Researchers measure the light emitted by a sub-Neptune planet's atmosphere

For more than a decade, astronomers have been trying to get a closer look at GJ 1214b, an exoplanet 40 light-years away from Earth. Their biggest obstacle is a thick layer of haze that blankets the planet, shielding it from the probing eyes of space telescopes and stymying efforts to study its atmosphere.

NASA's new James Webb Space Telescope (JWST) solved that issue. The telescope's infrared technology allows it to see planetary objects and features that were previously obscured by hazes, clouds or space dust, aiding astronomers in their search for habitable planets and early galaxies.

A team of researchers used JWST to observe GJ 1214b's atmosphere by measuring the heat it emits while orbiting its host star. Their results, published in the journal Nature on May 10, 2023, represent the first time anyone has directly detected the light emitted by a sub-Neptune exoplanet -- a category of planets that are larger than Earth but smaller than Neptune.

Though GJ 1214b is far too hot to be habitable, researchers discovered that its atmosphere likely contains water vapor -- possibly even significant amounts -- and is primarily composed of molecules heavier than hydrogen. University of Maryland Associate Professor of Astronomy Eliza Kempton, lead author of the Nature study, said their findings mark a turning point in the study of sub-Neptune planets like GJ 1214b.

"I've been on a quest to understand GJ 1214b for more than a decade," Kempton said. "When we received the data for this Nature paper, we could see the light from the planet just disappear when it went behind its host star. That had never before been seen for this planet or for any other planet of its class, so JWST is really delivering on its promise."

A 'new light'

Sub-Neptunes are the most common type of planet in the Milky Way, though none exist in our solar system. Despite the murkiness of GJ 1214b's atmosphere, Kempton and her co-authors determined the planet was still their best chance of observing a sub-Neptune's atmosphere because of its bright but small host star.

In their Nature paper, the researchers measured the infrared light that GJ 1214b emitted over the course of about 40 hours -- the time it takes the planet to orbit its star. As day turns to night, the amount of heat that shifts from one side of a planet to the other depends largely on what its atmosphere is made of. Known as a phase curve observation, this research method opened a new window into the planet's atmosphere.

"JWST operates at longer wavelengths of light than previous observatories, which gives us access to the heat emitted by the planet and allows us to create a map of the planet's temperature," Kempton said. "We finally got to see GJ 1214b in a new light."

By measuring the movement and fluctuation of heat, the researchers determined that GJ 1214b does not have an atmosphere dominated by hydrogen.

Potential water world?

The question of whether GJ 1214b contains water has long interested astronomers. Previous observations by NASA's Hubble Space Telescope suggested that GJ 1214b could be a water world -- a loose term for any planet that contains a significant amount of water.

The latest JWST data revealed traces of water, methane or some mix of the two. These substances match a subtle absorption of light seen in the wavelength range observed by JWST. Further studies will be needed to determine the exact makeup of the planet's atmosphere, but Kempton said the evidence remains consistent with the possibility of large amounts of water.

"GJ 1214b, based on our observations, could be a water world," Kempton said. "We think we detect water vapor, but it's challenging because water vapor absorption overlaps with methane absorption, so we can't say 100% that we detected water vapor and not methane. However, we see this evidence on both hemispheres of the planet, which heightens our confidence that there really is water there."

Reflecting on the findings

The researchers made another surprising discovery in their study: GJ 1214b is incredibly reflective. The planet was not as hot as expected, which tells researchers that something in the atmosphere is reflecting light.

Kempton said there is plenty of room for follow-up studies, including ones that take a closer look at the high-altitude aerosols that form the haze -- or possibly clouds -- in GJ 1214b's atmosphere. Previously, researchers thought it might be a dark, soot-like substance that absorbs light. However, the discovery that the exoplanet is reflective raises new questions.

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Human eyes really do play 'tricks' on the mind, say experts

A new study has shown that the human visual system can 'trick' the brain into making inaccurate assumptions about the size of objects in the world around them.

The research findings could have implications for many aspects of everyday life, such as driving, how eye witness accounts are treated in the criminal justice system, and security issues, such as drone sightings.

The research team from the University of York and Aston University presented participants with photographs of full-scale railway scenes, which had the upper and lower parts of the image blurred, as well photographs of small-scale models of railways that were not blurred.

Participants were asked to compare each image and decide which was the 'real' full-scale railway scene. The results were that participants perceived that the blurred real trains were smaller than the models.

Dr Daniel Baker, from the University of York's Department of Psychology, said: "In order for us to determine the real size of objects that we see around us, our visual system needs to estimate the distance to the object.

"To arrive at an understanding of absolute size it can take into account the parts of the image that are blurred out -- a bit like the out-of-focus areas that a camera produces -- which involves a bit of complicated mathematics to give the brain the knowledge of spatial scale.

"This new study, however, shows that we can be fooled in our estimates of object size. Photographers take advantage of this using a technique called 'tilt-shift miniaturisation', that can make life-size objects appear to be scale models."

The findings demonstrate that the human visual system is highly flexible -- sometimes capable of accurate perception of size by exploiting what is known as 'defocus blur', but at other times subject to other influences and failing to make sense of real-world object size.

Professor Tim Meese, from Aston University, said: "Our results indicate that human vision can exploit defocus blur to infer perceptual scale but that it does this crudely.

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Earth's first animals had particular taste in real estate

Even without body parts that allowed for movement, new research shows -- for the first time -- that some of Earth's earliest animals managed to be picky about where they lived.

These creatures from the Ediacaran Period, roughly 550 million years ago, are strangely shaped soft-bodied animals that lived in the sea. Researchers have long considered them enigmatic.

"It's not like studying dinosaurs, which are related to birds that we can observe today," said Phillip C. Boan, UC Riverside paleontology graduate student and lead author of the new study. "With these animals, because they have no modern descendants, we're still working out basic questions about how they lived, such as how they reproduced and what they ate."

For this particular research project, the researchers focused on understanding where in the sea the animals spent their lives.

The ancient sea was also a largely foreign place compared to today's marine environments. It was dominated by a mat on the sea floor composed of bacteria and layers of other organic materials. In addition, predatory creatures were uncommon.

Given the alien nature of Ediacaran Earth, the researchers were surprised to find an animal that lived much the way barnacles do today. A new Paleobiology paper details how Obamus coronatus, named for the former U.S. president, opted to live on specific parts of the sea floor in the company of other Obamus.

The animal averaged about a half-inch in diameter and was "shaped like a French cruller donut with ribbons on top," Boan said. It did not move of its own accord, and likely spent its entire life embedded in its preferred spot on the sea floor.

"We think about the very oldest animals and maybe you wouldn't expect them to be so picky. But Obamus only occurs where there is a thick mat, and it's a pretty sophisticated way of making a living for something so very old," said Mary Droser, UCR distinguished professor of paleontology and study co-author.

In 2018, Droser's laboratory named the Obamus in honor of Barack Obama's passion for science. Her group discovered it at an extraordinarily well-preserved fossil site in the Australian Outback, at what is now called Nilpena Ediacara National Park.

A series of storms buried the Ediacaran sea floor at Nilpena in layers of sediment, helping preserve sandstone impressions of entire animal communities that lived together there. "This way, we're able to piece together whole ecosystems," Droser said. "Looking at them is like snorkeling around on the ancient sea floor, instead of looking at a single animal in a fish tank."

For this project, the research team selected three animals found in relatively large numbers at Nilpena, and examined how they were geographically distributed.

The other two animals, Tribrachidium and Rugoconites, are also immobile creatures with no modern descendants. "They are tri-radially symmetrical, like the Mercedes Benz logo," Boan said. "And they would have lived their entire lives embedded in the sea floor, as Obamus did."

Distribution for these other two animals was varied. Sometimes they could be found living in the company of other organisms like themselves, but not in every instance. However, Obamus displayed a clear preference.

"This is really the first example of a habitat-selective Ediacaran creature, the first example of a macroscopic animal doing this," Boan said. "But how did they get where they wanted to go? This is a question we don't yet know the answer to."

The research team theorizes that Obamus were likely motivated by the need to reproduce.

"There are a limited number of reproductive strategies, especially for animals like these," Droser said. "There are more strategies today, and they're more elaborate now. But the same ones used today were still being used 550 million years ago."

Obamus likely spread itself via selective larva that preferred locations with thick microbial mat and near other Obamus. "We don't entirely understand how Obamus offspring spread out, but we know that when they picked a place to live, it was very specific," Boan said.

A deeper understanding of how life on Earth developed over time can give researchers insight into how life could develop on another planet. For this reason, Droser's lab is funded by NASA's Exobiology program.

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Nose shape gene inherited from Neanderthals

Humans inherited genetic material from Neanderthals that affects the shape of our noses, finds a new study led by UCL researchers.

The new Communications Biology study finds that a particular gene, which leads to a taller nose (from top to bottom), may have been the product of natural selection as ancient humans adapted to colder climates after leaving Africa.

Co-corresponding author Dr Kaustubh Adhikari (UCL Genetics, Evolution & Environment and The Open University) said: "In the last 15 years, since the Neanderthal genome has been sequenced, we have been able to learn that our own ancestors apparently interbred with Neanderthals, leaving us with little bits of their DNA.

"Here, we find that some DNA inherited from Neanderthals influences the shape of our faces. This could have been helpful to our ancestors, as it has been passed down for thousands of generations."

The study used data from more than 6,000 volunteers across Latin America, of mixed European, Native American and African ancestry, who are part of the UCL-led CANDELA study, which recruited from Brazil, Colombia, Chile, Mexico and Peru. The researchers compared genetic information from the participants to photographs of their faces -- specifically looking at distances between points on their faces, such as the tip of the nose or the edge of the lips -- to see how different facial traits were associated with the presence of different genetic markers.

The researchers newly identified 33 genome regions associated with face shape, 26 of which they were able to replicate in comparisons with data from other ethnicities using participants in east Asia, Europe, or Africa.

In one genome region in particular, called ATF3, the researchers found that many people in their study with Native American ancestry (as well as others with east Asian ancestry from another cohort) had genetic material in this gene that was inherited from the Neanderthals, contributing to increased nasal height. They also found that this gene region has signs of natural selection, suggesting that it conferred an advantage for those carrying the genetic material.

First author Dr Qing Li (Fudan University) said: "It has long been speculated that the shape of our noses is determined by natural selection; as our noses can help us to regulate the temperature and humidity of the air we breathe in, different shaped noses may be better suited to different climates that our ancestors lived in. The gene we have identified here may have been inherited from Neanderthals to help humans adapt to colder climates as our ancestors moved out of Africa."

Co-corresponding author Professor Andres Ruiz-Linares (Fudan University, UCL Genetics, Evolution & Environment, and Aix-Marseille University) added: "Most genetic studies of human diversity have investigated the genes of Europeans; our study's diverse sample of Latin American participants broadens the reach of genetic study findings, helping us to better understand the genetics of all humans."

The finding is the second discovery of DNA from archaic humans, distinct from Homo sapiens, affecting our face shape. The same team discovered in a 2021 paper that a gene influencing lip shape was inherited from the ancient Denisovans.

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Clearest snapshot of human genomic diversity

For more than 20 years, scientists have relied on the human reference genome, a consensus genetic sequence, as a standard against which to compare other genetic data. Used in countless studies, the reference genome has made it possible to identify genes implicated in specific diseases and trace the evolution of human traits, among other things.

But it has always been a flawed tool. One of its biggest problems is that about 70 percent of its data came from a single man of predominantly African-European background whose DNA was sequenced during the Human Genome Project, the first effort to capture all of a person's DNA. As a result, it can tell us little about the 0.2 to one percent of genetic sequence that makes each of the seven billion people on this planet different from each other, creating an inherent bias in biomedical data believed to be responsible for some of the health disparities affecting patients today. Many genetic variants found in non-European populations, for instance, aren't represented in the reference genome at all.

For years, researchers have called for a resource more inclusive of human diversity with which to diagnose diseases and guide medical treatments. Now scientists with the Human Pangenome Reference Consortium have made groundbreaking progress in characterizing the fraction of human DNA that varies between individuals. As they recently published in Nature, they've assembled genomic sequences of 47 people from around the world into a so-called pangenome in which more than 99 percent of each sequence is rendered with high accuracy.

Layered upon each other, these sequences revealed nearly 120 million DNA base pairs that were previously unseen.

While it's still a work in progress, the pangenome is public and can be used by scientists around the world as a new standard human genome reference, says The Rockefeller University's Erich D. Jarvis, one of the primary investigators.

"This complex genomic collection represents significantly more accurate human genetic diversity than has ever been captured before," he says. "With a greater breadth and depth of genetic data at their disposal, and greater quality of genome assemblies, researchers can refine their understanding of the link between genes and disease traits, and accelerate clinical research."

Sourcing diversity

Completed in 2003, the first draft of the human genome was relatively imprecise, but it became sharper over the years thanks to filled-in gaps, corrected errors, and advancing sequencing technology. Another milestone was reached last year, when the final eight percent of the genome -- mainly tightly coiled DNA that doesn't code for protein and repetitive DNA regions -- was finally sequenced.

Despite this progress, the reference genome remained imperfect, especially with respect to the critical 0.2 to one percent of DNA representing diversity. The Human Pangenome Reference Consortium (HPRC), a government-funded collaboration between more than a dozen research institutions in the United States and Europe, was launched in 2019 to address this problem.

At the time, Jarvis, one of the consortium's leaders, was honing advanced sequencing and computational methods through the Vertebrate Genomes Project, which aims to sequence all 70,000 vertebrate species. His and other collaborating labs decided to apply these advances for high-quality diploid genome assemblies to revealing the variation within a single vertebrate: Homo sapiens.

To collect a diversity of samples, the researchers turned to the 1000 Genomes Project, a public database of sequenced human genomes that includes more than 2500 individuals representing 26 geographically and ethnically varied populations. Most of the samples come from Africa, home to the planet's largest human diversity.

"In many other large human genome diversity projects, the scientists selected mostly European samples," Jarvis says. "We made a purposeful effort to do the opposite. We were trying to counteract the biases of the past."

It's likely that gene variants that could inform our knowledge of both common and rare diseases can be found among these populations.

Mom, dad, and child

But to broaden the gene pool, the researchers had to create crisper, clearer sequences of each individual-and the approaches developed by members of the Vertebrate Genome Project and associated consortiums were used to solve a longstanding technical problem in the field.

Every person inherits one genome from each parent, which is how we end up with two copies of every chromosome, giving us what's known as a diploid genome. And when a person's genome is sequenced, teasing apart parental DNA can be challenging. Older techniques and algorithms have routinely made errors when merging parental genetic data for an individual, resulting in a cloudy view. "The differences between mom's and dad's chromosomes are bigger than most people realize," Jarvis says. "Mom may have 20 copies of a gene and dad only two."

With so many genomes represented in a pangenome, that cloudiness threatened to develop into a thunderstorm of confusion. So the HPRC homed in a method developed by Adam Phillippy and Sergey Koren at the National Institutes of Health on parent-child "trios" -- a mother, a father, and a child whose genomes had all been sequenced. Using the data from mom and dad, they were able to clear up the lines of inheritance and arrive at a higher-quality sequence for the child, which they then used for pangenome analysis.

New variations

The researchers' analysis of 47 people yielded 94 distinct genome sequences, two for each set of chromosomes, plus the sex Y chromosome in males.

They then used advanced computational techniques to align and layer the 94 sequences. Of the 120 million DNA base pairs that were previously unseen or in a different location than they were noted to be in the previous reference, about 90 million derive from structural variations, which are differences in people's DNA that arise when chunks of chromosomes are rearranged -- moved, deleted, inverted, or with extra copies from duplications.

It's an important discovery, Jarvis notes, because studies in recent years have established that structural variants play a major role in human health, as well as in population-specific diversity. "They can have dramatic effects on trait differences, disease, and gene function," he says. "With so many new ones identified, there's going to be a lot of new discoveries that weren't possible before."

Filling gaps

The pangenome assembly also fills in gaps that were due to repetitive sequences or duplicated genes. One example is the major histocompatibility complex (MHC), a cluster of genes that code proteins on the surface of cells that help the immune system recognize antigens, such as those from the SARS-CoV-2 virus.

"They're really important, but it was impossible to study MHC diversity using the older sequencing methods," Jarvis says. "We're seeing much greater diversity than we expected. This new information will help us understand how immune responses against specific pathogens vary among people." It could also lead to better methods to match organ transplant donors with and patients, or identify people at risk for developing autoimmune disease.

The team has also uncovered surprising new characteristics of centromeres, which lie at the cruxes of chromosomes and conduct cell division, pulling apart as cells duplicate. Mutations in centromeres can lead to cancers and other diseases.

Despite having highly repetitive DNA sequences, "centromeres are so diverse from one haplotype to another, that they can account for more than 50 percent of the genetic differences between people or maternal and paternal haplotypes even within one individual," Jarvis says. "The centromeres seem to be one of the most rapidly evolving parts of the chromosome."

Relationship building

The current 47-people pangenome is just a starting point, however. The HPRC's ultimate goal is to produce high-quality, nearly error-free genomes from at least 350 individuals from diverse populations by mid-2024, a milestone that would make it possible to capture rare alleles that confer important adaptive traits. Tibetans, for example, have alleles related to oxygen use and UV light exposure that enable them to live at high altitudes.

A major challenge in collecting this data will be to gain trust from communities that have seen past abuses of biological data; for example, there are no samples in the current study from Native American nor Aboriginal peoples, who have been long been disregarded or exploited by scientific studies. But you don't have to go far back in time to find examples of unethical use of genetic data: Just a few years ago, DNA samples from thousands of Africans in multiple countries were commercialized without the donors' knowledge, consent, or benefit.

These offenses have sown mistrust against scientists among many populations. But by not being included, some of these groups could remain genetically obscure, leading to a perpetuation of the biases in the data -- and to continued disparities in health outcomes.

Read more at Science Daily

Webb looks for Fomalhaut's asteroid belt and finds much more

Astronomers used NASA's James Webb Space Telescope to image the warm dust around a nearby young star, Fomalhaut, in order to study the first asteroid belt ever seen outside of our solar system in infrared light. But to their surprise, the dusty structures are much more complex than the asteroid and Kuiper dust belts of our solar system. Overall, there are three nested belts extending out to 14 billion miles (23 billion kilometers) from the star; that's 150 times the distance of Earth from the Sun. The scale of the outermost belt is roughly twice the scale of our solar system's Kuiper Belt of small bodies and cold dust beyond Neptune. The inner belts -- which had never been seen before -- were revealed by Webb for the first time.

The belts encircle the young hot star, which can be seen with the naked eye as the brightest star in the southern constellation Piscis Austrinus. The dusty belts are the debris from collisions of larger bodies, analogous to asteroids and comets, and are frequently described as 'debris disks.' "I would describe Fomalhaut as the archetype of debris disks found elsewhere in our galaxy, because it has components similar to those we have in our own planetary system," said András Gáspár of the University of Arizona in Tucson and lead author of a new paper describing these results. "By looking at the patterns in these rings, we can actually start to make a little sketch of what a planetary system ought to look like -- If we could actually take a deep enough picture to see the suspected planets."

The Hubble Space Telescope and Herschel Space Observatory, as well as the Atacama Large Millimeter/submillimeter Array (ALMA), have previously taken sharp images of the outermost belt. However, none of them found any structure interior to it. The inner belts have been resolved for the first time by Webb in infrared light. "Where Webb really excels is that we're able to physically resolve the thermal glow from dust in those inner regions. So you can see inner belts that we could never see before," said Schuyler Wolff, another member of the team at the University of Arizona.

Hubble, ALMA, and Webb are tag-teaming to assemble a holistic view of the debris disks around a number of stars. "With Hubble and ALMA, we were able to image a bunch of Kuiper Belt analogs, and we've learned loads about how outer disks form and evolve," said Wolff. "But we need Webb to allow us to image a dozen or so asteroid belts elsewhere. We can learn just as much about the inner warm regions of these disks as Hubble and ALMA taught us about the colder outer regions."

These belts most likely are carved by the gravitational forces produced by unseen planets. Similarly, inside our solar system Jupiter corrals the asteroid belt, the inner edge of the Kuiper Belt is sculpted by Neptune, and the outer edge could be shepherded by as-yet-unseen bodies beyond it. As Webb images more systems, we will learn about the configurations of their planets.

Fomalhaut's dust ring was discovered in 1983 in observations made by NASA's Infrared Astronomical Satellite (IRAS). The existence of the ring has also been inferred from previous and longer-wavelength observations using submillimeter telescopes on Mauna Kea, Hawaii, NASA's Spitzer Space Telescope, and Caltech's Submillimeter Observatory.

"The belts around Fomalhaut are kind of a mystery novel: Where are the planets?" said George Rieke, another team member and U.S. science lead for Webb's Mid-Infrared Instrument (MIRI), which made these observations. "I think it's not a very big leap to say there's probably a really interesting planetary system around the star."

"We definitely didn't expect the more complex structure with the second intermediate belt and then the broader asteroid belt," added Wolff. "That structure is very exciting because any time an astronomer sees a gap and rings in a disk, they say, 'There could be an embedded planet shaping the rings!'"

Webb also imaged what Gáspár dubs "the great dust cloud," which may be evidence for a collision occurring in the outer ring between two protoplanetary bodies. This is a different feature from a suspected planet first seen inside the outer ring by Hubble in 2008. Subsequent Hubble observations showed that by 2014 the object had vanished. A plausible interpretation is that this newly discovered feature, like the earlier one, is an expanding cloud of very fine dust particles from two icy bodies that smashed into each other.

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Cleanup of inactive Gulf of Mexico wells estimated at $30 billion

Wetlands, coastal areas and offshore waters near Alabama, Louisiana and Texas have more inactive oil and gas wells than producing ones, and the cost to permanently plug and abandon them could be $30 billion, University of California, Davis, researchers suggest.

A paper published today in the journal Nature Energy examines the cost to plug 14,000 wells that are inactive, have not produced for five years and are unlikely to be reactivated in the Gulf of Mexico region, which is the epicenter of U.S. offshore oil and gas operations.

The wells could pose future environmental and financial risks to the public, and the cost differential for plugging onshore wells versus those in offshore waters is large, said Mark Agerton, an assistant professor at UC Davis and lead author of the paper.

Leaks from wells closer to shore are more likely to damage coastal ecosystems and release greenhouse gases like methane into the atmosphere, compared to wells in deep waters. The study found that more than 90% of inactive wells are in shallow areas, and the cost to plug those would be $7.6 billion, or 25% of a total $30 billion.

Informing policy decisions

"The wells aren't supposed to be leaking into the environment, but sometimes they do," said Agerton, of the Department of Agricultural and Resource Economics. "How do you get the most environmental benefit for the least amount of money?"

The findings could help states decide cleanup priorities, especially as they access $4.7 billion in federal money authorized by the Infrastructure Investment and Jobs Act. That money is set aside for methane reduction programs, including cleanup of old oil and gas wells, said Gregory Upton, an associate research professor at the Louisiana State University Center for Energy Studies and co-author of the paper.

"States have a pretty good idea of what it costs to plug these wells on land, but there is really a lot of uncertainty as to what the costs were for these offshore wells," Upton said during a media briefing about the paper.

Liability for cleaning up wells abandoned in federal waters falls to prior owners if the current owner becomes insolvent and is unable to cover costs. Large American oil companies currently own or have owned 88% of the wells in federal Gulf of Mexico waters and would legally shoulder cleanup liabilities before taxpayers, Agerton said.

But in state waters, each jurisdiction handles liability differently, and prior ownership doesn't come into play. States oversee plugging programs for orphaned wells whose owners have gone bankrupt, though the cost to plug an abandoned offshore well increases with the length of the well and the depth of the water.

"The bulk of the costs comes from plugging wells in deeper water where the environmental consequences are less than for a shallow well closer to shore," Agerton said. "That money is probably better spent on state waters where they can't go after prior owners for cleanup costs and it's going to be a cheaper cleanup job with more environmental benefit."

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Evidence of Ice Age human migrations from China to the Americas and Japan

Scientists have used mitochondrial DNA to trace a female lineage from northern coastal China to the Americas. By integrating contemporary and ancient mitochondrial DNA, the team found evidence of at least two migrations: one during the last ice age, and one during the subsequent melting period. Around the same time as the second migration, another branch of the same lineage migrated to Japan, which could explain Paleolithic archeological similarities between the Americas, China, and Japan. The study appears May 9 in the journal Cell Reports.

"The Asian ancestry of Native Americans is more complicated than previously indicated," says first author Yu-Chun Li, a molecular anthropologist at the Chinese Academy of Sciences. "In addition to previously described ancestral sources in Siberia, Australo-Melanesia, and Southeast Asia, we show that northern coastal China also contributed to the gene pool of Native Americans."

Though it was long assumed that Native Americans descended from Siberians who crossed over the Bering Strait's ephemeral land bridge, more recent genetic, geological, and archeological evidence suggests that multiple waves of humans journeyed to the Americas from various parts of Eurasia.

To shed light on the history of Native Americans in Asia, a team of researchers from the Chinese Academy of Sciences followed the trail of an ancestral lineage that might link East Asian Paleolithic-age populations to founding populations in Chile, Peru, Bolivia, Brazil, Ecuador, Mexico, and California. The lineage in question is present in mitochondrial DNA, which can be used to trace kinship through the female line.

The researchers scoured over 100,000 contemporary and 15,000 ancient DNA samples from across Eurasia to eventually identify 216 contemporary and 39 ancient individuals belonging to the rare lineage. By comparing the accumulated mutations, geographic locations, and carbon-dated age of each of these individuals, the researchers were able to trace the lineage's branching path. They identified two migration events from northern coastal China to the Americas, and in both cases, they think that the travelers probably set dock in America via the Pacific coast rather than by crossing the inland ice-free corridor (which would not have opened at the time).

The first radiation event occurred between 19,500 and 26,000 years ago during the Last Glacial Maximum, when ice sheet coverage was at its greatest and conditions in northern China were likely inhospitable for humans. The second radiation occurred during the subsequent deglaciation or melting period, between 19,000 and 11,500 years ago. There was a rapid increase in human populations at this time, probably due to the improved climate, which may have fueled expansion into other geographical regions.

The researchers also uncovered an unexpected genetic link between Native Americans and Japanese people. During the deglaciation period, another group branched out from northern coastal China and traveled to Japan. "We were surprised to find that this ancestral source also contributed to the Japanese gene pool, especially the indigenous Ainus," says Li.

This discovery helps to explain archeological similarities between the Paleolithic peoples of China, Japan, and the Americas. Specifically, the three regions share similarities in how they crafted stemmed projectile points for arrowheads and spears. "This suggests that the Pleistocene connection among the Americas, China, and Japan was not confined to culture but also to genetics," says senior author Qing-Peng Kong, an evolutionary geneticist at the Chinese Academy of Sciences.

Though the study focused on mitochondrial DNA, complementary evidence from Y chromosomal DNA suggests that male ancestors of Native Americans also lived in northern China at around the same time as these female ancestors.

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Kangaroo Island ants 'play dead' to avoid predators

They're well known for their industrious work, but now a species of ant on Kangaroo Island is also showing that it is skilled at 'playing dead', a behaviour that University of South Australia researchers believe is a recorded world first.

Accidentally discovered as researchers were checking pygmy-possum and bat nest boxes on Kangaroo Island, a colony of Polyrhachis femorata ants appeared to be dead… until one moved.

Researchers believe the ants were 'playing dead' as a defensive strategy to avoid potential danger.

Published by CSIRO, this is the first time that a whole colony of ants has been recorded feigning death, and the first record of the Polyrhachis femorata ant species for South Australia.

Wildlife ecologist, UniSA's Associate Professor S. 'Topa' Petit, says she was surprised to discover a colony of what appeared to be dead ants in one of the nest boxes.

"The mimicry was perfect," Assoc Professor Petit says. "When we opened the box, we saw all these dead ants…and then one moved slightly.

"This sort of defensive immobility is known among only a few ant species -- in individuals or specific casts -- but we don't know of other instances when it's been observed for entire colonies.

"In some of the boxes containing colonies of Polyrhachis femorata, some individuals took a while to stop moving, and others didn't stop. The triggers for the behaviour are difficult to understand."

Assoc Prof Petit says that nest boxes may present an opportunity to study the ants' death-feigning behaviours, which are of great interest to many behavioural ecologists investigating a diversity of animal species.

The discovery was made during the Kangaroo Island Nest Box Project, where 901 box cavities have been monitored across 13 diverse properties as part of wildlife recovery efforts following the devastating 2020 bushfires.

Co-researcher at the Kangaroo Island Research Station, Peter Hammond, says that he used to call the Nest Box Project 'Friends of the Invertebrates', because invertebrates were often the only occupants of the bat and pygmy-possum nest boxes.

"We are learning a lot about invertebrates as well as targeted vertebrates," Hammond says.

"Most of our several hundred boxes are on burnt ground, but we also have some on unburnt properties as controls because our aim is to determine the value of nest boxes in bushfire recovery.

"Polyrhachis femorata is strongly associated with the critically endangered Narrow-Leaf Mallee community, where it colonised several boxes very quickly. However, we also have records for two other properties further west, indicating that the ants will use other habitats.

"We believe that the Polyrhachis femorata species was strongly affected by the bushfires."

Assoc Prof Petit says there is a lot to discover about this species.

"Polyrhachis femorata is a beautiful arboreal ant that tends to be quite shy, but little else is known about its ecology or behaviour," Assoc Prof Petit says.

"We have a relatively unknown world of ants under our feet and in the trees. Ants provide crucial ecosystem services and are a vital part of functional ecosystems on Kangaroo Island and elsewhere.

"It is very exciting that such an endearing species as Polyrhachis femorata is living on Kangaroo Island and we look forward to finding out more about its ecology.

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Galactic bubbles are more complex than imagined

Astronomers have revealed new evidence about the properties of the giant bubbles of high-energy gas that extend far above and below the Milky Way galaxy's center.

In a study recently published inNature Astronomy, a team led by scientists at The Ohio State University was able to show that the shells of these structures -- dubbed "eRosita bubbles" after being found by the eRosita X-ray telescope -are more complex than previously thought.

Although they bear a striking similarity in shape to Fermi bubbles, eRosita bubbles are larger and more energetic than their counterparts. Known together as the "galactic bubbles" due to their size and location, they provide an exciting opportunity to study star formation history as well as reveal new clues about how the Milky Way came to be, said Anjali Gupta, lead author of the study and a former postdoctoral researcher at Ohio State who is now a professor of astronomy at Columbus State Community College.

These bubbles exist in the gas that surrounds galaxies, an area which is called the circumgalactic medium.

"Our goal was really to learn more about the circumgalactic medium, a place very important in understanding how our galaxy formed and evolved," Gupta said. "A lot of the regions that we were studying happened to be in the region of the bubbles, so we wanted to see how different the bubbles are when compared to the regions which are away from the bubble."

Previous studies had assumed that these bubbles were heated by the shock of gas as it blows outward from the galaxy, but this paper's main findings suggest the temperature of the gas within the bubbles isn't significantly different from the area outside of it.

"We were surprised to find that the temperature of the bubble region and out of the bubble region were the same," said Gupta. Additionally, the study demonstrates that these bubbles are so bright because they're filled with extremely dense gas, not because they are at hotter temperatures than the surrounding environment.

Gupta and Smita Mathur, co-author of the study and a professor of astronomy at Ohio State, did their analysis using observations made by the Suzaku satellite, a collaborative mission between NASA and the Japanese Aerospace Exploration Agency.

By analyzing 230 archival observations made between 2005 and 2014, researchers were able to characterize the diffuse emission -- the electromagnetic radiation from very low density gas -- of the galactic bubbles, as well as the other hot gases that surround them.

Although the origin of these bubbles has been debated in scientific literature, this study is the first that begins to settle it, said Mathur. As the team found an abundance of non-solar neon-oxygen and magnesium-oxygen ratios in the shells, their results strongly suggest that galactic bubbles were originally formed by nuclear star-forming activity, or the injection of energy by massive stars and other kinds of astrophysical phenomena, rather than through the activities of a supermassive black hole.

"Our data supports the theory that these bubbles are most likely formed due to intense star formation activity at the galactic center, as opposed to black hole activity occurring at the galactic center," Mathur said. To further investigate the implications their discovery may have for other aspects of astronomy, the team hopes to use new data from other upcoming space missions to continue characterizing the properties of these bubbles, as well as work on novel ways to analyze the data they already have.

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Detailed image of the human retina

What cell types are found in which human tissue, and where? Which genes are active in the individual cells, and which proteins are found there? Answers to these questions and more are to be provided by a specialised atlas -- in particular how the different tissues form during embryonic development and what causes diseases. In creating this atlas, researchers aim to map not only tissue directly isolated from humans, but also structures called organoids. These are three-dimensional clumps of tissue that are cultivated in the laboratory and develop in a way similar to human organs, but on a small scale.

"The advantage of organoids is that we can intervene in their development and test active substances on them, which allows us to learn more about healthy tissue as well as diseases," explains Barbara Treutlein, Professor of Quantitative Developmental Biology at the Department of Biosystems Science and Engineering at ETH Zurich in Basel.

To help produce such an atlas, Treutlein, together with researchers from the Universities of Zurich and Basel, has now developed an approach to gather and compile a great deal of information about organoids and their development. The research team applied this approach to the organoids of the human retina, which they derived from stem cells.

Many proteins visible simultaneously

At the heart of the methods the scientists used for their approach was the 4i technology: iterative indirect immunofluorescence imaging. This new imaging technique can visualise several dozen proteins in a thin tissue section at high resolution using fluorescence microscopy. The 4i technology was developed a few years ago by Lucas Pelkmans, a professor at the University of Zurich and coauthor of the study that has just been published in the scientific journal Nature Biotechnology. It is in this study that the researchers applied this method to organoids for the first time.

Typically, researchers use fluorescence microscopy to highlight three proteins in a tissue, each with a different fluorescent dye. For technical reasons, it is not possible to stain more than five proteins at a time. In 4i technology, three dyes are used, but these are washed from the tissue sample after measurements have been taken, and three new proteins are stained. This step was performed 18 times, by a robot, and the process took a total of 18 days. Lastly, a computer merges the individual images into a single microscopy image on which 53 different proteins are visible. They provide information on the function of the individual cell types that make up the retina; for example, rods, cones, and ganglion cells.

The researchers have supplemented this visual information of retinal proteins with information on which genes are read in the individual cells.

High spatial and temporal resolution

The scientists performed all these analyses on organoids that were of different ages and thus at different stages of development. In this way, they were able to create a time series of images and genetic information that describes the entire 39-week development of retinal organoids. "We can use this time series to show how the organoid tissue slowly builds up, where which cell types proliferate and when, and where the synapses are located. The processes are comparable to those of retinal formation during embryonic development," says Gray Camp, a professor at the University of Basel and a senior author of this study.

The researchers published their image information and more findings on retinal development on a publicly accessible website: EyeSee4is.

Further tissue types planned

So far, the scientists have been studying how a healthy retina develops, but in the future, they hope to deliberately disrupt development in retinal organoids with drugs or genetic modifications. "This will give us new insights into diseases such as retinitis pigmentosa, a hereditary condition that causes the retina's light-sensitive receptors to gradually degenerate and ultimately leads to blindness," Camp says. The researchers want to find out when this process begins and how it can be stopped.

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Atmospheric research provides clear evidence of human-caused climate change signal associated with CO2 increases

New research provides clear evidence of a human "fingerprint" on climate change and shows that specific signals from human activities have altered the temperature structure of Earth's atmosphere.

Differences between tropospheric and lower stratospheric temperature trends have long been recognized as a fingerprint of human effects on climate. This fingerprint, however, neglected information from the mid to upper stratosphere, 25 to 50 kilometers above the Earth's surface.

"Including this information improves the detectability of a human fingerprint by a factor of five. Enhanced detectability occurs because the mid to upper stratosphere has a large cooling signal from human-caused CO2 increases, small noise levels of natural internal variability, and differing signal and noise patterns," according to the journal article, "Exceptional stratospheric contribution to human fingerprints on atmospheric temperature," published in the Proceedings of the National Academy of Sciences (PNAS). Noise in the troposphere can include day-to-day weather, interannual variability arising from El Niños and La Niñas, and longer-term natural fluctuations in climate. In the upper stratosphere, the noise of variability is smaller, and the human-caused climate change signal is larger, so the signal can be much more easily distinguished.

"Extending fingerprinting to the upper stratosphere with long temperature records and improved climate models means that it is now virtually impossible for natural causes to explain satellite-measured trends in the thermal structure of the Earth's atmosphere," the paper states.

"This is the clearest evidence there is of a human-caused climate change signal associated with CO2 increases," according to lead author Benjamin Santer, an adjunct scientist in the Physical Oceanography Department at the Woods Hole Oceanographic Institute (WHOI) in Massachusetts.

"This research undercuts and rebuts claims that recent atmospheric and surface temperature changes are natural, whether due to the Sun or due to internal cycles in the climate system. A natural explanation is virtually impossible in terms of what we are looking at here: changes in the temperature structure of the atmosphere," added Santer, who has worked on climate fingerprinting for more than 30 years. "This research puts to rest incorrect claims that we don't need to treat climate change seriously because it is all natural."

The research was motivated by earlier work by Suki Manabe and Richard Wetherald, who in 1967 used a simple climate model to study how CO2 from fossil fuel burning might change atmospheric temperature. Their modeling found a very distinctive feature: an increase in CO2 levels led to more trapping of heat in the troposphere (the lowest layer of Earth's atmosphere) and less heat escaping higher up into the stratosphere (the layer above the troposphere), thus warming the troposphere and cooling the stratosphere. This prediction of tropospheric warming and stratospheric cooling in response to increasing CO2 has been confirmed many times by more complex models and verified by comparing model results with global-mean atmospheric temperature observations from weather balloons and satellites.

Although these earlier studies considered global-mean temperature changes in the middle and upper stratosphere, roughly 25 to 50 kilometers above Earth's surface, they did not look at detailed patterns of climate change in this layer. This region can be better studied now because of improved simulations and satellite data. The new research is the first to search for human-caused climate change patterns -- also called "fingerprints" -- in the middle and upper stratosphere.

"The human fingerprints in temperature changes in the mid to upper stratosphere due to CO2 increases are truly exceptional because they are so large and so different from temperature changes there due to internal variability and natural external forcing. These unique fingerprints make it possible to detect the human impact on climate change due to CO2 in a short period of time (~10 -- 15 years) with high confidence," stated co-author Qiang Fu, a professor in the Department of Atmospheric Sciences at the University of Washington.

"The world has been reeling under climate change, so being as confident as possible of the role of carbon dioxide is critical," said co-author Susan Solomon, Martin Professor of Environmental Studies at the Massachusetts Institute of Technology. "The fact that observations show not only a warming troposphere but also a strongly cooling upper stratosphere is unique tell-tale evidence that nails the dominant role of carbon dioxide in climate change and greatly increases confidence."

Santer said that although it is intellectually gratifying to be able to extend fingerprinting higher up into the atmosphere to test the prediction by Manabe and Wetherald, it is also deeply concerning.

"As someone who tries to understand the kind of world that future generations are going to inhabit, these results make me very worried. We are fundamentally changing the thermal structure of Earth's atmosphere, and there is no joy in recognizing that," Santer said.

"This study shows that the real world has changed in a way that simply cannot be explained by natural causes," Santer added. "We now face important decisions, in the United States and globally, on what to do about climate change. I hope those decisions are based on our best scientific understanding of the reality and seriousness of human effects on climate."

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Viruses could reshuffle the carbon cycle in a warming world

Microbes play important roles in ecosystems, and these roles are changing with global warming. Scientists also now know that most types of microbes are infected by viruses, but they know relatively little about how these viral infections could change how microbes react to warming. In this study, scientists describe many different ways that increasing temperatures could affect viruses and their microbial hosts. These changes could ultimately affect the responses of whole ecosystems to warming. The work exposes several important gaps in researchers' current knowledge about the connections between viruses, warming, and ecosystem functioning. Filling these gaps is crucial for understanding and predicting the effects of climate change on ecosystems.

This study creates a roadmap for understanding the many different ways that viruses could modify the effects of warming on communities of microbes. Viruses likely have strong effects on processes with microbes and the ways ecosystems function. Incorporating these previously ignored effects into ecosystem models will help scientists improve their predictions of how ecosystems could respond to climate change.

Microorganisms play integral roles in ecosystems by controlling the flow of energy and matter through processes like photosynthesis (carbon uptake), respiration (carbon release), and decomposition (carbon recycling). Climate change is currently altering how ecosystems function by changing how organisms operate within microbial food webs. Scientists know that viruses can have strong impacts on microbial processes, but they have less knowledge of how these impacts will change with future warming.

In this study, scientists from Duke University, the University of Tennessee Knoxville, the Netherlands Institute of Ecology, and Oak Ridge National Laboratory reviewed the potential impacts of warming on viruses and how these might alter scientific understanding of ecosystem responses to climate change. Warming likely affects several different stages of the viral infection cycle, as well as virus-host dynamics. However, there are still many gaps in our understanding about these effects. Because viruses are ubiquitous across all habitats and have strong effects on microbial functioning, filling these gaps is critical to understanding how warming will affect the flow of energy and matter within ecosystems. The researchers' preliminary models show that viruses could potentially tip the scales on natural carbon balances, causing some ecosystems to switch from being net carbon sources (releasing more carbon than they store) to being net carbon sinks (absorbing carbon). This study shows how incorporating viruses into predictive models can lead to new and unexpected effects on ecosystems in response to climate change.

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Researchers discover that the ice cap is teeming with microorganisms

There are no plants, and only very few animals: people rarely come here. The large glaciers in Greenland have long been perceived as ice deserts. Gigantic ice sheets where conditions for life are extremely harsh.

But now, it seems, we have been wrong. There is much more life on the glaciers than we thought.

Headed by Professor Alexandre Anesio, a group of researchers from the Department of Environmental Science at Aarhus University have discovered that the glaciers are teeming with life. Microbes that have adapted to life on the ice. And not just one or two species. Several thousand different species.

"A small puddle of melt-water on a glacier can easily have 4,000 different species living in it. They live on bacteria, algae, viruses and microscopic fungi. It's a whole ecosystem that we never knew existed until recently," says Alexandre Anesio.

What do the microbes live on?

Over the past 50 years, researchers have repeatedly been surprised by the hardiness of life. Life has been found several kilometres underground -- where there is neither sun nor oxygen. Billions of microorganisms "eat" minerals in the bedrock and so can survive.

Researchers have shown that life can even survive in space. In 2007, European researchers placed a colony of more than 3,000 microscopic water bears (tardigrades) outside a satellite and sent them into orbit around the Earth. The orbit lasted 10 days, after which the satellite returned to Earth. No less than 68 per cent of the microbes survived the vacuum of space and the lethal radiation.

Therefore, it might not come as a surprise that life also thrives on the glaciers. After all there is sun, oxygen and water. Nevertheless, until recently, researchers believed that the ice had too little nourishment to sustain life. But they were wrong.

There is nourishment. Just in incredibly small quantities, explains Alexandre Anesio.

Black algae

One of the microorganisms on the ice that the researchers spent most time investigating is a small black algae. The algae grows on top of the ice and tinges it black. There is a reason why the black algae so interesting for the researchers.

"When the ice darkens, it becomes more difficult to reflect sunlight. Instead, heat from the sun's rays is absorbed by the ice, which starts to melt. The more the ice melts, the warmer the temperature on Earth. The algae therefore play an important role in global warming," says Alexandre Anesio.

In recent years, larger and larger areas of the ice have become stained by the algae, making the ice melt even faster. Alexandre Anesio has calculated that the algae are increasing the ice melt by about 20 per cent.

The algae on the ice also existed before people kicked off global warming through industrialisation. However, climate change means spring arrives ever earlier to the Arctic and as a result the algae have a longer season to grow and spread.

"The algae spread a little more every year. When I travel to Greenland, I now see vast areas where the ice is completely dark because of the algae," he says.

Looking for an algaecide

Alexandre Anesio and his colleagues are spending a lot of time on the black algae because they are trying to find out whether the algae growth can be slowed down in some way or another.

The is a balance In most ecosystems -- a kind of equilibrium -- because the various organisms keep each other in check. So Alexandre Anesio wants to learn more about the relationship between the different microbes.

"The various microorganisms on the ice affect each other. Some leave nutrition that others live off. Small viral particles attack and consume bacteria. We believe that some of the fungal spores could eat the black algae. This is what we're looking for," he says.

However, he stresses that, even if they do find a way to curb algae growth, this will not solve climate change. Although it could slow it down.

Algae growth is a consequence of our releasing too many greenhouse gases into the atmosphere. And this is where the problem must be solved. We need to focus on slowing down our emissions.

The same pigment as in black tea

Algae is found virtually everywhere. In the sea, in lakes, on trees and rocks, and even as small spores in the air. Most algae are greenish. Like plants and trees, they are green because of chlorophyll. A molecule that enables them to photosynthesise.

But it's different for the black algae.

"Because the algae live on the ice, they're bombarded with sunlight and radiation. To protect themselves, they produce a lot of black pigment. It's actually the same pigment as in black tea. The pigment forms a protective layer outside the algae and protects the chlorophyll molecules against the dangerous radiation," says Alexandre Anesio. When the pigment absorbs the sun's rays, it generates heat. This heat makes the ice around the algae melt. And this actually benefits the algae. They need both water and micronutrients from the ice to live.

And they can only use the water when it is liquid.

NASA also has an eye on his research

Alexandre Anesio's research into life on the ice is important for a better understanding of climate change. However, NASA is also following his research results closely. The results may be crucial in the hunt for life in space.

"NASA has approached us several times because we're working with life that lives in one of the most inhospitable places on Earth. If life thrives on and under the ice, there's a probability that we'll also find life in the ice on Mars or Jupiter's and Saturn's ice moons, for example," he says.

Before NASA sent their Perseverance rover to Mars, they even invited Alexandre Anesio to a meeting.

"They were afraid that the rover would take with it microbes from Earth. Microbes that may be able to survive on Mars and pollute the samples they were going to take from Mars. So, they wanted to know what conditions life can survive in. What are the boundaries for life?"

Can give an indication of what they should look for

NASA is so interested in the research of life in the ice because we haven't found liquid water on any other planets in the solar system. Not yet, anyway. But we've found plenty of ice.

However, there is evidence to suggest that there are liquid oceans beneath the frozen surface of Saturn's moon, Enceladus and Jupiter's moon, Europa -- and one of the necessities of life, as we know it, is liquid water.

Therefore, NASA and other space agencies are very interested in learning more about the type of life that can live on and under the ice. Because organisms that resemble those in Greenland are probably those they'll be looking for on the ice moons.

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The evolution of honey bee brains

Researchers have proposed a new model for the evolution of higher brain functions and behaviors in the Hymenoptera order of insects. The team compared the Kenyon cells, a type of neuronal cell, in the mushroom bodies (a part of the insect brain involved in learning, memory and sensory integration) of "primitive" sawflies and sophisticated honey bees. They found that three diverse, specialized Kenyon cell subtypes in honey bee brains appear to have evolved from a single, multifunctional Kenyon cell-subtype ancestor. In the future, this research could help us better understand the evolution of some of our own higher brain functions and behaviors.

Are you "busy as a bee," a "social butterfly" or a "fly on the wall"? There are many ways we compare our behavior to that of insects, and as it turns out there may be more to it than just fun idioms. Studying insects could help us understand not only how their behavior has evolved, but also the behavior of highly evolved animals, including ourselves. Mammalian brains are big and complex, so it is difficult to identify which behaviors and neural and genetic changes have co-developed over time. By comparison, insect brains are much smaller and simpler, making them useful models for study.

"In 2017, we reported that the complexity of Kenyon cell (KC) subtypes in mushroom bodies in insect brains increases with the behavioral diversification in Hymenoptera (a large and varied order of insects)" explained Professor Takeo Kubo from the Graduate School of Science at the University of Tokyo and co-author of the current study. "In other words, the more KC subtypes an insect has, the more complex its brain and the behaviors it may exhibit. But we didn't know how these different subtypes evolved. That was the stimulus for this new study."

The team from the University of Tokyo and Japan's National Agriculture and Food Research Organization (NARO) chose two Hymenoptera species as representatives for different behaviors: the solitary turnip sawfly (which has a single KC subtype) and the sophisticated, social honey bee (which has three KC subtypes). As the sawfly has a more "primitive" brain, it is thought to contain some ancestral properties of the honey bee brain. To uncover the potential evolutionary pathways between them, the researchers used transcriptome analysis to identify the gene expression profiles (the genetic activity) of the various KC subtypes and speculate their functions.

"I was surprised that each of the three KC subtypes in the honey bee showed comparable similarity to the single KC type in the sawfly," said Assistant Professor Hiroki Kohno, co-author from the Graduate School of Science. "Based on our initial comparative analysis of several genes, we had previously supposed that additional KC subtypes had been added one by one. However, they appear to have been separated from a multifunctional ancestral type, through functional segregation and specialization." As the number of KC subtypes increased, each subtype almost equally inherited some distinct properties from an ancestral KC. These then modified in different ways, resulting in their varied present-day functions.

The researchers wanted a specific behavioral example of how ancestral KC functions are present in both the sawfly and the honey bee. So, they trained sawflies to engage in a common honey bee behavior test, where they learn to associate an odor stimulus with a reward. Although challenging at first, the team was eventually able to engage the sawflies in the memory task. The researchers then manipulated a gene called CaMKII in sawfly larvae, which in honey bees is associated with forming long-term memory, a KC function. When the larvae became adults, their long-term memory was impaired, indicating that the gene plays a similar role in both sawflies and honey bees. Although CaMKII was expressed (i.e., was active) across the entire single KC subtype in sawflies, in honey bees, it was preferentially expressed in only one KC subtype. This suggests that the role of CaMKII in long-term memory was passed down to the specific KC subtype in the honey bee.

Despite differences in the size and complexity of insect and mammalian brains, there are commonalities in terms of function and the basic architecture of the nervous system. That is why the model proposed in this study for the evolution and diversification of KC subtypes may help towards better understanding the evolution of our own behavior. Next, the team is interested in studying KC types acquired in parallel with social behaviors, such as the honey bee's "waggle dance."

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Researchers develop model for how the brain acquires essential omega-3 fatty acids

Researchers at the UCLA David Geffen School of Medicine, the Howard Hughes Medical Institute at UCLA and the National Institutes of Health have developed a zebrafish model that provides new insight into how the brain acquires essential omega-3 fatty acids, including docosahexaenoic acid (DHA) and linolenic acid (ALA). Their findings, published in Nature Communications,have the potential to improve understanding of lipid transport across the blood-brain barrier and of disruptions in this process that can lead to birth defects or neurological conditions. The model may also enable researchers to design drug molecules that are capable of directly reaching the brain.

Omega-3 fatty acids are considered essential because the body cannot make them and must obtain them through foods, such as fish, nuts and seeds. DHA levels are especially high in the brain and important for a healthy nervous system. Infants obtain DHA from breastmilk or formula, and deficiencies of this fatty acid have been linked to problems with learning and memory. To get to the brain, omega-3 fatty acids must pass through the blood-brain barrier via the lipid transporter Mfsd2a, which is essential for normal brain development. Despite its importance, scientists did not know precisely how Mfsd2a transports DHA and other omega-3 fatty acids.

In the study, the research team provides images of the structure of zebrafish Mfsd2a, which is similar to its human counterpart. The snapshots are the first to detail precisely how fatty acids move across the cell membrane. The study team also identified three compartments in Mfsd2a that suggest distinct steps required to move and flip fatty acids through the transporter, as opposed to movement through a linear tunnel or along the surface of the protein complex. The findings provide key information on how Mfsd2a transports omega-3 fatty acids into the brain and may enable researchers to optimize drug delivery via this route. The study also provides foundational knowledge on how other members of this transporter family, called the major facilitator superfamily (MFS), regulate important cellular functions.

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Tiny microbes could brew big benefits for green biomanufacturing

A research team led by Lawrence Berkeley National Laboratory (Berkeley Lab) and UC Berkeley has engineered bacteria to produce new-to-nature carbon products that could provide a powerful route to sustainable biochemicals.

The advance -- which was recently announced in the journal Nature -- uses bacteria to combine natural enzymatic reactions with a new-to-nature reaction called the "carbene transfer reaction." This work could also one day help reduce industrial emissions because it offers sustainable alternatives to chemical manufacturing processes that typically rely on fossil fuels.

"What we showed in this paper is that we can synthesize everything in this reaction -- from natural enzymes to carbenes -- inside the bacterial cell. All you need to add is sugar and the cells do the rest," said Jay Keasling, a principal investigator of the study and CEO of the Department of Energy's Joint BioEnergy Institute (JBEI).

Carbenes are highly reactive carbon-based chemicals that can be used in many different types of reactions. For decades, scientists have wanted to use carbene reactions in the manufacturing of fuels and chemicals, and in drug discovery and synthesis.

But these carbene processes could only be carried out in small batches via test tubes and required expensive chemical substances to drive the reaction.

In the new study, the researchers replaced expensive chemical reactants with natural products that can be produced by an engineered strain of the bacteria Streptomyces. Because the bacteria use sugar to produce chemical products through cellular metabolism, "this work enables us to perform the carbene chemistry without toxic solvents or toxic gases typically used in chemical synthesis," said first author Jing Huang, a Berkeley Lab postdoctoral researcher in the Keasling Lab. "This biological process is much more environmentally friendly than the way chemicals are synthesized today," Huang said.

During experiments at JBEI, the researchers observed the engineered bacterium as it metabolized and converted sugars into the carbene precursor and the alkene substrate. The bacterium also expressed an evolved P450 enzyme that used those chemicals to produce cyclopropanes, high-energy molecules that could potentially be used in the sustainable production of novel bioactive compounds and advanced biofuels. "We can now perform these interesting reactions inside the bacterial cell. The cells produce all of the reagents and the cofactors, which means that you can scale this reaction to very large scales" for mass manufacturing, Keasling said.

Recruiting bacteria to synthesize chemicals could also play an integral role in reducing carbon emissions, Huang said. According to other Berkeley Lab researchers, close to 50% of greenhouse gas emissions come from the production of chemicals, iron and steel, and cement. Limiting global warming to 1.5 degrees Celsius above pre-industrial levels will require severely cutting greenhouse gas emissions in half by 2030, says a recent report by the Intergovernmental Panel on Climate Change.

Huang said that while this fully integrated system can be envisioned for a large number of carbene donor molecules and alkene substrates, it is not yet ready for commercialization.

"For every new advance, someone needs to take the first step. And in science, it can take years before you succeed. But you have to keep trying -- we can't afford to give up. I hope our work will inspire others to continue searching for greener, sustainable biomanufacturing solutions," Huang said.

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Scientists present evidence for a billion-years arms race between viruses and their hosts

Researchers have proposed a new evolutionary model for the origin of a kingdom of viruses called Bamfordvirae, suggesting a billion-years evolutionary arms race between two groups within this kingdom and their hosts.

Their study, published today as a Reviewed Preprint in eLife, provides what the editors say are convincing analyses that advance our understanding of the deep evolutionary history of viruses, the interaction between viruses and the first eukaryotes (organisms with cells that include a nucleus), and the diversification of viral lineages.

Viruses in the kingdom Bamfordvirae make up one of the most diverse groups that infect living organisms. They include the Nucleocytoplasmic Large DNA viruses (NCLDVs; the largest viruses characterised to date), virophages (viral parasites of other viruses), adenoviruses (common viruses that cause cold and flu-like symptoms), and Mavericks and Polinton-like viruses (both virus-like mobile genetic elements that colonise the genomes of their hosts).

There are two main hypotheses for the origins of these viruses: the 'nuclear-escape' and 'virophage-first' hypotheses. The nuclear-escape hypothesis says that a Maverick-like ancestor originated with hosts (endogenous), escaped from the host cell nucleus and gave rise to adenoviruses and NCLDVs. In contrast, the virophage-first hypothesis suggests that NCLDVs co-evolved with early virophages. Mavericks then evolved from virophages that became endogenous, with adenoviruses escaping from the host nucleus at a later stage.

"Despite these proposed scenarios, the diversification of viruses in the Bamfordvirae kingdom remains a major open question in virus evolution. To gain a better understanding of their history, we wanted to test the predictions made by both the nuclear-escape and virophage-first models, and consider alternative scenarios regarding the origin of different lineages," says José Gabriel Niño Barreat, Postdoctoral Research Assistant at the University of Oxford, UK. Barreat is a co-author of the study alongside Aris Katzourakis, Professor of Evolution and Genomics at the University of Oxford's Department of Biology.

Barreat and Katzourakis used two hypothesis-testing methods (maximum-likelihood and Bayesian frameworks) to compare the plausibility of the nuclear-escape versus alternative evolutionary scenarios. They focused on four key proteins shared by viruses in this lineage which are involved in the formation of viral capsids: major and minor capsid proteins, DNA-packaging ATPase, and protease. They applied another two methods that use genetic data to estimate rooted phylogenies, to infer the evolutionary trajectory of the different lineages. Then, they assessed whether adenoviruses and NCLDVs descended from a common ancestor, as predicted by the nuclear-escape scenario.

Their analyses revealed strong evidence against a sister relationship between adenoviruses and NCLDVs, as suggested by the nuclear-escape hypothesis. Instead, the findings suggest that adenoviruses descended from a common ancestor with Mavericks, to the exclusion of NCLDVs. At odds with a virophage-first scenario, the researchers found that the most recent common ancestor of Mavericks and adenoviruses was not a virophage. However, their work does not rule out the virophage-first hypothesis completely, making it the one best supported by current phylogenetic analyses.

Additionally, their work provides support for the positioning of the Bamfordvirae ancestral root between virophages and the other viral lineages. This positioning pointed the team towards a new model for the evolutionary origins of these viruses.

"The model proposes that the Bamfordvirae ancestor did not originate from an invasion of the eukaryotic cell nucleus, and that it was a non-virophage DNA virus with a small genome," says co-author Aris Katzourakis. "The lifestyle of virophages would have evolved at a later stage as these became specialised parasites of the ancestral NCLDVs." Katzourakis adds that the relative timing of events suggests the most recent common ancestor of the Bamfordvirae kingdom existed more than a billion years ago, extending to the initial stages of eukaryotic life. However, an absolute timescale for the precise dating of these events is not currently available.

Another limitation of the study is that the phylogenetic signal in the protein data analysed may have been obscured by the deep divergences and extreme diversity in this lineage. However, the authors were able to robustly distinguish between alternative scenarios, and the focus on the origin and development of the viral capsid provides a simple way to explain the available data.

"This work contributes to our knowledge on how viruses evolve different evolutionary strategies, for example to become parasites of other viruses like virophages, or viral giants like NCLDVs," Barreat says. "As well as playing important roles in Earth's ecosystems, it is becoming increasingly clear that viruses may have contributed to major evolutionary transitions during the history of life. Therefore, understanding the deep evolutionary history of viruses provides more context for these ancient interactions and the actors involved."

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Vanishing glaciers threaten alpine biodiversity

With glaciers melting at unprecedented rates due to climate change, invertebrates that live in the cold meltwater rivers of the European Alps will face widespread habitat loss, warn researchers.

Many of the species are likely to become restricted to cold habitats that will only persist higher in the mountains, and these areas are also likely to see pressures from the skiing and tourism industries or from the development of hydroelectric plants.

The research study -- led jointly by the University of Leeds and University of Essex -- calls on conservationists to consider new measures to protect aquatic biodiversity.

Invertebrates -- key role in ecosystems

The invertebrates, which include stoneflies, midges and flatworms, play a key role in nutrient cycling and organic matter transfer to fish, amphibians, birds and mammals in the wider Alpine ecosystem.

Using glacier, landscape and biodiversity mapping data collected across the Alps, scientists from across Europe simulated how key invertebrate populations across the mountain range are likely to change between now and 2100 because of climate change.

As the climate warms, the modelling predicted the invertebrate species would seek out colder conditions in the highest parts of the mountain range. In the future, these colder areas are also likely to be prioritised for skiing or tourism or the development of hydropower plants.

Lee Brown, Professor of Aquatic Science at the University of Leeds who co-led the research, said: "Conservationists need to be thinking about how protected area designations must evolve to take into account the effects of climate change.

"It may be that some species will have to be moved to refuge areas if we want to safeguard their survival as many of them are not strong fliers so they cannot disperse easily through the mountains."

Alpine climate is changing rapidly

The research, involving a collaboration between nine European research institutions, brought together data on invertebrate species distribution in the Alps, an area that covers more than 34,000 square kilometres, and mapped it alongside expected changes to glaciers and river flows.

There was sufficient data to model what was likely to happen to 19 invertebrate species, mainly aquatic insects, that live in the cold-water regions of the Alps.

Dr Jonathan Carrivick, from the School of Geography at Leeds who co-led the research, said: "We have quantified that as glaciers melt and retreat, the rivers running through the Alps will experience major changes in their water source contributions.

"In the short term, some will carry more water and some new tributary rivers will form, but over several decades from now -- most rivers will become drier, flow slower and become more stable, and there could even have periods in a year when there is no water flow. Additionally, most water in Alpine rivers will also be warmer in the future."

Losers and winners

By the turn of the century, the modelling predicts that most of the species would have experienced "consistent losses" of habitat.

Those hardest hit are expected to be the non-biting midges, Diamesa latitarsis grp., D. steinboecki, and D. bertrami; the stonefly, Rhabdiopteryx alpina; and mayfly, Rhithrogena nivata.

However, several species are expected to benefit from the habitat changes, including the flatworm, Crenobia alpina and the flat headed may fly, Rhithrogena loyolaea.

Other species would find refuge in new locations. The scientists predict the stonefly Dictyogenus alpinus and the caddisfly Drusus discolor will be able to survive in the Rhone valley in southeast France while other species will be lost from the rivers that flow into the Danube basin.

Conservation

Writing in the paper, the researchers describe the "substantial work" that is necessary to protect the biodiversity in rivers that are being fed by retreating glaciers. The locations where glaciers still exist late in the 21st century are likely to be prioritised for hydropower dam construction and ski resort development.

Dr Martin Wilkes, from the University of Essex and who co-led the research, said: "The losses we predict for Alpine biodiversity by the end of this century relate to just one of several possible climate change scenarios.

"Decisive action by world leaders to reduce greenhouse gas emissions could limit the losses. On the other hand, inaction could mean that the losses happen sooner than we predict."

Understanding how invertebrate populations respond to climate changes is key to understanding how biodiversity in high mountainous areas can be affected, and the techniques developed in the study could be applied to other mountain environments.

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Scientist uncovers roots of antibiotic resistance

Bacteria naturally adapt to various environmental stimuli and as they mutate, these changes can make them resistant to drugs that would kill or slow their growth.

In a recent article published in PLoS Genetics, UCF College of Medicine microbiologist Dr. Salvador Almagro-Moreno uncovers the evolutionary origins of antimicrobial resistance (AMR) in bacteria. His studies on the bacterium that causes cholera, Vibrio cholerae, provide insight into deciphering what conditions must occur for infectious agents to become resistant.

"How AMR occurs in bacterial populations and the pathways leading to these new traits are still poorly understood," he said. "This poses a major public health threat as antimicrobial resistance is on the rise."

Dr. Almagro-Moreno studied genetic variants of a protein found in bacterial membranes called OmpU. Using computational and molecular approaches, his team found that several OmpU mutations in the cholera bacteria led to resistance to numerous antimicrobial agents. This resistance included antimicrobial peptides that act as defenses in the human gut. The researchers found that other OmpU variants did not provide these properties, making the protein an ideal system for deciphering the specific processes that occur to make some bacteria resistant to antimicrobials.

By comparing resistant and antibiotic sensitive variants, the researchers were able to identify specific parts of OmpU associated with the emergence of antibiotic resistance. They also discovered that the genetic material encoding these variants, along with associated traits, can be passed between bacterial cells, increasing therisk of spreading AMR in populations under antibiotic pressure.

By understanding how mutations occur, researchers can better understand and develop therapeutics to combat resistant infections. Dr. Almagro-Moreno is also looking at environmental factors such as pollution and warming of the oceans, as possible causes of resistant bacteria. "We are studying the genetic diversity ofenvironmental populations, including coastal Florida isolates, to develop a new approach to understandinghow antimicrobial resistance evolves," he explained.

Read more at Science Daily