Now Northwestern University researchers have developed a new technology that makes it easier to eavesdrop on our body’s inner conversations.

While the body’s chemical signals are incredibly faint — making them difficult to detect and analyze — the researchers have developed a new method that boosts signals by more than 1,000 times. Transistors, the building block of electronics, can boost weak signals to provide an amplified output. The new approach makes signals easier to detect without complex and bulky electronics.

By enabling amplification of weak biochemical signals, the new approach brings modern medicine one step closer to real-time, on-site diagnostics and disease monitoring.

The research was published Saturday (March 24) in the journal Nature Communications.

“If we could reliably measure biochemical signals in the body, we could incorporate those sensors into wearable technologies or implants that have a small footprint, less burden and don’t require expensive electronics,” said Northwestern’s Jonathan Rivnay, the study’s senior author. “But extracting high-quality signals has remained a challenge. With limited power and space inside the body, you need to find ways to amplify those signals.”

Rivnay is a professor of biomedical engineering at Northwestern’s McCormick School of Engineering. Xudong Ji, a post-doctoral researcher in Rivnay’s laboratory, is the paper’s first author.

While they communicate vital information packed with potential to guide diagnoses and treatment, many chemical sensors produce weak signals. In fact, health care professionals often cannot decipher these signals without removing a sample (blood, sweat, saliva) and running it through high-tech laboratory equipment. Usually, this equipment is expensive and perhaps even located off-site. And results can take an excruciatingly long time to return.

Rivnay’s team, however, aims to sense and amplify these hidden signals without ever leaving the body.

Other researchers have explored electrochemical sensors for biosensing using aptamers, which are single strands of DNA engineered to bind to specific targets. After successfully binding to a target of interest, aptamers act like an electronic switch, folding into a new structure that triggers an electrochemical signal. But with aptamers alone, the signals are often weak and highly susceptible to noise and distortion if not tested under ideal and well-controlled conditions.

To bypass this issue, Rivnay’s team equipped an amplifying component onto a traditional electrode-based sensor and developed an electrochemical transistor-based sensor with new architecture that can sense and amplify the weak biochemical signal. In this new device, the electrode is used to sense a signal, but the nearby transistor is dedicated to amplifying the signal. The researchers also incorporated a built-in, thin-film reference electrode to make the amplified signals more stable and reliable.

“We combine the power of the transistor for local amplification with the referencing you get from well-established electrochemical methods,” Ji said. “It’s the best of both worlds because we’re able to stably measure the aptamer binding and amplify it on site.”

To validate the new technology, Rivnay’s team turned to a common cytokine, a type of signaling protein, that regulates immune response and is implicated in tissue repair and regeneration. By measuring the concentration of certain cytokines near a wound, researchers can assess how quickly a wound is healing, if there is a new infection or whether or not other medical interventions are required.

In a series of experiments, Rivnay and his team were able to amplify the cytokines’ signal by three-to-four orders of magnitude compared with traditional electrode-based aptamer sensing methods. Although the technology performed well in experiments to sense cytokine signaling, Rivnay says it should be able to amplify signals from any molecule or chemical, including antibodies, hormones or drugs, where the detection scheme uses electrochemical reporters.

“This approach is broadly applicable and doesn’t have a specific use case,” Rivnay said. “The big vision is to implement our concept into implantable biosensors or wearable devices that can both sense a problem and then respond it.”

The study, “Organic electrochemical transistors as on-site signal amplifier for electrochemical aptamer-based sensing,” was supported by the Defense Advanced Research Projects Agency (grant number D20AC00002).

The approach uses an innovative copper-containing polymeric filter and essentially converts CO₂ into sodium bicarbonate (aka baking soda) that can be released harmlessly into the ocean. This new hybrid material, or filter, is called DeCarbonHIX (i.e., decarbonization through hybrid ion exchange material), and is described in a paper recently published in the journal Science Advances.

The research, which demonstrated a 300 percent increase in the amount of carbon captured compared with existing direct air capture methods, has garnered international attention from media outlets like the BBC, CNN, Fast Company, and The Daily Beast, and professional organizations like the American Chemical Society. SenGupta himself has been fielding interest in the technology from companies based in Brazil, Ireland, and the Middle East.

“The climate crisis is an international problem,” says SenGupta, who is a professor of chemical and biomolecular engineering and civil and environmental engineering in Lehigh’s P.C. Rossin College of Engineering and Applied Science. “And I believe we have a responsibility to build direct air capture technology in a way that it can be implemented by people and countries around the world. Anyone who can operate a cell phone should be able to operate this process. This is not technology for making money. It’s for saving the world.”

The work is yet another extension of SenGupta’s personal and professional commitment to developing technologies that benefit humanity, and in particular, marginalized communities around the world. His research on water science and technology has included drinking water treatment methodologies, desalination, municipal wastewater reuse, and resource recovery. He invented the first reusable, arsenic-selective hybrid anion exchanger nanomaterial (HAIX-Nano), and as a result, more than two million people around the world now drink arsenic-safe water. Two of his patents have been recognized as “Patents for Humanity” by the US patent and Trademark Office.

His invention of DeCarbonHIX was the outcome of an ongoing CO₂-driven wastewater desalination project funded by the Bureau of Reclamation under the jurisdiction of the U.S. Department of the Interior. SenGupta and his students were on the lookout for a reliable supply of CO₂ even in remote places. That quest led the way to the field of direct air capture, or DAC, and the creation of DeCarbonHIX. This subject was the dissertation topic for environmental engineering student Hao Chen ’23 PhD, who successfully defended his PhD in March and will receive his doctorate in May.

Capturing carbon at lower concentrations

The most abundant of the greenhouse gasses contributing to global warming is carbon dioxide. In 2021, global emissions of CO₂ rose by 6 percent from the previous year — to 36.3 gigatons, according to the International Energy Agency. Just one gigaton (equal to 1 billion tons) is the equivalent of the mass of all land mammals on earth.

Emissions from greenhouse gasses have increased global temperatures by approximately 1.1 degrees Celsius above pre-industrial levels, according to the Intergovernmental Panel on Climate Change. In its 2021 working group report, the IPCC estimates the average yearly temperature over the next 20 years is expected to rise by at least 1.5 degrees Celsius. The warmer the earth gets, the greater the fallout in terms of rising sea levels, extreme storm events, and ecological disruption, all of which have repercussions on global health, security, and stability.

“The worst part of this crisis is that people who are marginalized, who are poor, will suffer 10 times more than those who contributed to this situation,” says SenGupta.

There are three ways to reduce CO₂, he says. The first — government action — can reduce emissions, but that won’t address what’s already in the air.

“The second way is removing it from point sources, places like chimneys and stacks where carbon dioxide is being emitted in huge amounts,” he says. “The good thing about that is you can remove it at very high concentrations, but it only targets emissions from specific sources.”

The newest method is called direct air capture, which, he says, “allows you to remove CO₂ from anywhere, even your own backyard.”

With DAC, chemical processes remove CO₂ from the atmosphere, after which it’s typically stored underground. However, says SenGupta, the technology is limited by its capacity. It can’t capture enough CO2 to overcome the energy cost of running the process.

“If you’re capturing carbon dioxide from a chimney at a plant, the amount of CO₂ in the air can be upwards of 100,000 parts per million,” he says. “At that concentration, it’s easy to remove. But generally speaking, the CO2 level in the air is around 400 parts per million. That’s very high from a climate change point of view, but for removal purposes, we consider that ultra-dilute. Current filter materials just can’t collect enough of it.”

Another challenge with DAC involves storage. After the CO₂ is captured, it’s dissolved, put under pressure, liquified, and typically stored miles underground. A DAC operation must then be located in an area with enough geological storage — and stability. A country like Japan, for instance, can’t pump CO₂ underground because the area is prone to earthquakes.

Seeing a solution in seawater

SenGupta has developed a DAC method that overcomes both the capture problem and the issue of storage.

For the capture problem, he developed DeCarbonHIX — a mechanically strong, chemically stable sorbent (a material used to absorb liquids or gasses) — that contains copper.

“The copper changes an intrinsic property of the parent polymer material and enhances the capturing capacity by 300 percent,” he says. “We showed that for direct air capture from air with 400 parts per million of CO₂, we achieve capacity, meaning capacity is no longer a function of how much carbon dioxide is in the air. The filter will get saturated completely at any concentration, which means you can perform DAC in your backyard, in the middle of the desert, or in the middle of the ocean.”

The ocean is actually SenGupta’s solution to the storage problem. His DAC process starts with air blowing through the filter to capture CO₂. Once the filter is saturated with gas molecules (determined by measuring the amount of gas going into the filter versus coming out of it), seawater is passed through the filter. The seawater converts the carbon dioxide to sodium bicarbonate (you likely know it as baking soda, but lose the visual as we’re talking about a dissolved solution here). The dissolved sodium bicarbonate is then released directly into the ocean, what Sengupta calls “an infinite sink.”

“And it has no adverse impact on the ocean whatsoever,” says SenGupta. “It doesn’t change the salinity at all.”

In fact, he says, the sodium bicarbonate, which is slightly alkaline, may improve the health of the ocean. That’s because elevated levels of CO₂ in the atmosphere have gradually reduced the pH of the ocean, causing acidification. More acidic waters harm the growth and reproduction of marine life like corals and plankton and can create catastrophic collapses in the food chain.

“Sodium bicarbonate may reverse that lowering of pH,” he says.

It’s worth noting, he says, that like existing DAC processes, DeCarbonHIX can also be desorbed with hot water or steam, and pure CO₂ can be recovered, compressed, and stored underground in geological storage.

“In reality, this new filter material offers a dual mode of desorption and sequestration.”

In a study published in Current Biology, Tulane psychology professor Jonathan Fadok, PhD, and postdoctoral researcher Lydia Smith-Osborne looked at two forms of psychosocial stress — social isolation and social instability — and how they manifest themselves based on social rank.

They conducted their research on adult female mice, putting them in pairs and allowing them to form a stable social relationship over several days. In each pair, one of the mice had high, or dominant social status, while the other was considered the subordinate with relatively low social status. After establishing a baseline, they monitored changes in behavior, stress hormones and neuronal activation in response to chronic social stress.

“We analyzed how these different forms of stress impact behavior and the stress hormone corticosterone (an analogue of the human hormone, cortisol) in individuals based on their social rank,” said Fadok, an assistant professor in the Tulane Department of Psychology and the Tulane Brain Institute. “We also looked throughout the brain to identify brain areas that are activated in response to psychosocial stress.”

“We found that not only does rank inform how an individual responds to chronic psychosocial stress, but that the type of stress also matters,” said Smith-Osborne, a DVM/PhD and the first author on the study.

She discovered that mice with lower social status were more susceptible to social instability, which is akin to ever-changing or inconsistent social groups. Those with higher rank were more susceptible to social isolation, or loneliness.

There were also differences in the parts of the brain that became activated by social encounters, based upon the social status of the animal responding to it and whether they had experienced psychosocial stress.

“Some areas of a dominant animal’s brain would react differently to social isolation than to social uncertainty, for example,” Smith-Osborne said. “And this was also true for subordinates. Rank gave the animals a unique neurobiological ‘fingerprint’ for how they responded to chronic stress.”

Do the researchers think the results can translate to people? Perhaps, Fadok said.

“Overall, these findings may have implications for understanding the impact that social status and social networks have on the prevalence of stress-related mental illnesses such as generalized anxiety disorder and major depression,” he said. “However, future studies that use more complex social situations are needed before these results can translate to humans.”

They published their results on March 30 in Geophysical Research Letters.

The team’s finding could also shed light on another phenomenon: the small shock sometimes felt when touching a metal doorknob. Called spark discharge, it occurs when a voltage difference is created between a body and a conductor. In a series of lab experiments in the 1960s, scientists discovered that spark discharges produce X-rays — just as lightning does. More than 60 years later, scientists are still conducting lab experiments to better understand the mechanism underpinning this process.

Lightning consists in part of relativistic electrons, which emit spectacular high-energy bursts of X-rays with tens of mega electron-volt energies called terrestrial gamma-ray flashes (TGFs). Researchers have created simulations and models to explain the TGF observations, but there is a mismatch between simulated and actual sizes, according to lead author Victor Pasko, Penn State professor of electrical engineering. Pasko and his team mathematically modeled the TGF phenomenon to better understand how it can occur in observed compact space.

“The simulations are all very big — usually several kilometers across — and the community has difficulty reconciling this right now with actual observations, because when lightning propagates, it’s very compact,” Pasko said, explaining that lightning’s space channel is typically several centimeters in scale, with electric discharge activity producing X-rays expanding around tips of these channels up to 100 meters in extreme cases. “Why is that source so compact? It’s been a puzzle until now. Since we’re working with very small volumes, it may also have implications for the lab experiments with spark discharges underway since the 1960s.”

Pasko said that they developed the explanation for how an electric field amplifies the number of electrons, driving the phenomenon. The electrons scatter on individual atoms, which constitute the air, as they experience acceleration. As the electrons move, most of them go forward as they gain energy and multiply, similar to a snow avalanche, allowing them to produce more electrons. As the electrons avalanche, they produce X-rays, which launch the photons backward and produce new electrons.

“From there, the question we wanted to answer mathematically was, ‘What is the electric field you need to apply in order to just replicate this, to launch just enough X-rays backwards to allow amplification of these select electrons?'” Pasko said.

The mathematical modeling established a threshold for the electric field, according to Pasko, which confirmed the feedback mechanism that amplifies the electron avalanches when X-rays emitted by the electrons travel backward and generate new electrons.

“The model results agree with the observational and experimental evidence indicating that TGFs originate from relatively compact regions of space with spatial extent on the order of 10 to 100 meters,” Pasko said.

In addition to describing high-energy phenomena related to lightning, Pasko said the work may eventually help to design new X-ray sources. The researchers said they plan to examine the mechanism using different materials and gases, as well as different applications of their findings.

The other authors on the paper are Reza Janalizadeh, a postdoctoral scholar in the Penn State Department of Electrical Engineering; Sebastien Celestin of the University of Orleans in Orleans, France; Anne Bourdon, of Ecole Polytechnique in Palaiseau, France; and Jaroslav Jansky of the University of Defense in Brno, Czechia.

The National Science Foundation funded this work.

New research led by Penn State reveals that the stem region of the spike protein became progressively tighter over time, and the team thinks this likely improved the virus’s ability to transmit through nasal droplets and infect host cells once in the body. The team said the stem region of the protein that emerged in the most recent Omicron variants is as rigid as it can get, which could mean that newer vaccines may be effective for longer than the ones that targeted the original variant.

“We wanted to see how the spike protein morphed structurally as it evolved from the original wild-type strain of the virus, through the alpha, delta and most recently Omicron variants,” said Ganesh Anand, associate professor of chemistry and of biochemistry and molecular biology, Penn State. “We found that the spike protein was initially more flexible at the stem region, which is where the spike protein is bundled together, but over time, mutations caused the protein to become progressively tighter and more rigid, and we think it’s now as rigid as it can get. This is important because it means that vaccines that are developed to target the current variant with these rigid spike proteins are likely to be effective for much longer than previous vaccines against the more flexible wild-type strain.”

To study how the spike protein changed with each of the new variants, the team studied the virus in vitro (in a test tube) using a technique called amide hydrogen/deuterium exchange mass spectrometry.

Anand explained that the SARS-CoV-2 spike protein is composed of three chain molecules called monomers that are bound together to form a trimer. The spike protein is made up of two subunits, an S1 and S2 subunit. The S1 subunit contains a receptor binding domain while the S2 subunit contains the stem region responsible for bundling the trimer.

“It is analogous to a tree, with the stem forming the trunk and the receptor binding domain forming the branches,” said Anand.

The team’s results, which published in the journal eLife, revealed that the spike protein stem first became more rigid with the D614G mutation, which is common to all SARS-CoV-2 variants. The stem became progressively more twisted with the emergence of new mutations in subsequent variants, and the Omicron BA.1 variant showed the largest magnitude increase in stabilization relative to preceding variants.

Why would the virus benefit from a tighter core?

“We did not study the virus in patients, so we cannot determine if the changes we observed in the spike protein directly affected the newer variants such as Omicron’s ability to transmit more readily; however, we can say that the changes likely made the virus more fit, which could translate to better transmission,” said Anand. “A tighter core could likely make the virus more stable in nasal droplets and faster at binding to and entering host cells. So, for example, what initially took about 11 days to develop an infection after exposure now takes only about four days.”

Anand noted that one of the reasons the vaccines have not been able to fully neutralize the virus is because they were generated against the spike protein of the original wild-type variant.

“The latest bivalent booster — which targets newer variants — helps, but people who never got this booster aren’t receiving this more targeted protection,” he said. “Future vaccines that focus specifically on Omicron are likely to be effective for longer.”

Finally, Anand said that the spike protein has now become so tightly twisted that it is unlikely to structurally change further at the stem region.

“There are limits to how much it can tighten,” he said. “I think that we can have some cautious optimism, in that we’re not going to continuously have variants emerging, at least tightening is not going to be a mechanism.”

Other Penn State authors on the paper include chemistry graduate students Sean Braet, Theresa Buckley and Varun Venkatakrishnan. Kim-Marie Dam, postdoctoral research fellow, and Pamela Bjorkman, assistant professor of biology and biological engineering, Caltech, also are authors.

“When you look around the world today, you can see ants on nearly every continent occupying all these different habitats, and even different dimensions of those habitats — some ants live underground, some live in the canopies of trees. We’re trying to understand how they were able to diversify from a single common ancestor to occupy all these different spaces,” says Matthew Nelsen, a research scientist at the Field Museum in Chicago and lead author of the paper.

Scientists already knew that ants and flowering plants, or angiosperms, both originated around 140 million years ago and subsequently became more prevalent and spread to new habitats. Nelsen and his colleagues wanted to find evidence that the two groups’ evolutionary paths were linked.

To find that link, Nelsen and his co-authors (Corrie Moreau at Cornell University, Kevin Boyce at Stanford University, and Richard Ree at the Field Museum) compared the climates that 1,400 modern ant species inhabit, including data on temperature and precipitation. They coupled this information with a time-scaled reconstruction of the ant family tree, based on genetic information and ant fossils preserved in amber. Many ant behaviors, like where they build their nests and what habitats they live in, appear to be deeply ingrained in their species’ lineages, to the point that scientists are able to make pretty good guesses about prehistoric ants’ lives based on their modern relatives. These data, when paired with similar information about plants, helped bring the early ants’ world into focus.

About 60 million years ago, ants lived primarily in forests and built their nests underground. “Around this time, some of the plants in these forests evolved to exhale more water vapor out through tiny holes in their leaves — they made the whole place a lot wetter, so the environment became more like a rainforest,” says Nelsen. In this wetter environment, some of the ants began moving their nests out from underground and up into the trees. (They weren’t the only ones moving to the trees, either — frogs, snakes, and epiphytic plants, similar to the bromeliads and air plants we have today, also took to the trees around this time, helping create new arboreal communities.)

Some of the flowering plants living in these forests began to spread outward, inching their way into more arid regions and adapting to thrive in drier conditions. Nelsen and his colleagues’ work suggests that when flowering plants left the forests, some of the ants followed. The plants may have provided an incentive for the ants in the form of food. “Other scientists have shown that plants in these arid habitats were evolving ways of making food for ants — including things like elaiosomes, which are like fleshy appendages on the seeds,” says Nelsen. And when ants take the seeds to get the elaiosomes, they help disperse them: a win for the parent plants.

The researchers say that by showing how plants helped shape the evolution and spread of ants is especially important in light of the climate and biodiversity crises we’re facing.

“This study shows the important role that plants play in shaping ecosystems,” says Nelsen. “Shifts in plant communities — such as those we are seeing as a consequence of historic and modern climate change — can cascade and impact the animals and other organisms relying on these plants.”

The Australian continent is dominated by dry ecosystems and widely varying precipitation patterns. Generally, at the end of the dry season — when the first rains begin to fall — CO₂ emissions over Australia rise sharply. “This effect is well-known at the local level, but it was never observed at the continental level,” states Eva-Marie Metz, a doctoral candidate in Prof. Butz’s working group at the Institute of Environmental Physics at Heidelberg University. Data on the atmospheric CO₂ concentrations obtained from the Greenhouse Gases Observing Satellite (GOSAT) were analysed. Using the satellite data from 2009 to 2018, the scientists found that the seasonal pattern of CO₂ concentrations over Australia was much more dynamic than previously assumed.

Until now, the lack of measurement data on ground hampered uncovering the mechanisms that cause these variations. The research team fed the GOSAT satellite data into an atmospheric inversion model, which is used to estimate the CO₂ flux at the ground level. It became clear that there must be an undiscovered mechanism of CO₂ release in Australian terrestrial ecosystems, according to Dr Sanam Vardag, whose group also conducts research at the Institute of Environmental Physics of Heidelberg University. Further studies showed that the concentrations of CO₂ always rise when dry soils are rewetted by heavy rainfall. This causes the so-called “Birch Effect,” reports Dr Vardag. Soil microbes that are inactive when dry are reactivated by the moisture and multiply, causing the soil to “breathe” and release CO₂. Plant photosynthesis does not begin until later, so carbon dioxide is not bound at the end of the dry season, thus causing the seasonally rapid rise in CO₂ that the international team of researchers was able to discern on the continental level.

Their investigations have provided an explanation on how the variations in the carbon fluxes from land to atmosphere occur. According to Prof. Butz, these results are significant because they suggest that dry regions — such as are dominant in Australia — have a greater influence on the variations of the global carbon cycle than previously believed. “Our findings, the first on a continental scale, can be used for climate modelling and thus contribute to a better understanding of the global climate-carbon feedbacks,” explains the Heidelberg researcher.

The research results were published in the journal “Science.” In addition to the environmental physicists from Heidelberg, researchers from the Max Planck Institute for Biogeochemistry in Jena and from the Max Planck Institute for Meteorology in Hamburg as well as from Australia, Canada, China, France, Japan, the United Kingdom, and the USA participated in the research. Funding was provided by the German Research Foundation, among others.

Even images obtained by the world’s best ground-based telescopes are blurry due to the atmosphere’s shifting pockets of air. While seemingly harmless, this blur obscures the shapes of objects in astronomical images, sometimes leading to error-filled physical measurements that are essential for understanding the nature of our universe.

Now researchers at Northwestern University and Tsinghua University in Beijing have unveiled a new strategy to fix this issue. The team adapted a well-known computer-vision algorithm used for sharpening photos and, for the first time, applied it to astronomical images from ground-based telescopes. The researchers also trained the artificial intelligence (AI) algorithm on data simulated to match the Vera C. Rubin Observatory’s imaging parameters, so, when the observatory opens next year, the tool will be instantly compatible.

While astrophysicists already use technologies to remove blur, the adapted AI-driven algorithm works faster and produces more realistic images than current technologies. The resulting images are blur-free and truer to life. They also are beautiful — although that’s not the technology’s purpose.

“Photography’s goal is often to get a pretty, nice-looking image,” said Northwestern’s Emma Alexander, the study’s senior author. “But astronomical images are used for science. By cleaning up images in the right way, we can get more accurate data. The algorithm removes the atmosphere computationally, enabling physicists to obtain better scientific measurements. At the end of the day, the images do look better as well.”

The research will be published March 30 in the Monthly Notices of the Royal Astronomical Society.

Alexander is an assistant professor of computer science at Northwestern’s McCormick School of Engineering, where she runs the Bio Inspired Vision Lab. She co-led the new study with Tianao Li, an undergraduate in electrical engineering at Tsinghua University and a research intern in Alexander’s lab.

When light emanates from distant stars, planets and galaxies, it travels through Earth’s atmosphere before it hits our eyes. Not only does our atmosphere block out certain wavelengths of light, it also distorts the light that reaches Earth. Even clear night skies still contain moving air that affects light passing through it. That’s why stars twinkle and why the best ground-based telescopes are located at high altitudes where the atmosphere is thinnest.

“It’s a bit like looking up from the bottom of a swimming pool,” Alexander said. “The water pushes light around and distorts it. The atmosphere is, of course, much less dense, but it’s a similar concept.”

The blur becomes an issue when astrophysicists analyze images to extract cosmological data. By studying the apparent shapes of galaxies, scientists can detect the gravitational effects of large-scale cosmological structures, which bend light on its way to our planet. This can cause an elliptical galaxy to appear rounder or more stretched than it really is. But atmospheric blur smears the image in a way that warps the galaxy shape. Removing the blur enables scientists to collect accurate shape data.

“Slight differences in shape can tell us about gravity in the universe,” Alexander said. “These differences are already difficult to detect. If you look at an image from a ground-based telescope, a shape might be warped. It’s hard to know if that’s because of a gravitational effect or the atmosphere.”

To tackle this challenge, Alexander and Li combined an optimization algorithm with a deep-learning network trained on astronomical images. Among the training images, the team included simulated data that matches the Rubin Observatory’s expected imaging parameters. The resulting tool produced images with 38.6% less error compared to classic methods for removing blur and 7.4% less error compared to modern methods.

When the Rubin Observatory officially opens next year, its telescopes will begin a decade-long deep survey across an enormous portion of the night sky. Because the researchers trained the new tool on data specifically designed to simulate Rubin’s upcoming images, it will be able to help analyze the survey’s highly anticipated data.

For astronomers interested in using the tool, the open-source, user-friendly code and accompanying tutorials are available online.

“Now we pass off this tool, putting it into the hands of astronomy experts,” Alexander said. “We think this could be a valuable resource for sky surveys to obtain the most realistic data possible.”

The study, “Galaxy image deconvolution for weak gravitational lensing with unrolled plug-and-play ADMM,” used computational resources from the Computational Photography Lab at Northwestern University.

Shigella infections cause fever, stomach pain, and prolonged, sometimes bloody diarrhea for as long as a week. The bacteria sicken 450,000 people each year in the US alone. Although most people recover on their own, children and those with weakened immune systems are at risk of Shigella infections spreading to their bloodstream and causing kidney damage. Shigella infections are a significant cause of sickness and disability, but it’s difficult to study the bacteria because it only sickens primates like humans and apes — not animals easy to study in a lab. The bacteria cannot infect more typical lab animals such as mice.

Previous research had looked at how Shigella interacts with gasdermin-B, a critical part of our immune system that helps protect us against infection. Gasdermin-B is member of a protein family called gasdermin, which includes gasdermin-A, -B, -C, -D, -E and -F. It was thought that when gasdermin-B detects an invader, such as bacteria, it begins to poke holes in the cell’s wall, causing it to burst open and release chemicals that induce inflammation and call reinforcements from the immune system. But the past research studies on gasdermin-B were contradictory; some confirmed its role in cell death during infection, but others contradicted the idea.

UConn School of Medicine immunologist Jianbin Ruan and a team of colleagues from UConn Health wanted to clarify whether gasdermin-B actually does cause cell death in the case of microbial invasion; they also wanted to figure out why it doesn’t do this when Shigella is the invader.

The team needed to take a close look at gasdermin-B. They expressed the protein, purified it, and then cooled the protein down to very low temperatures so it would hold still while they took pictures of it with an electron microscope.

“We collected hundreds of thousands of images to build the 3D models of protein molecules at the atomic level. Through these models we will understand what these proteins look like and how they do their job,” said Chengliang Wang, research fellow in the Ruan lab and first author of the study.

Their research confirms previous research and provides evidence that Shigella bacteria grab onto a specific segment of gasdermin-B in humans. However, the mouse version of the protein has a different shape that prevents Shigella from latching onto it, resulting in the rapid clearance of the bacteria and preventing infection. This finding helps explain why Shigella is unable to infect mice.

Since human gasdermin-B can be configured in six slightly differing proteins, or isoforms, the team expressed all six then looked at how these isoforms behaved inside cells, and they found something surprising: some of the isoforms of gasdermin-B did indeed poke holes to cause cell death — but other isoforms did not.

“Previously, people didn’t understand why studies contradicted each other. We show that only two of the isoforms of gasdermin-B cause pyroptosis, or cell death,” says Ruan. Those two isoforms contain a specific protein segment that is absent in the other gasdermin-B isoforms, as shown by their cryogenic electron microscopy structure.

The finding may explain many mysteries of cell death, and life. Cancer cells, for example, are notoriously long lived and unlikely to die via pyroptosis. It may be that these cancer cells express only gasdermin-B isoforms that don’t poke holes in cell walls.

However, we don’t yet know what these other isoforms are doing. It may be that the different isoforms of gasdermin-B play significant and distinctive roles depending on where they are in the body, and different cell types preferentially express different isoforms.

“The protein structures that our team discovered have significant implications for drug development. Specifically, they can inform the design of small molecule drugs that modulate gasdermin-B activity,” explains Ruan. “These drugs could potentially be used to treat a range of conditions, including cancer, inflammatory and autoimmune diseases, and infectious diseases by either suppressing or enhancing the immune response. Our findings thus hold promise for the development of novel therapies to address these pressing medical needs.”

The researchers, including several scientists from the University of Colorado Boulder, published their findings today in the journal Science.

To tell the stories of horses in the West, the team closely examined about two dozen sets of animal remains found at sites ranging from New Mexico to Kansas and Idaho. The researchers come from 15 countries and multiple Native American groups, including the Lakota, Comanche and Pawnee nations.

“What unites everyone is the shared vision of telling a different kind of story about horses,” said William Taylor, a corresponding author of the study and curator of archaeology at the CU Museum of Natural History. “Focusing only on the historical record has underestimated the antiquity and the complexity of Indigenous relationships with horses across a huge swath of the American West.”

For many of the scientists involved, the research holds deep personal significance, added Taylor, who grew up in Montana where his grandfather was a rancher.

“We’re looking at parts of the country that are extraordinarily important to the people on this project,” he said.

The researchers drew on archaeozoology, radiocarbon dating, DNA sequencing and other tools to unearth how and when horses first arrived in various regions of today’s United States. Based on the team’s calculations, Indigenous communities were likely riding and raising horses as far north as Idaho and Wyoming by at least the first half of the 17th Century — as much as a century before records from Europeans had suggested.

Groups like the Comanche, in other words, may have begun to form deep bonds with horses mere decades after the animals arrived in the Americas on Spanish boats.

The results line up with a wide range of Indigenous oral histories.

“All this information has come together to tell a bigger, broader, deeper story, a story that natives have always been aware of but has never been acknowledged,” said Jimmy Arterberry, co-author of the new study and tribal historian of the Comanche Nation in Oklahoma.

Study co-author Carlton Shield Chief Gover agreed, noting that the love of horses may be one thing that extends across societies and borders.

“People are fascinated by horses. They’ve grown up with horses,” said Shield Chief Gover, a citizen of the Pawnee Nation of Oklahoma and curator for public anthropology at the Indiana University Museum of Archaeology and Anthropology. “We can talk to one another through our shared love of an animal.”

Mud Pony

For many Native American communities that shared love goes a long way back.

The Pawnee, for example, tell the story of “Mud Pony,” a boy who began seeing visions of strange creatures in his sleep.

“He makes these little mud figurines of these animals he sees in his dreams, and, overnight, they become alive,” Shield Chief Gover said. “That’s how you get horses.”

European historical records from the colonial period, however, have tended to favor a more recent origin story for horses in the West. Many scholars have suggested that Native American communities didn’t begin caring for horses until after the Pueblo Revolt of 1680. During this event, Pueblo people in what is today New Mexico temporarily overthrew Spanish rule, releasing European livestock in the process.

Taylor, also an assistant professor of anthropology at CU Boulder, and his colleagues didn’t think it fit as an origin story for the relationships between humans and horses in the West: “We thought: There’s something fishy about this story.”

Clues in bone

With funding from the U.S. National Science Foundation (NSF), they formed an equine dream team that includes archaeologists from the University of Oklahoma and University of New Mexico. Geneticist Ludovic Orlando and Lakota scholar Yvette Running Horse Collin took part from the University of Toulouse.

“This research demonstrates how multiple different types of data can be integrated to address the fascinating historical question of how and when horses spread across the West,” said NSF Archaeology program director John Yellen.

The researchers began collecting as much data as they could on horses remains from the West. DNA evidence, for example, suggests that most Indigenous horses had descended from Spanish and Iberian horses, with British horses becoming more common in the 18^th and 19^th Centuries.

“Our analyses show it was born and raised locally,” Taylor said. “It was cared for, and when that animal passed, there was extraordinary significance to that event.”

The remains of this horse, along with several others from the study, also seemed to date back to around the turn of the 17th Century, decades before the start of the Pueblo Revolt.

How animals like it arrived in Wyoming isn’t clear, but it’s likely that Europeans weren’t involved in their initial transport.

Shield Chief Gover explained that few Indigenous people will be surprised by the results of the study. But the team’s findings may help to illustrate for academic scientists just how important these animals were to the history of Indigenous peoples. The Pawnee, who lived in Nebraska, for example, rode horses on twice-a-year buffalo hunts, traveling farther and faster into the “sea of grass” of the Great Plains. Comanche also galloped on horseback to hunt buffalo, while owning a lot of horses was a sign of wealth.

“I don’t want to diminish the reverence and the respect we have for horses,” Arterberry said. “We see them as gifts the Creator gave us, and, because of that, we survived and thrived and became who we are today.”

Respecting horses

Study co-author Chance Ward, a master’s student in Museum and Field Studies at CU Boulder, would like to see the archaeology community begin to treat those relationships with more respect. He was born and raised on the Cheyenne River Reservation in South Dakota, which is home to four bands of the Lakota Nation. Ward grew up listening to his mother’s childhood stories about riding ponies in the Bear Creek community. His father’s parents started a ranch on the reservation where members of the family practice rodeo today.

He explained that many researchers don’t handle animal remains with the same care they reserve for cultural objects and human remains.

“They tend to be thrown into a box or bag where they hit against each other and break,” Ward said. “This project is a chance for us as Native people to put our voices out there and take better care of important and sacred animals in museum collections.”