Wednesday, May 18, 2022

“Natural Immunity” from Omicron is Weak and Limited

The new study shows that infection with Omicron does not protect against other variants of COVID-19. In this photo, clear zones on the purple background show the SARS-CoV-2 virus escaping from neutralizing antibodies in patient blood samples.
Credit: Gladstone Institutes

In unvaccinated people, infection with the Omicron variant of SARS-CoV-2 provides little long-term immunity against other variants, according to a new study by researchers at Gladstone Institutes and UC San Francisco (UCSF), published today in the journal Nature.

In experiments using mice and blood samples from donors who were infected with Omicron, the team found that the Omicron variant induces only a weak immune response. In vaccinated individuals, this response—while weak—helped strengthen overall protection against a variety of COVID-19 strains. In those without prior vaccination, however, the immune response failed to confer broad, robust protection against other strains.

“In the unvaccinated population, an infection with Omicron might be roughly equivalent to getting one shot of a vaccine,” says Melanie Ott, MD, PhD, director of the Gladstone Institute of Virology and co-senior author of the new work. “It confers a little bit of protection against COVID-19, but it’s not very broad.”

Banned Contaminants Still Threaten Endangered California Condors

Condors at Pinnacles National Park in central California.
Photo courtesy of San Diego Zoo Wildlife Alliance

A new study has found contaminants that were banned decades ago are still imperiling critically endangered California condors. The condors may be at increased risk for reproductive impairment because they consume dead marine mammals along the California coast.

The research, led by San Diego State University (SDSU) and San Diego Zoo Wildlife Alliance (SDZWA) scientists, in collaboration with Centro de Investigación Científica y de Educación Superior de Ensenada and the National Oceanographic and Atmospheric Administration, found that marine mammals stranded on the California coast harbor relatively high levels of halogenated organic contaminants (HOCs). Researchers detected more than 400 contaminants in samples taken from stranded marine mammals that California condors may feed on.

On the California coast, the marine mammals had an estimated seven times more DDT and 3.5 times more PCBs than their counterparts in Baja California, Mexico. Other lesser-studied compounds were also detected. One group of these compounds was estimated to be 148 times more abundant in California marine mammals compared to those in Baja California.

The study, published in the journal Environmental Science & Technology, also reveals that coastal condors have more contaminants in their blood than inland condors, which lack a marine mammal diet.

Choline makes key nutrients available for baby development

Choline Molecule 
Choline occurs in foods as a free molecule and in the form of phospholipids, especially as phosphatidylcholines. Choline is highest in organ meats and egg yolks though it is found to a lesser degree in non-organ meats, grains, vegetables, fruit and dairy products.

The nutrient choline – shown to have long-term benefits for children whose mothers consume it during pregnancy – also helps the body more efficiently use an omega 3 fatty acid that is essential for fetal brain, cognition and vision development, a new study finds.

The study was published in the American Journal of Clinical Nutrition.

The findings show that choline supplementation supports cellular metabolism to more efficiently handle and release the omega 3 fatty acid, DHA, from a pregnant individual’s liver. Once released into the bloodstream, DHA can be delivered into all the tissues, including the placenta.

“During pregnancy, mom is primed to get nutrients out of the liver and make them available to the baby, so by supplementing choline and DHA [together], we are increasing DHA bioavailability,” said senior author Marie Caudill, professor of nutritional sciences in the College of Agriculture and Life Sciences. Kevin Klatt, Ph.D. ’18, a research scientist and registered dietitian at the University of California, Berkeley, is the paper’s first author.

Rainforest trees may have been dying faster since the 1980s because of climate change

Northeast Australia's relict tropical rainforest are one of the oldest most isolated rainforests in the world.
Photo credit: Alexander Schenkin

Tropical trees in Australia’s rainforests have been dying at double the previous rate since the 1980s, seemingly because of climate impacts, according to the findings of a long-term international study published in Nature today. This research has found the death rates of tropical trees have doubled in the last 35 years, as global warming increases the drying power of the atmosphere.

Deterioration of such forests reduces biomass and carbon storage, making it increasingly difficult to keep global peak temperatures well below the target 2 °C, as required by the Paris Agreement. Today’s study, led by researchers from the Smithsonian Environmental Research Center and Oxford University, and French National Research Institute for Sustainable Development (IRD), has used uniquely long data records from across Australia’s rainforests.

It finds average tree death rates in these forests have doubled over the past four decades. Researchers found trees are living around half as long, which is a pattern consistent across species and sites across the region. And the impacts can be seen as far back as the 1980s, according to the team.

Researchers Use Galaxy as a ‘Cosmic Telescope’ to Study Heart of the Young Universe

An artist’s rendering shows how a cluster of galaxies (lensing cluster) acts as a gravitational lens that magnifies and extends the light from a background galaxy.
Image: W. M. Keck Observatory/Adam Makarenko

A unique new instrument, coupled with a powerful telescope and a little help from nature, has given researchers the ability to peer into galactic nurseries at the heart of the young universe.

After the big bang some 13.8 billion years ago, the early universe was filled with enormous clouds of neutral diffuse gas, known as Damped Lyman-α systems, or DLAs. These DLAs served as galactic nurseries, as the gases within slowly condensed to fuel the formation of stars and galaxies. They can still be observed today, but it isn’t easy.

“DLAs are a key to understanding how galaxies form in the universe, but they are typically difficult to observe since the clouds are too diffuse and don’t emit any light themselves,” says Rongmon Bordoloi, assistant professor of physics at North Carolina State University and corresponding author of the research.

Currently, astrophysicists use quasars – supermassive black holes that emit light – as “backlight” to detect the DLA clouds. And while this method does allow researchers to pinpoint DLA locations, the light from the quasars only acts as small skewers through a massive cloud, hampering efforts to measure their total size and mass.

But Bordoloi and John O’Meara, chief scientist at the W.M. Keck Observatory in Kamuela, Hawaii, found a way around the problem by using a gravitationally lensed galaxy and integral field spectroscopy to observe two DLAs – and the host galaxies within – that formed around 11 billion years ago, not long after the big bang.

“Gravitationally lensed galaxies refer to galaxies that appear stretched and brightened,” Bordoloi says. “This is because there is a gravitationally massive structure in front of the galaxy that bends the light coming from it as it travels toward us. So, we end up looking at an extended version of the object – it’s like using a cosmic telescope that increases magnification and gives us better visualization.

“The advantage to this is twofold: One, the background object is extended across the sky and bright, so it is easy to take spectrum readings on different parts of the object. Two, because lensing extends the object, you can probe very small scales. For example, if the object is one light year across, we can study small bits in very high fidelity.”

Spectrum readings allow astrophysicists to “see” elements in deep space that are not visible to the naked eye, such as diffuse gaseous DLAs and the potential galaxies within them. Normally, gathering the readings is a long and painstaking process. But the team solved that issue by performing integral field spectroscopy with the Keck Cosmic Web Imager.

Integral field spectroscopy allowed the researchers to obtain a spectrum at every single pixel on the part of the sky it targeted, making spectroscopy of an extended object on the sky very efficient. This innovation combined with the stretched and brightened gravitationally lensed galaxy allowed the team to map out the diffuse DLA gas in the sky at high fidelity. Through this method the researchers were able to determine not only the size of the two DLAs, but also that they both contained host galaxies.

“I’ve waited most of my career for this combination: a telescope and instrument powerful enough, and nature giving us a bit of lucky alignments to study not one but two DLAs in a rich new way,” O’Meara says. “It’s great to see the science come to fruition.”

The DLAs are huge, by the way. With diameters greater than 17.4 kiloparsecs, they’re more than two thirds the size of the Milky Way galaxy today. For comparison, 13 billion years ago, a typical galaxy would have a diameter of less than 5 kiloparsecs. A parsec is 3.26 light years, and a kiloparsec is 1,000 parsecs, so it would take light about 56,723 years to travel across each DLA.

“But to me, the most amazing thing about the DLAs we observed is that they aren’t unique – they seem to have similarities in structure, host galaxies were detected in both, and their masses indicate that they contain enough fuel for the next generation of star formation,” Bordoloi says. “With this new technology at our disposal, we are going to be able to dig deeper into how stars formed in the early universe.”

The work appears in Nature and was supported by the National Aeronautics and Space Administration, the W.M. Keck Foundation and the National Science Foundation. The Australian Research Council Centre of Excellence for All Sky Astrophysics in 3 Dimensions (ASTRO 3D) also contributed to the work.

Source/Credit: North Carolina State University | Tracey Peake

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Spying on Thousands of Neurons in the Brain’s Vision Center Simultaneously

Scientists tracked how individual neurons (white dots)
across the mouse visual center responded when the
animals saw an image on a screen.
That let the team trace the sequence
of events triggered when the eyes detect an important sight.
Credit: S. Ebrahimi et al./Nature 2022
Using a custom-built microscope to peer into the mouse brain, scientists have tracked the activity of single neurons across the entire visual cortex.

These recordings, made in the tenths of seconds after the animals saw a cue on a screen, expose the complex dynamics involved in making sense of what the eyes see. In an unprecedented combination of breadth and detail, the results describe the behavior of more than 21,000 total neurons in six mice over five days, Howard Hughes Medical Institute Investigator Mark Schnitzer’s team reports in the journal Nature on May 18, 2022.

His team is the first to get a glimpse of individual cells’ activity occurring at the same time throughout eight parts of the brain involved in vision. “People have studied these brain areas before, but prior imaging studies did not have cellular resolution across the entire visual cortex,” says Schnitzer, a neuroscientist at Stanford University.

The work highlights the dramatic sequence of events that unfolds in the brain from the instant it receives messages from the eyes until it decides how to respond to that sight. The researchers’ far-reaching but fine-grained imaging approach made it possible for them to collect an “incredible” set of data, says Tatiana Engel, a computational neuroscientist at Cold Spring Harbor Laboratory who was not involved in the study.

A component for brain-inspired computing

Scientists aim to perform machine-learning tasks more efficiently with processors that emulate the working principles of the human brain.
Image: Unsplash

Researchers from ETH Zurich, Empa and the University of Zurich have developed a new material for an electronic component that can be used in a wider range of applications than its predecessors. Such components will help create electronic circuits that emulate the human brain and that are more efficient than conventional computers at performing machine-learning tasks.

Compared with computers, the human brain is incredibly energy-efficient. Scientists are therefore drawing on how the brain and its interconnected neurons function for inspiration in designing innovative computing technologies. They foresee that these brain-inspired computing systems will be more energy-efficient than conventional ones, as well as better at performing machine-learning tasks.

Much like neurons, which are responsible for both data storage and data processing in the brain, scientists want to combine storage and processing in a single type of electronic component, known as a memristor. Their hope is that this will help to achieve greater efficiency because moving data between the processor and the storage, as conventional computers do, is the main reason for the high energy consumption in machine-learning applications.

At-Risk Sea Life in the Atlantic Needs Better Protection from an Increase in Shipping


Researchers at the University of Portsmouth have discovered that rates of shipping in the North East Atlantic area rose by 34 per cent in a five-year period.

Even more noticeable, and of major concern to scientists, is the rate of shipping growth in Marine Protected Areas. Analysis of vessel movements in these delicate environments shows an increase of 73 per cent in the same time period.

The report, which was published in Marine Pollution Bulletin, is the first detailed survey of shipping activity in the North East Atlantic. Researchers used data from over 530 million vessel positions recorded by Automatic identification Systems (AIS). They looked at the change in shipping between 2013 and 2017 across ten distinct vessel types.

In total the study area covered 1.1 million km2, including waters off Belgium, Denmark, France, Germany, Iceland, Ireland, The Netherlands, Norway, Portugal, Spain, and the UK.

Renewed monitoring effort is needed to ensure that protective measures are adequate to conserve species under threat in a changing environment.

For Plant-based Proteins, Soy is a Smart Choice

Tofu, flour, milk, and sauce are just some of the products that can be made from the versatile plant protein soy

Soy – the versatile protein source that comes from the species of legumes known as soybeans – is becoming a popular alternative to meat and dairy products, and for good reason. Whether you are trying to eat healthier, eat more sustainably, or both, College of Agriculture, Health and Natural Resources Department of Nutritional Sciences researcher Yangchao Luo and his research group recently published an article in the Journal of Agriculture and Food Research exploring qualities that make soy a versatile and nutritious choice.

What makes soy such a popular source of plant-based meat (and dairy) alternatives?

In comparison to other plant-based proteins, soy protein provides the most complete nutrients in terms of amino acids, compared to animal sources. Soy contains almost every amino acid, with only one minor exception, methionine, which is an essential amino acid, and what we call a limiting amino acid. Other plant-based proteins may miss two, three, or even four different essential amino acids. You can easily get all essential amino acids in a meal by mixing plant-based proteins or by pairing soy-based proteins with grains.

Upon extrusion process, soy-based proteins undergo a series of physicochemical changes to form fibrous anisotropic structure, the texture of which becomes very similar to meat products. When modified chemically or enzymatically, soy protein can further develop sensory characteristics that can mimic real meat. This is very easy to do for soy protein, but more challenging for many other plant proteins. A lot of food companies nowadays are trying to develop meat alternatives, and soy-based protein is just the top choice for the food industries.

Ultrahigh piezoelectric performance demonstrated in ceramic materials

The ability of piezoelectric materials to convert mechanical energy into electrical energy and vice versa makes them useful for various applications from robotics to communication to sensors. A new design strategy for creating ultrahigh-performing piezoelectric ceramics opens the door to even more beneficial uses for these materials, according to a team of researchers from Penn State and Michigan Technological University.

“For a long time, piezoelectric polycrystalline ceramics have shown limited piezoelectric response in comparison to single crystals,” said Shashank Priya, associate vice president for research and professor of materials science and engineering at Penn State and co-author of the study published in the journal Advanced Science. “There are many mechanisms that limit the magnitude of piezoelectricity in polycrystalline ceramic materials. In this paper, we demonstrate a novel mechanism that allows us to enhance the magnitude of the piezoelectric coefficient several times higher than is normally expected for a ceramic.”

The piezoelectric coefficient, which describes the level of a material's piezoelectric response, is measured in picocoulombs per Newton.

“We achieved close to 2,000 picocoulombs per Newton, which is a significant advance, because in polycrystalline ceramics, this magnitude has always been limited to around 1,000 picocoulombs per Newton,” Priya said. "2,000 was considered an unreachable target in the ceramics community, so achieving that number is very dramatic.”

Tuesday, May 17, 2022

Rice chemists skew the odds to prevent cancer

A new paper by a Rice University lab shows how to increase the odds of identifying cancer-causing mutations before tumors take hold. Authors are, from left, Cade Spaulding, Anatoly Kolomeisky and Hamid Teimouri.
Credit: Rice University

The path to cancer prevention is long and arduous for legions of researchers, but new work by Rice University scientists shows that there may be shortcuts.

Rice chemist Anatoly Kolomeisky, lead author and postdoctoral researcher Hamid Teimouri and research assistant Cade Spaulding are developing a theoretical framework to explain how cancers caused by more than one genetic mutation can be more easily identified and perhaps stopped.

Essentially, it does so by identifying and ignoring transition pathways that don’t contribute much to the fixation of mutations in a cell that goes on to establish a tumor.

A study in the Biophysical Journal describes their analysis of the effective energy landscapes of cellular transformation pathways implicated in a variety of cancers. The ability to limit the number of pathways to the few most likely to kick-start cancer could help to find ways to halt the process before it ever really starts.

“In some sense, cancer is a bad-luck story,” said Kolomeisky, a professor of chemistry and of chemical and biomolecular engineering. “We think we can decrease the probability of this bad luck by looking for low-probability collections of mutations that typically lead to cancer. Depending on the type of cancer, this can range between two mutations and 10.”

Technology allows amputees to control a robotic arm with their mind

University of Minnesota Department of Biomedical Engineering Associate Professor Zhi Yang shakes hands with research participant Cameron Slavens, who tested out the researchers' robotic arm system. With the help of industry collaborators, the researchers have developed a way to tap into a patient’s brain signals through a neural chip implanted in the arm, effectively reading the patient’s mind and opening the door for less invasive alternatives to brain surgeries.
Credit: Neuroelectronics Lab, University of Minnesota

University of Minnesota Twin Cities researchers have developed a more accurate, less invasive technology that allows amputees to move a robotic arm using their brain signals instead of their muscles.

Many current commercial prosthetic limbs use a cable and harness system that is controlled by the shoulders or chest, and more advanced limbs use sensors to pick up on subtle muscle movements in a patient’s existing limb above the device. But both options can be cumbersome, unintuitive, and take months of practice for amputees to learn how to move them.

Researchers in the University’s Department of Biomedical Engineering, with the help of industry collaborators, have created a small, implantable device that attaches to the peripheral nerve in a person’s arm. When combined with an artificial intelligence computer and a robotic arm, the device can read and interpret brain signals, allowing upper limb amputees to control the arm using only their thoughts.

Scent dogs detect coronavirus reliably from skin swabs

Scent dog Silja at the Helsinki-Vantaa airport.
Credit: Egil Björkman

The rapid and accurate identification and isolation of patients with coronavirus infection is an important part of global pandemic management. The current diagnosis of coronavirus infection is based on a PCR test that accurately and sensitively identifies coronavirus from other pathogens. However, PCR tests are ill-suited for screening large masses of people because of, among other things, their slow results and high cost.

Researchers from the Faculties of Veterinary Medicine and Medicine at the University of Helsinki and from Helsinki University Hospital jointly designed a triple-blind, randomized, controlled study set-up to test the accuracy of trained scent detection dogs where none of the trio – dog, dog handler or researcher – knew which of the sniffed skin swab samples were positive and which negative. The study also analyzed factors potentially interfering with the ability of the dogs to recognize a positive sample.

The three-faceted study has now been published in the journal BMJ Global Health. The study provides valuable information on the use of scent dogs in pandemic control.

Scientists Nail Down 'Destination' for Protein That Delivers Zinc

Brookhaven Lab biologist Crysten Blaby and postdoctoral fellow Nicolas Grosjean and colleagues ran genetic experiments, biochemical assays, and computational modeling studies that identified ZNG1 as a zinc chaperone protein.
Credit: Brookhaven National Laboratory

Most people don’t think much about zinc. But all living things need zinc for survival. This trace element helps many proteins fold into the right shapes to do their jobs. And in proteins known as enzymes, zinc helps catalyze chemical reactions—including many important for providing energy to cells. If zinc is absent, people, pets, and plants don’t thrive.

That’s one reason biologists at the U.S. Department of Energy’s Brookhaven National Laboratory are so interested in this element.

“We're looking for ways to grow bioenergy plants—either plants that produce biofuels or whose biomass can be converted into fuel—and doing it on land that is not suitable for growing food crops,” said Brookhaven Lab biologist Crysten Blaby, who also holds an adjunct appointment at Stony Brook University. “So, we’re interested in strategies nature uses to survive when zinc and other micronutrients are lacking.”

In a paper just published in the journal Cell Reports, Blaby and her colleagues describe one such strategy: a so-called “chaperone” protein that delivers zinc to where it’s needed, which could be especially important when access to zinc is limited. Though scientists, including Blaby, have long suspected the existence of a zinc chaperone, the new research provides the first definitive evidence by identifying a “destination” for its deliveries.

A new mathematical model of cellular movement

A new mathematical model describes how cells change their shape during movement and suggests that the movement is mainly driven by the contraction of the skeletal proteins, called “myosin.” The image shows the shape of cells at various speeds as predicted by the model. Non-moving cells are circular but become asymmetric as they begin to move. The colors indicate the concentration of myosin in the cell with red indicating a higher concentration.
Credit: C. Alex Safsten, Penn State

A mathematical model that describes how cells change their shape during movement suggests that the movement is mainly driven by the contraction of the skeletal proteins, called “myosin.” The new model developed at Penn State can help researchers to better understand the various biological processes where cellular movement plays a key role and also could inform the development of artificial systems that mimic biological processes.

“The focus of this work is on the development of minimal mathematical models that are simple enough to be amenable to rigorous analysis but still capture key biological phenomena,” said Leonid Berlyand, professor of mathematics at Penn State and the leader of this research team. “The point of our model is to capture the onset of cell motion driven by myosin contraction with focus on analyzing the stability of this motion observed in experiments.”

For large bone injuries, it’s Sonic hedgehog to the rescue

After surgical rib resection (top), a cartilage and bone bridge form (second from top) and then resolve (third from top) and remodel to regenerate the missing tissue in the gap (bottom). Blue shows cartilage matrix; red shows mineralized matrix.
Images by Stephanie Kuwahara and Max Serowoky/ Mariani Lab

A USC Stem Cell study in NPJ Regenerative Medicine presents intriguing evidence that large bone injuries might trigger a repair strategy in adults that recapitulates elements of skeletal formation in utero. Key to this repair strategy is a gene with a fittingly heroic name: Sonic hedgehog.

In the study, first author Maxwell Serowoky, a PhD student in the USC Stem Cell laboratory of Francesca Mariani, and his colleagues took a close look at how mice are able to regrow large sections of missing rib—an ability they share with humans, and one of the most impressive examples of bone regeneration in mammals.

To their surprise, the scientists observed an increase in the activity of Sonic hedgehog (Shh), which plays an important role in skeletal formation in embryos, but hasn’t previously been linked to injury repair in adults.

In their experiments, Shh appeared to play a necessary role in healing the central region of large sections of missing ribs, but not in closing small-scale fractures.

New Approach Allows for Faster Ransomware Detection

Photo credit: Michael Geiger

Engineering researchers have developed a new approach for implementing ransomware detection techniques, allowing them to detect a broad range of ransomware far more quickly than previous systems.

Ransomware is a type of malware. When a system is infiltrated by ransomware, the ransomware encrypts that system’s data – making the data inaccessible to users. The people responsible for the ransomware then extort the affected system’s operators, demanding money from the users in exchange for granting them access to their own data.

Ransomware extortion is hugely expensive, and instances of ransomware extortion are on the rise. The FBI reports receiving 3,729 ransomware complaints in 2021, with costs of more than $49 million. What’s more, 649 of those complaints were from organizations classified as critical infrastructure.

Monday, May 16, 2022

Extraterrestrial stone brings first supernova clues to Earth

A 3-gram sample of the Hypatia stone. Researchers found a consistent pattern of 15 elements in the Hypatia stone. The pattern is completely unlike anything in our solar system or our solar neighborhood, in the Milky Way.
Credit: Romano Serra 

New chemistry ‘forensics’ indicate that the stone named Hypatia from the Egyptian desert could be the first tangible evidence found on Earth of a supernova type Ia explosion. These rare supernovas are some of the most energetic events in the universe.

This is the conclusion from a new study published in the journal Icarus, by Jan Kramers, Georgy Belyanin and Hartmut Winkler of the University of Johannesburg, and others.

Since 2013, Belyanin and Kramers have discovered a series of highly unusual chemistry clues in a small fragment of the Hypatia Stone.

In new research, they eliminated 'cosmic suspects' for the origin of the stone in a painstaking process. They have pieced together a timeline stretching back to the early stages of the formation of Earth, our Sun and the other planets in our solar system.

Cutting air pollution emissions would save 50,000 U.S. lives, $600 billion each year

Image by Ralf Vetterle from Pixabay

Eliminating air pollution emissions from energy-related activities in the United States would prevent more than 50,000 premature deaths each year and provide more than $600 billion in benefits each year from avoided illness and death, according to a new study by University of Wisconsin–Madison researchers.

Published today in the journal GeoHealth, the study reports the health benefits of removing dangerous fine particulates released into the air by electricity generation, transportation, industrial activities and building functions like heating and cooking — also major sources of carbon dioxide emissions that cause climate change, since they predominantly rely on burning fossil fuels like coal, oil, and natural gas.

“Our work provides a sense of the scale of the air quality health benefits that could accompany deep decarbonization of the U.S. energy system,” says Nick Mailloux, lead author of the study and a graduate student at the Center for Sustainability and the Global Environment in UW–Madison’s Nelson Institute for Environmental Studies. “Shifting to clean energy sources can provide enormous benefit for public health in the near term while mitigating climate change in the longer term.”

Validation brings new predictive capability to global megafire smoke impacts

Recent megafires in Australia and British Columbia have injected unprecedented amounts of smoke into the stratosphere. Modeling led by Los Alamos National Laboratory will help predict the effects of similar future events.
Credit: David Peterson, FIREX-AQ

New research modeling smoke from two recent megafires sets the stage for better forecasting of how emissions from these global-scale events will behave and impact temperatures. As huge wildfires become more common under climate change, increased attention has focused on the intensity and duration of their emissions, which rival those of some volcano eruptions.

Megafires in British Columbia in 2017 and Australia in 2019-2020 injected massive amounts of smoke into the stratosphere, allowing first-ever detailed satellite- and ground-based measurements of such cataclysms. Using that data for validation, a Los Alamos National Laboratory–led team modeled the behavior and impacts of the smoke as it rose from the lower atmosphere into the high-riding stratosphere, then circulated the globe. The research appeared in the Journal of Geophysical Research – Atmospheres.

Lighting up breast tumors during surgery

Scanning electron microscopy image of a breast cancer cell.
Credit: Bruce Wetzel & Harry Schaefer,
courtesy of the National Cancer Institute.
Nearly 13 percent of women born in the U.S. today will develop breast cancer at some point during their lives. Treatment for early-stage disease often includes breast-conserving surgery, where the tumor and some surrounding healthy tissues (the tumor margin) are removed. However, around 20 percent of these surgeries require a second operation, generally because cancer cells are found within the tumor margins.

Now, NIBIB-funded researchers are developing an imaging method that would allow surgeons to better identify cancerous cells in the tumor margins during surgery. This technique could lead to a reduction in follow-up breast cancer surgeries and reduce rates of breast cancer recurrence. Results were recently published in eBioMedicine, a publication of The Lancet.

“Today, surgeons primarily rely on their sense of sight and touch to distinguish between healthy and cancerous tissues during surgery, which may lead to incomplete removal of the tumor,” said Tatjana Atanasijevic, Ph.D., manager of the NIBIB program in Molecular Probes and Imaging Agents. “This imaging technique provides real-time visual feedback during surgery, allowing surgeons to better gauge the breast tumor margins, and ultimately optimizing surgical excision.”

The technique relies on a method known as near-infrared imaging, which utilizes probes that fluoresce under near-infrared light. These fluorescent probes can allow clinicians to visualize features beyond the tissue surface, such as blood vessels or tumors, which can help to guide surgical procedures. However, there aren’t many near-infrared agents that are approved for clinical use by the U.S. Food and Drug Administration (FDA), and those that are approved are non-specific, meaning that they don’t home in on a specific target in the body. Further, the only near-infrared probe approved for surgery, indocyanine green (ICG), doesn't stay in the bloodstream for very long and therefore its utility for image-guided tumor resection is somewhat limited.

Green robotics start-up signs deal with energy giant

University of Bristol alumni and founders of Perceptual Robotics: Chief Operating Officer Dimitris Nikolaidis, Chief Technical Officer Kevin Driscoll-Lind and Chief Executive Officer Kostas Karachalios
Credit: University of Bristol

A start-up with University of Bristol roots has signed a deal with energy giant Enel to help keep its estimated 9,000 turbines spinning.

Perceptual Robotics use autonomous drones and artificial intelligence to detect damage in wind turbines early.

Now the company, founded by three Bristol alumni, has landed a deal to inspect turbines owned by Enel Green Power, a subsidiary of Enel, which is one of the biggest energy companies in the world.

Enel Green Power will use the data to carry out preventative maintenance - reducing costs and turbine stoppages while increasing safety.

Meanwhile, research published today shows that Perceptual Robotics’ technology is 14% better at detecting damage than expert humans carrying out the same inspections.

Perceptual Robotics says it can reduce the cost of wind turbine blade maintenance by 30%.

Kostas Karachalios, CEO of Perceptual Robotics, who studied for a Master of Engineering (MEng) at Bristol, said: “The task of inspecting and maintaining these structures is becoming ever more challenging, as the industry is increasingly recognized.

Using Bacteria to Accelerate CO2 Capture in Oceans

Berkeley Lab researcher Peter Agbo was awarded a grant for a carbon capture project under the Lab’s Carbon Negative Initiative.
Credit: Marilyn Sargent/Berkeley Lab

You may be familiar with direct air capture, or DAC, in which carbon dioxide is removed from the atmosphere in an effort to slow the effects of climate change. Now a scientist at Lawrence Berkeley National Laboratory (Berkeley Lab) has proposed a scheme for direct ocean capture. Removing CO2 from the oceans will enable them to continue to do their job of absorbing excess CO2 from the atmosphere.

Experts mostly agree that combating climate change will take more than halting emissions of climate-warming gases. We must also remove the carbon dioxide and other greenhouse gases that have already been emitted, to the tune of gigatons of CO2 removed each year by 2050 in order to achieve net zero emissions. The oceans contain significantly more CO2 than the atmosphere and have been acting as an important carbon sink for our planet.

Deaths from Alcohol Use Disorder Surged During Pandemic

Deaths related to alcohol use disorder dramatically increased over projections during the COVID-19 pandemic, Cedars-Sinai investigators found

Deaths involving alcohol use disorder increased dramatically during the pandemic, according to a new study by Cedars-Sinai investigators. The study also found that young adults 25 to 44 years old experienced the steepest upward trend in alcohol use disorder mortality.

In the study, published in the peer-reviewed journal JAMA Network Open, investigators used predictive modeling to compare expected—also called projected—alcohol use disorder mortality rates to actual rates. They found that alcohol use disorder-related mortality rates increased among all ages and sexes during the pandemic.

“During the first few months of the pandemic, my colleagues and I saw increased numbers of patients being treated for acute

alcohol use-related conditions in the intensive care unit and throughout the medical center,” said Yee Hui Yeo, MD, MSc, lead author of the study. “We also became aware of reports from single centers of elevated alcohol use-related complications. That prompted us to think, maybe this is a significant public health crisis.”

Ancient grains

Laura Motta, University of Michigan paleoethnobotanist, shows peas excavated from the Karanis site in Egypt.
Image credit: Eric Bronson, Michigan Photography

For a long time, researchers believed the diets of ancient people were nutritionally poor.

Everyday ancient Mediterranean civilizations relied on a diet of grains and pulses (chickpeas, lentils and other members of the bean family). Researchers thought this food lacked micronutrients such as zinc and iron, while also containing components that inhibit the uptake of what nutrients the food did have.

But a University of Michigan pilot study on crops grown in Egypt during Roman times suggests that ancient grains were more nutrient dense than grains grown in the same region today. Now, building on that study, U-M is part of a five-university consortium to receive a €3.7 million grant (about $3.85 million), called the AGROS project, awarded by the Belgian program Excellence of Science.

The researchers will use cutting-edge technologies to examine the nutritional profile of the food and how its nutrients changed based on the historical methods of food preparation.

Transgender mental health in crisis

Trans and LGBTIQA+ organizations across Australia are facing huge demand from the trans community for inclusive and affirming mental health services.
Image: The Gender Spectrum Collection

Australia’s transgender (trans) community is experiencing depression and thoughts of self-harm at levels never before seen, but many are not getting the help they need because they’re afraid to access mainstream services, a new study has shown.

Authored by the University of Melbourne’s Trans Health Research Group, the Trans in the Pandemic: Stories of Struggle and Resilience in the Australia Trans Community report has found 61 per cent of the 1019 people surveyed in 2020 experienced clinical depression – that’s twice the national rate and much higher than before the COVID-19 pandemic.

The team also found 49 per cent of trans people experienced thoughts of self-harm or suicide compared to 14.9 per cent for the general Australian population who reported thoughts of self-harm or suicide in the initial months of the pandemic.

The survey was carried out in May and June 2020, when there was concern the trans community may be disproportionately affected by social distancing restrictions, and healthcare and employment disruptions.

Report lead author Sav Zwickl said it was already well-established prior to the pandemic that the trans community faced numerous health disparities and was one of the most medically and socially marginalized groups in society.

Sunday, May 15, 2022

Experimental COVID-19 vaccine provides mutation-resistant T cell protection in mice

Marulasiddappa Suresh
Credit: UWM
A second line of defense — the immune system’s T cells — may offer protection from COVID-19 even when vaccine-induced antibodies no longer can, according to new research out of the University of Wisconsin School of Veterinary Medicine.

The researchers discovered that a new, protein-based vaccine against the original version of the COVID-19 virus was able to teach mouse T cells how to recognize and kill cells infected with new, mutated versions of the virus. This T cell protection worked even when antibodies lost their ability to recognize and neutralize mutated SARS-CoV-2, the virus that causes COVID-19.

“Antibodies prevent COVID-19 infection, but if new variants escape these antibodies, T cells are there to provide a second line of protection,” explains lead scientist Marulasiddappa Suresh, a professor of immunology and associate dean for research at the School of Veterinary Medicine.

The study, published in the Proceedings of the National Academy of Sciences, investigates the role of T cells, a specialized type of white blood cell, in defending against COVID-19 when antibodies fail.

When you receive a COVID-19 vaccine, your body learns to produce antibodies, proteins in the immune system that bind to and neutralize SARS-CoV-2. These antibodies circulate in the blood stream and protect you from illness by patrolling the nostrils, airways and lungs and wiping out the virus before it can cause infection or disease.

Thursday, May 12, 2022

The genetic origins of the world's first farmers clarified

Ancient DNA extraction in Mainz’s lab. Work done in sterile conditions to avoid contamination from modern DNA.
Credit: Joachim Burger / JGU

The genetic origins of the first agriculturalists in the Neolithic period long seemed to lie in the Near East. A new study published in the journal Cell shows that the first farmers actually represented a mixture of Ice Age hunter-gatherer groups, spread from the Near East all the way to south-eastern Europe. Researchers from the University of Bern and the SIB Swiss Institute of Bioinformatics as well as from the Johannes Gutenberg University Mainz and the University of Fribourg were involved in the study. The method they developed could help reveal other human evolution patterns with unmatched resolution. 

The first signs of agriculture and a sedentary lifestyle are found in the so-called 'Fertile Crescent', a region in the Near East where people began to settle down and domesticate animals and plants about 11,000 years ago. The question of the origin of agriculture and sedentism has occupied researchers for over 100 years: did farming spread from the Near East through cultural diffusion or through migration? Genetic analyses of prehistoric skeletons so far supported the idea that Europe's first farmers were descended from hunter-gatherer populations in Anatolia. While that may well be the case, this new study shows that the Neolithic genetic origins cannot clearly be attributed to a single region. Unexpected and complex population dynamics occurred at the end of the Ice Age, and led to the ancestral genetic makeup of the populations who invented agriculture and a sedentary lifestyle i.e. the first Neolithic farmers. 

The first farmers emerged from a mixing process starting 14,000 years ago 

Previous analyses had suggested that the first Neolithic people were genetically different from other human groups from that time. Little was known about their origins. Nina Marchi, one of the study's first authors from the Institute of Ecology and Evolution at the University of Bern and SIB says: "We now find that the first farmers of Anatolia and Europe emerged from a population admixed between hunter-gatherers from Europe and the Near East." According to the authors, the mixing process started around 14,000 years ago, which was followed by a period of extreme genetic differentiation lasting several thousand years. 

A novel approach to model population history from prehistoric skeletons 

The Klein7 individual from the Kleinhadersdorf site in the Lower Austrian Weinviertel, whose genome was analyzed in the paper.
Credit: BDA / Christine Neugebauer-Maresch


This research was made possible by combining two techniques: the production of high-quality ancient genomes from prehistoric skeletons, coupled with demographic modeling on the resulting data. The research team coined the term "demo genomic modeling" for this purpose. "It is necessary to have genome data of the best possible quality so that the latest statistical genomic methods can reconstruct the subtle demographic processes of the last 30 thousand years at high resolution", says Laurent Excoffier, one of the senior authors of the study. Laurent Excoffier is a professor at the Institute of Ecology and Evolution at the University of Bern and group leader at SIB. He initiated the project together with Joachim Burger of the Johannes Gutenberg University in Mainz and Daniel Wegmann of the University of Fribourg. Nina Marchi adds: "Simply comparing the similarity of different ancient genomes is not enough to understand how they evolved. We had to reconstruct the actual histories of the populations studied as accurately as possible. This is only possible with complex population genetic statistics." 

Interdisciplinary key to solve such ancient puzzles 

Joachim Burger of the University of Mainz and second senior author emphasizes the necessity of interdisciplinarity: "It took close to ten years to gather and analyze the skeletons suitable for such a study. This was only possible by collaborating with numerous archaeologists and anthropologists, who helped us to anchor our models historically". The historical contextualization was coordinated by Maxime Brami, who works with Burger at Johannes Gutenberg University. The young prehistorian was surprised by some of the study's findings: "Europe's first farmers seem to be descended from hunter-gatherer populations that lived all the way from the Near East to the Balkans. This was not foreseeable archaeologically". 

Towards a general model of human population evolution 

Genetic data from fossils (skeletons) are badly damaged and must be processed accordingly using bioinformatics, as Daniel Wegmann from the University of Fribourg and group leader at SIB explains: "The high-resolution reconstruction of the prehistory of the Europeans was only possible thanks to methods that we specifically developed to analyze
ancient fossil genomes." Joachim Burger adds: "With these approaches, we have not only elucidated the origins of the world's first Neolithic populations, but we have established a general model of the evolution of human populations in Southwest Asia and Europe." 

"Of course, spatial and temporal gaps remain, and this does not imply the end of studies on the evolution of humans in this area", concludes Laurent Excoffier. Thus, the team's research plan is already set; they want to supplement their demographic model with genomes from the later phases of the Neolithic and Bronze Ages to provide an increasingly detailed picture of human evolution. 

Source/Credit: University of Bern

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Wednesday, May 11, 2022

International project aims to understand and protect endangered sea turtles

A hawksbill sea turtle (Eretmochelys imbricata)
Credit: Kate Charles, Ocean Spirits Inc

A partnership of organizations and universities in the UK and Grenada has launched a new project looking into the challenges and threats facing two endangered marine species.

Marine conservationists in the two countries will be working to understand more about hawksbill sea turtles (Eretmochelys imbricata) and green sea turtles (Chelonia mydas).

This will include using a variety of field techniques to fully appreciate their behaviors and habitats, and ultimately, the partners hope to develop a series of measures that can be used to support the sustainable conservation of the species now and in the future.

The research is being funded by the Oscar Montgomery Environmental Foundation (OMEF), a charity launched in 2020 as a legacy to a young man who was passionate about the marine environment.

He died, aged just 17, and the charity set up in his memory aims to support, advocate and raise awareness of environmental issues, largely marine, and support projects and research which work to conserve and enhance the global environment.

Powering the moon

An artistic rendering of a resilient microgrid for a lunar base camp
might look like. Sandia National Laboratories engineers are working with
NASA to design the system controller for the microgrid.
Illustration by Eric Lundin
Sandia National Laboratories is well-known for designing reliable and resilient microgrids for military bases and vital city services. Now, Sandia researchers are working with NASA to design one for the moon.

This is not the first time Sandia has partnered with NASA to power equipment on the moon. In fact, Sandia provided the technical direction for the radioisotope thermoelectric generators that powered the lunar experiments placed by many of the Apollo missions.

NASA’s plan for its concept Artemis lunar base is that it will serve as a technology proving ground for the eventual human exploration of Mars, said Jack Flicker, a Sandia electrical engineer. The base camp concept consists of a habitation unit — complete with room for up to four astronauts — as well as the potential for separate mining and fuel processing, called in-situ resource utilization, facilities. Early Artemis missions will include short stays at the base camp with the goal to build up to stays of two months at a time.

The mining and processing facilities could produce rocket fuel, water, oxygen and other materials needed for extended exploration of the lunar surface while decreasing supply needs from Earth. This facility will be located far away from the base camp — so other science and technology activities conducted there won’t be disrupted — but the electrical grid for the two units will be connected during emergencies for resiliency and robustness, Flicker added.

Precision oncology helps prostate cancer patients

Brain metastasis of prostate cancer with selected intratumoral areas (pink and white circles) for undergoing molecular analyses.
Credit: Antonio Rodriguez, Dept. of Pathology and DBMR

Researchers at the University of Bern and University Hospital Bern have achieved a breakthrough in a particularly aggressive form of prostate cancer. In tissue samples from advanced brain metastases, they were able to establish the genetic profile of the cancer cells. These findings show for the first time that affected patients could benefit from target treatment, from which they have so far not been eligible.

Around 6,600 men are diagnosed with prostate cancer in Switzerland every year. It is the second most common cause of cancer-related death in men after lung cancer. Dangerous are advanced stages in which cancer cells have spread to other organs and form so-called metastases. However, unlike other cancers such as breast or lung cancer, the extremely dangerous metastases in the brain are very rare in prostate cancer. Only 1.5 percent of advanced cases have been diagnosed as brain metastatic prostate cancer (PCBM), according to a 2020 review study. As a result, PCBM cases have been poorly studied.

What Makes Some More Afraid of Change Than Others?

Being fearless can help wildlife, specifically birds, find new food sources, explore new nesting areas and help them adapt to changes in their environment; but being afraid can also help protect them from dangerous novel things in their environment such as cars. Scientists have discovered significant differences in how the brain works in two distinct personality types: those who act fearless and those who seem afraid of new things.

Humans are undoubtedly altering the natural environment. But how wild animals respond to these changes is complex and unclear. In a new study published today, scientists have discovered significant differences in how the brain works in two distinct personality types: those who act fearless and those who seem afraid of new things. Being fearless can help wildlife, specifically birds, find new food sources, explore new nesting areas and help them adapt to changes in their environment; but being afraid can also help protect them from dangerous novel things in their environment such as cars.

“Our study provides interesting and important evidence that some of the behavior differences could be led by gene expression,” said LSU Department of Biological Sciences Assistant Professor Christine Lattin, who is the lead author on the paper published by PLOS ONE today.

Tuesday, May 10, 2022

Astronomers find ‘gold standard’ star in Milky Way

The star HD 222925 is a ninth-magnitude star located toward the southern constellation Tucana.
Image credit: The STScI Digitized Sky Survey

In our sun’s neighborhood of the Milky Way Galaxy is a relatively bright star, and in it, astronomers have been able to identify the widest range of elements in a star beyond our solar system yet.

The study, led by University of Michigan astronomer Ian Roederer, has identified 65 elements in the star, HD 222925. Forty-two of the elements identified are heavy elements that are listed along the bottom of the periodic table of elements.

Identifying these elements in a single star will help astronomers understand what’s called the “rapid neutron capture process,” or one of the major ways by which heavy elements in the universe were created. Their results are posted on arXiv and have been accepted for publication in the Astrophysical Journal Supplement Series.

“To the best of my knowledge, that’s a record for any object beyond our solar system. And what makes this star so unique is that it has a very high relative proportion of the elements listed along the bottom two-thirds of the periodic table. We even detected gold,” Roederer said. “These elements were made by the rapid neutron capture process. That’s really the thing we’re trying to study: the physics in understanding how, where and when those elements were made.”

Ice-capped volcanoes slower to erupt, study finds

Undergraduate researcher Lilian Lucas, left, and geology professor Patricia Gregg found that additional pressure from thick overlying glacial ice can make volcanic systems more stable and slower to erupt than volcanoes without ice. 
Photo by Fred Zwicky

The Westdahl Peak volcano in Alaska last erupted in 1992, and continued expansion hints at another eruption soon. Experts previously forecasted the next blast to occur by 2010, but the volcano – located under about 1 kilometer of glacial ice – has yet to erupt again. Using the Westdahl Peak volcano as inspiration, a new volcanic modeling study examined how glaciers affect the stability and short-term eruption cycles of high-latitude volcanic systems – some of which exist along major air transportation routes.

The study, led by University of Illinois Urbana-Champaign undergraduate researcher Lilian Lucas, with graduate student Jack Albright, former graduate student Yan Zhan and geology professor Patricia Gregg, used finite element numerical modeling to study the stability of the rock that surrounds volcanic systems – but with a new twist. The team accounted for the additional pressure from glacial ice volcanoes when forecasting the timing of eruptions.

“Volcanic forecasting involves a lot of variables, including the depth and size of a volcano’s magma chamber, the rate at which magma fills that chamber and the strength of the rocks that contain the chamber, to name a few,” Lucas said. “Accounting for overlying pressure from polar ice caps is another critical, yet poorly understood, variable.”

Research breakthrough means warp speed ‘Unruh effect’ can finally be tested in lab settings

SFLORG Stock image

A major hurdle for work at the forefront of fundamental physics is the inability to test cutting-edge theories in a laboratory setting. But a recent discovery opens the door for scientists to see ideas in action that were previously only understood in theory or represented in science fiction.

One such theory is on the Unruh effect. When astronauts in a spacecraft undergo super strong acceleration and see the light of stars stream by, then the Unruh effect is an additional warm glow on top of the streaming light. First predicted by Canadian physicist Bill Unruh, this effect is closely related to the glow from black holes predicted by Stephen Hawking. This is because black holes strongly accelerate everything towards them.

“Black holes are believed to be not entirely black,” says Barbara Šoda, a PhD student in physics at the University of Waterloo. “Instead, as Stephen Hawking discovered, black holes should emit radiation. This is because, while nothing else can escape a black hole, quantum fluctuations of radiation can.”

Similar to how the Hawking effect needs a black hole, the Unruh effect requires enormous accelerations to produce a significant glow. The Unruh effect was therefore thought to be so weak that it would be impossible to measure with the acceleration that can be achieved in experiments with current technology.

Soil Microbes Use Different Pathways to Metabolize Carbon

Credit: Victor O. Leshyk/Northern Arizona University
Much of what scientists think about soil metabolism may be wrong. New evidence from Northern Arizona University suggests that microbes in different soils use different biochemical pathways to process nutrients, respire and grow. The study, published in Plant and Soil, upends long-held assumptions in the field of soil ecology and calls for more investigation and higher-resolution methods to be applied to what has been a black box for the field.

“As ecologists, we generally don’t think about soil metabolism in terms of pathways,” said Paul Dijkstra, research professor of biology in the Center for Ecosystem Science and Society at NAU and lead author of the study. “But we now have evidence that metabolism differs from soil to soil. We’re the first to see that.”

“We’ve learned that biochemistry—more specifically, the metabolic pathways the soil microbiota chooses—matters, and it matters a lot,” said co-author Michaela Dippold, a professor of bio-geosphere interactions at University of Tübingen in Germany. “Our field urgently needs to develop experimental approaches that quantify maintenance energy demand and underlying respiration in a robust way. It’s a challenge to which future soil ecology research will have to respond.”

Study finds cells take out the trash before they divide

MIT researchers have discovered that before cells start to divide, they toss waste products. In this image, the magenta represents DNA, and the green represents a lysosomal marker on the surface of the cells, which is an indicator of lysosomal exocytosis.
Credits: Courtesy of the researchers / Massachusetts Institute of Technology

MIT researchers have discovered that before cells start to divide, they do a little cleanup, tossing out molecules that they appear not to need anymore.

Using a new method, they developed for measuring the dry mass of cells, the researchers found that cells lose about 4 percent of their mass as they enter cell division. The researchers believe that this emptying of trash helps cells to give their offspring a “fresh start,” without the accumulated junk of the parent cell.

“Our hypothesis is that cells might be throwing out things that are building up, toxic components or just things that don’t function properly that you don’t want to have there. It could allow the newborn cells to be born with more functional contents,” says Teemu Miettinen, an MIT research scientist and the lead author of the new study.

Scott Manalis, the David H. Koch Professor of Engineering in the departments of Biological Engineering and Mechanical Engineering, and a member of the Koch Institute for Integrative Cancer Research, is the senior author of the paper, which appears today in eLife. MIT biological engineering undergraduates Kevin Ly and Alice Lam are also authors of the paper.

Fossils reveal tropically hot North America 95 million years ago

Cretaceous oysters of the genus Pycnodonte investigated in the new study. These specimens were collected in San Miguel County, Colorado (top left), Kane County, Utah (top right), Big Horn County, Wyoming (bottom left), and Natrona County, Wyoming (bottom right), with a penny for scale.
Image credit: Matt Jones

A new University of Michigan study that used fossil oyster shells as paleothermometers found the shallow sea that covered much of western North America 95 million years ago was as warm as today’s tropics.

The study provides the first direct temperature data from that vast mid-latitude sea during the height of the Cretaceous Thermal Maximum, one of the planet’s hottest climate intervals of the past several hundred million years.

The findings, published online May 9 in the journal Geology, also hint at what may be in store for future generations unless emissions of heat-trapping greenhouse gases are reined in.

“These data indicate that the North American interior during the peak of the Cretaceous greenhouse was as warm as the hottest conditions in the modern-day tropics—imagine the climate of Bali, Indonesia, in places like Utah or Wyoming,” said study lead author Matt Jones, a former University of Michigan postdoctoral researcher now at the Smithsonian Institution’s National Museum of Natural History.

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