Mystery of icy plumes that may foretell deadly supercell storms

 

An Above Anvil Cirrus Plume emanates from the top of a storm.
(Image credit: NASA)

The most devastating tornadoes are often preceded by a cloudy plume of ice and water vapor billowing above a severe thunderstorm. New research reveals the mechanism for these plumes could be tied to “hydraulic jumps” – a phenomenon Leonardo Da Vinci observed more than 500 years ago.

When a cloudy plume of ice and water vapor billows up above the top of a severe thunderstorm, there’s a good chance a violent tornado, high winds or hailstones bigger than golf balls will soon pelt the Earth below.

A new Stanford University-led study, published Sept. 10 in Science, reveals the physical mechanism for these plumes, which form above most of the world’s most damaging tornadoes.

Previous research has shown they’re easy to spot in satellite imagery, often 30 minutes or more before severe weather reaches the ground. “The question is, why is this plume associated with the worst conditions, and how does it exist in the first place? That’s the gap that we are starting to fill,” said atmospheric scientist Morgan O’Neill, lead author of the new study.

The research comes just over a week after supercell thunderstorms and tornadoes spun up among the remnants of Hurricane Ida as they barreled into the U.S. Northeast, compounding devastation wrought across the region by record-breaking rainfall and flash floods.

Understanding how and why plumes take shape above powerful thunderstorms could help forecasters recognize similar impending dangers and issue more accurate warnings without relying on Doppler radar systems, which can be knocked out by wind and hail – and have blind spots even on good days. In many parts of the world, Doppler radar coverage is nonexistent.

“If there’s going to be a terrible hurricane, we can see it from space. We can’t see tornadoes because they’re hidden below thunderstorm tops. We need to understand the tops better,” said O’Neill, who is an assistant professor of Earth system science at Stanford’s School of Earth, Energy & Environmental Sciences (Stanford Earth).

Supercell storms and exploding turbulence

The thunderstorms that spawn most tornadoes are known as supercells, a rare breed of storm with a rotating updraft that can hurtle skyward at speeds faster than 150 miles an hour, with enough power to punch through the usual lid on Earth’s troposphere, the lowest layer of our atmosphere.

In weaker thunderstorms, rising currents of moist air tend to flatten and spread out upon reaching this lid, called the tropopause, forming an anvil-shaped cloud. A supercell thunderstorm’s intense updraft presses the tropopause upward into the next layer of the atmosphere, creating what scientists call an overshooting top. “It’s like a fountain pushing up against the next layer of our atmosphere,” O’Neill said.

As winds in the upper atmosphere race over and around the protruding storm top, they sometimes kick up streams of water vapor and ice, which shoot into the stratosphere to form the tell-tale plume, technically called an Above-Anvil Cirrus Plume, or AACP.

The rising air of the overshooting top soon speeds back toward the troposphere, like a ball that accelerates downward after cresting aloft. At the same time, air is flowing over the dome in the stratosphere and then racing down the sheltered side.

Using computer simulations of idealized supercell thunderstorms, O’Neill and colleagues discovered that this excites a downslope windstorm at the tropopause, where wind speeds exceed 240 miles per hour. “Dry air descending from the stratosphere and moist air rising from the troposphere join in this very narrow, crazy-fast jet. The jet becomes unstable and the whole thing mixes and explodes in turbulence,” O’Neill said. “These speeds at the storm top have never been observed or hypothesized before.”

Hydraulic jump

Scientists have long recognized that overshooting storm tops of moist air rising into the upper atmosphere can act like solid obstacles that block or redirect airflow. And it’s been proposed that waves of moist air flowing over these tops can break and loft water into the stratosphere. But no research to date has explained how all the pieces fit together.

The new modeling suggests the explosion of turbulence in the atmosphere that accompanies plumed storms unfolds through a phenomenon called a hydraulic jump. The same mechanism is at play when rushing winds tumble over mountains and generate turbulence on the downslope side, or when water speeding smoothly down a dam’s spillway abruptly bursts into froth upon joining slower-moving water below.

Leonardo DaVinci observed the phenomenon in flowing water as early as the 1500s, and ancient Romans may have sought to limit hydraulic jumps in aqueduct designs. But until now atmospheric scientists have only seen the dynamic induced by solid topography. The new modeling suggests a hydraulic jump can also be triggered by fluid obstacles in the atmosphere made almost entirely of air and which are changing shape every second, miles above the Earth’s surface.

The simulations suggest the onset of the jump coincides with a surprisingly rapid injection of water vapor into the stratosphere, upwards of 7000 kilograms per second. That’s two to four times higher than previous estimates. Once it reaches the overworld, water may stay there for days or weeks, potentially influencing the amount and quality of sunlight that reaches Earth via destruction of ozone in the stratosphere and warming the planet’s surface. “In our simulations that exhibit plumes, water reaches deep into the stratosphere, where it possibly could have more of a long-term climate impact,” said co-author Leigh Orf, an atmospheric scientist at the University of Wisconsin-Madison.

According to O’Neill, high-altitude NASA research aircraft have only recently gained the ability to observe the three-dimensional winds at the tops of thunderstorms, and have not yet observed AACP production at close range. “We have the technology now to go verify our modeling results to see if they’re realistic,” O’Neill said. “That’s really a sweet spot in science.”

This research was supported by the National Science Foundation and the NASA Precipitation Measurement Mission and Ground Validation program.

Source/Credit: Stanford University/Josie Garthwaite

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Ancient sea ice core sheds light on modern climate change

 

A 170 m record of marine sediment cores extracted from Adélie Land in Antarctica by the Integrated Ocean Drilling Program is yielding new insights into the complicated relationship between sea ice and climate change.

In a new study published in Nature Geoscience, researchers at the University of Birmingham, have collaborated in an international project to identify how fluctuations in sea ice levels have interconnected with both algae blooms and weather events linked to El Nino over the past 12,000 years.

They found that Antarctic winds strongly affect the break-out and melting of sea ice, which in turn affects the levels of algae which can grow rapidly in surface waters when sea ice is reduced. Changes in the levels of algae growth in the waters surrounding the Antarctic are important enough to affect the global carbon cycle.

The researchers used techniques such as CT scan (computed tomography) imaging and analysis of microfossils and organic biomarkers, to examine the relationship between sea ice and large algae growth “bloom” events at annual timescales. The findings, produced in partnership with research institutes in New Zealand, Japan, France, Spain and the USA, span the entire Holocene period and have yielded a highly detailed picture of these relationships that can help predict future sea ice, climate and biological interactions.

The researchers found that algal bloom events occurred nearly every year before 4,500 years ago. However, a baseline shift to less frequent algal blooms and the type of algal production after 4.5 thousand years ago, saw bloom events responding to the El Nino Southern Oscillation (ENSO) and other climate cycles as sea-ice levels rapidly increased. Recent work by many of the same team links the expansion of sea ice at this time to glacial retreat and the development of the Ross Ice Shelf, which acts to cool Antarctic surface waters to create a “sea-ice factory”.

Dr James Bendle, of the University of Birmingham’s School of Geography, Earth and Environmental Science, is a co-author on the paper. He said: “While there’s a clear relationship between temperatures rising in the Arctic over recent decades and sea ice melting, the picture is more complex in the Antarctic. That’s because some areas of the Antarctic are warming, but in some areas sea ice has been increasing. Since sea ice reflects incoming sunlight, not only is the warming effect slowed down, but algae are unable to photosynthesize as easily. Climate models currently struggle to predict observed changes in sea ice for the Antarctic, and our findings will help climate researchers build more robust and detailed models.”

He added: “The relationship we have observed with these changing conditions and the ENSO wind fields is particularly significant. We know that El Nino amplifies the effects of climate change in some regions, so any insights linking this with Antarctic Sea ice is fascinating and has implications for how future long-term loss of sea ice may affect food webs in Antarctic waters, as well as carbon cycling processes within this globally important region.”


Dr Katelyn Johnson, of GNS Science, in New Zealand, is the lead author on the paper. She said: “While sea ice that persists from year to year can prevent these large algal blooms from occurring, sea ice that breaks out and melts creates a favorable environment for these algae to grow. These large algae ‘bloom events’ occur around the continent, form the base of the food webs and act as a carbon sink”.

“Unlike the Arctic where rising temperatures have led to reduced sea ice, the relationship in the Antarctic is less clear, as is the subsequent impact on primary productivity. Our new record provides a longer-term view of how sea ice and climate models like ENSO impact the frequency of these bloom events, allowing climate modelers to build more robust models.”

Source/Credit: University of Birmingham

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Moth wingtips an ‘acoustic decoy’ to thwart bat attack

 

The Atlas moth (Attacus atlas) has a strong anti-bat acoustic decoy at the tip of its forewings. Composite image with photograph on right half and acoustic tomography on the left. Color indicates echo strength on a dB scale and red indicates highest echo amplitude. Note the red highly reflecting stripe created by the rippled part of the wingtip.
Image Credit: Dr Thomas Neil and Professor Marc Holderied

Wingtips of certain species of silkmoth are structured to reflect sound and throw off attackers, according to a new study.

Researchers at the University of Bristol have discovered that the tips of some saturniid moth forewings are curiously rippled and folded. They found that these unique structures strongly reflect sound, meaning that a bat hunting using echolocation is more likely to attack the wingtip region of the moth over the body, potentially saving the moth’s life.

Photograph of the Chinese tussar moth (Antheraea pernyi).
This silkmoth has a strong wingtip decoy based on ripples. 
Image Credit: Dr Thomas Neil

They also discovered that the ripples and folds of the forewing tips have evolved to act as hemispheric and corner retroreflectors respectively, meaning that they reflect sound strongly back to its point of origin. Coupled together, the folds and ripples of these wingtips cover a huge range of incident sounds angles, meaning that over the entire wingbeat cycle of a flying moth and most possible positions of an attacking bat, the wingtip would consistently produce the strongest echoes. The acoustic protection of wingtips is even stronger than that of common hindwing decoys.

Professor Marc Holderied of Bristol’s School of Biological Sciences explained: “We have demonstrated that the folded and rippled wingtips on the forewings of some silkmoths act as acoustic decoys.

“Structurally, the wingtips act as acoustic retroreflectors, reflecting sound back to its source from numerous angles, meaning a bat would be more likely to strike the wingtip over the more vulnerable body of the moth.”

The findings, published today in Current Biology, are the latest revelation in the bat-moth acoustic arms race - the battle between bats which hunt moths using echolocation, and the subsequent evolution of different defensive strategies amongst moths to increase their chances of survival.

Photograph of the Chinese tussar moth (Antheraea pernyi).
This silkmoth has a strong wingtip decoy
based on ripples. Image Credit: Dr Thomas Neil

Towed acoustic decoys are a well-established defense amongst some silkmoths. These species have evolved elongated hindwings which terminate in a coiled and twisted end. The morphology of these elongated hindwings means that they generate very strong echoes, so much so that they will often divert a bat’s acoustic gaze towards them, away from the exposed body of the moth, causing the bat to strike the expendable tail of the moth or miss the moth all together.

Lead author Dr Thomas Neil said: “There are many silkmoths that do not have these elongated hindwings, and we were interested in how they might protect themselves from bats. Through our research we discovered that there are many silkmoths that have rippled and folded structures not on the tips of their elongated hindwings but on the tips of their forewings. These resembled the twisted hindwing structures seen in other moths and so we wanted to know if they might also serve as an acoustic decoy to thwart a bat’s attack.

“To test this theory, we used innovative acoustic tomography analysis. We recorded echoes from moths from over 10,000 angles, to compare whether the echoes coming from the wingtips of these moths were stronger than the echoes from the body. If the echoes coming from the rippled and folded wingtips were stronger than that of the body, this would indicate that they were indeed acoustic decoys.

“Conclusive support for the idea that the forewing reflector is an acoustic decoy comes from our finding that acoustic forewing decoys always evolved as an alternative to acoustic hindwing decoys, with there being no species known to possess both.”

Now the researchers will try and collect behavioral data to corroborate their findings in the lab. They plan to monitor bats and moths with varying levels of folded wing morphologies to see how much of a survival advantage it really gives them.

Prof Holderied added:“The results of this study introduce another exciting aspect to the story of the bat-moths acoustic arms race. We have identified a novel form of acoustic defense amongst silkmoths which may give them an advantage over hunting bats. Wider implications might include improved man-made anti radar and sonar decoy architectures.”

Source/Credit: University of Bristol

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ESO captures best images yet of peculiar “dog-bone” asteroid

 

These eleven images are of the asteroid Kleopatra, viewed at different angles as it rotates. The images were taken at different times between 2017 and 2019 with the Spectro-Polarimetric High-contrast Exoplanet REsearch (SPHERE) instrument on ESO’s VLT.   Kleopatra orbits the Sun in the Asteroid Belt between Mars and Jupiter. Astronomers have called it a “dog-bone asteroid” ever since radar observations around 20 years ago revealed it has two lobes connected by a thick “neck”. 
Credit / Source: ESO/Vernazza, Marchis et al./MISTRAL algorithm (ONERA/CNRS)

Using the European Southern Observatory’s Very Large Telescope (ESO’s VLT), a team of astronomers have obtained the sharpest and most detailed images yet of the asteroid Kleopatra. The observations have allowed the team to constrain the 3D shape and mass of this peculiar asteroid, which resembles a dog bone, to a higher accuracy than ever before. Their research provides clues as to how this asteroid and the two moons that orbit it formed.

“Kleopatra is truly a unique body in our Solar System,” says Franck Marchis, an astronomer at the SETI Institute in Mountain View, USA and at the Laboratoire d'Astrophysique de Marseille, France, who led a study on the asteroid — which has moons and an unusual shape — published today in Astronomy & Astrophysics. “Science makes a lot of progress thanks to the study of weird outliers. I think Kleopatra is one of those and understanding this complex, multiple asteroid system can help us learn more about our Solar System.”

Kleopatra orbits the Sun in the Asteroid Belt between Mars and Jupiter. Astronomers have called it a “dog-bone asteroid” ever since radar observations around 20 years ago revealed it has two lobes connected by a thick “neck”. In 2008, Marchis and his colleagues discovered that Kleopatra is orbited by two moons, named AlexHelios and CleoSelene, after the Egyptian queen’s children.

To find out more about Kleopatra, Marchis and his team used snapshots of the asteroid taken at different times between 2017 and 2019 with the Spectro-Polarimetric High-contrast Exoplanet REsearch (SPHERE) instrument on ESO’s VLT. As the asteroid was rotating, they were able to view it from different angles and to create the most accurate 3D models of its shape to date. They constrained the asteroid’s dog-bone shape and its volume, finding one of the lobes to be larger than the other, and determined the length of the asteroid to be about 270 kilometers or about half the length of the English Channel.

This image provides a size comparison of the asteroid Kleopatra with northern Italy.   The top half of the image shows a computer model of Kleopatra, a “dog-bone” shaped asteroid which orbits the Sun in the Asteroid Belt between Mars and Jupiter. End to end, Kleopatra is 270 kilometers long.   The bottom half of the image gives an aerial view of northern Italy, with the footprint Kleopatra would have if it were hovering above it.   
Credit / Sou: ESO/M. Kornmesser/Marchis et al.

In a second study, also published in Astronomy & Astrophysics and led by Miroslav Brož of Charles University in Prague, Czech Republic, the team reported how they used the SPHERE observations to find the correct orbits of Kleopatra’s two moons. Previous studies had estimated the orbits, but the new observations with ESO’s VLT showed that the moons were not where the older data predicted them to be.

“This had to be resolved,” says Brož. “Because if the moons’ orbits were wrong, everything was wrong, including the mass of Kleopatra.” Thanks to the new observations and sophisticated modelling, the team managed to precisely describe how Kleopatra’s gravity influences the moons’ movements and to determine the complex orbits of AlexHelios and CleoSelene. This allowed them to calculate the asteroid’s mass, finding it to be 35% lower than previous estimates.

Combining the new estimates for volume and mass, astronomers were able to calculate a new value for the density of the asteroid, which, at less than half the density of iron, turned out to be lower than previously thought. The low density of Kleopatra, which is believed to have a metallic composition, suggests that it has a porous structure and could be little more than a “pile of rubble”. This means it likely formed when material reaccumulated following a giant impact.

Kleopatra’s rubble-pile structure and the way it rotates also give indications as to how its two moons could have formed. The asteroid rotates almost at a critical speed, the speed above which it would start to fall apart, and even small impacts may lift pebbles off its surface. Marchis and his team believe that those pebbles could subsequently have formed AlexHelios and CleoSelene, meaning that Kleopatra has truly birthed its own moons.

The new images of Kleopatra and the insights they provide are only possible thanks to one of the advanced adaptive optics systems in use on ESO’s VLT, which is located in the Atacama Desert in Chile. Adaptive optics help to correct for distortions caused by the Earth’s atmosphere which cause objects to appear blurred — the same effect that causes stars viewed from Earth to twinkle. Thanks to such corrections, SPHERE was able to image Kleopatra — located 200 million kilometers away from Earth at its closest — even though its apparent size on the sky is equivalent to that of a golf ball about 40 kilometers away.

ESO’s upcoming Extremely Large Telescope (ELT), with its advanced adaptive optics systems, will be ideal for imaging distant asteroids such as Kleopatra. “I can’t wait to point the ELT at Kleopatra, to see if there are more moons and refine their orbits to detect small changes,” adds Marchis.

Source/Credit: ESO

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Released
09-09-21 12:00UTC

Biomarker predicts cognitive decline in Alzheimer’s disease

top-down view of a tau PET and MRI from a participant in the Northwestern study.
Warmer colors (red) indicate high Alzheimer's disease tau pathology.
(Image orientation: left is left, right is right).

 A biomarker in the brain predicts future cognitive decline in patients with the language form of Alzheimer’s disease 

Northwestern Medicine scientists discovered the buildup of tau protein in the brain predicts the amount of future cognitive decline over one year in individuals with AD. The study measured used a newer type of positron emission tomography (PET) imaging that shows the location of toxic tau protein in the brain. 

“Our new research shows tau PET imaging biomarkers can predict future decline in individuals with primary progressive aphasia due to AD,” said senior study author Emily Rogalski, associate director of Northwestern’s Mesulam Center for Cognitive Neurology and Alzheimer’s Disease. “These tau-based biomarkers may help predict the pace of progression of the disease and be important for early detection. They may eventually help us treat AD before we see symptoms.”

The higher the level of the bad form of tau in the brain, the worse a person’s cognitive performance, the study showed. The more tau protein a person had in a specific region of their brain, the more likely they were to have worse cognition a year later. The study also found the higher the level of tau, the more atrophy was occurring across the brain. 

The study was published Sept. 8 in Alzheimer’s and Dementia: The Journal of the Alzheimer’s Association.

Early diagnosis of AD is important because the Food & Drug Administration recently approved Biogen’s Aduhelm (aducanumab) to treat patients in the disease’s mild stages, and other drugs are in the development pipeline. 

“The presence and level of these biomarkers might give us a picture of how aggressive the disease is going to be, providing important markers necessary for precision-medicine interventions,” said lead author Adam Martersteck. He conducted the research as a neuroscience graduate student at Northwestern University Feinberg School of Medicine and now is a postdoctoral fellow at the University of California Berkeley.

The study was among the first to show the amount of tau pathology in the brain predicts subsequent cognitive decline over time.

The individuals in the study had Progressive Primary Aphasia (PPA), which is often caused by an early-onset form of AD. In PPA, the parts of the brain that control language and speech degenerate.

“It’s important to show that AD in primary progressive aphasia is similar to the more common late-onset AD that causes memory problems, so that participants with PPA can be included in clinical trials and offered all the same opportunities,” Martersteck said.

The finding about predictive decline from tau pathology is also applicable to more common forms of AD in which memory loss is the primary symptom. One theory is that toxic forms of AD accumulate and then trigger events resulting in brain cell degeneration. This research supports this theory. 

Participants from around the country were seen locally or flown to Chicago for MRI, tau PET imaging and cognitive testing at Northwestern’s Mesulam Center for Cognitive Neurology and Alzheimer's Disease. The 19 participants all had been diagnosed with PPA. 

As a growing proportion of Americans age, the prevalence of AD is expected to rise. An estimated 50 million people worldwide and 6 million in the U.S. have AD, with those numbers expected to triple in the next 30 years.

In the study, scientists measured toxic tau at baseline and tested participants on their ability to name objects. Participants returned a year later and were tested again on their ability to name objects. The more tau they had in the left anterior temporal lobe on PET imaging, the more likely they were to have worse cognition and a decline in their naming. 

“The next steps for the research are to determine if these measurements are reliable at the individual level to guide prognosis and intervention targets,” Rogalski said. “We know some individuals with PPA progress more rapidly than others, but factors driving fast versus slow progression have been difficult to ascertain. Reliable biomarkers are one key to solving this conundrum.” 

Other Northwestern study authors are Jaiashre Sridhar, Christina Coventry, Sandra Weintraub and Dr. Marsel Mesulam.

Source/Credit: Northwestern University

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Coral cryopreservation for breeding key to survival

 

Fragment of endangered Caribbean elkhorn coral grown from cryopreserved sperm.
(Photo credit: Chris Page)

Flash-frozen sperm collected from corals in Florida and Puerto Rico was used to fertilize coral eggs from hundreds of miles away in Curaçao. The juvenile corals raised from this trans-Caribbean coupling demonstrate the reproductive compatibility of coral colonies that would otherwise be too far apart to produce offspring in the wild and they represent the largest wildlife population ever raised from cryopreserved material.

A paper describing this study, by an international team of researchers, including Mary Hagedorn at the University of Hawaiʻi at Mānoa School of Ocean and Earth Science and Technology (SOEST), was published in the Proceedings of the National Academy of Sciences.

The technique could be used as a conservation tool by introducing genetic variation into endangered corals and potentially accelerating their adaptation to climate change.

“Most corals only attempt sexual reproduction once a year and the eggs and sperm are only viable for a short time period,” said Hagedorn, a research biologist at the Smithsonian Conservation Biology Institute and UH Mānoa’s Hawaiʻi Institute of Marine Biology. She is the lead author of this study, and has developed the technique to cryopreserve coral sperm in her laboratory at UH. “Cryopreservation allows us to breed corals with parentage from hundreds of miles apart.”

Assisted gene flow

“Corals are a vital foundation species for reef ecosystems,” said Iliana Baums, professor of biology at Penn State and one of the leaders of the research team. “Reefs provide habitat for astonishing species diversity, protect shorelines and are economically important for fisheries, but they are suffering in many places due to warming ocean waters. Without intervention, we will continue to lose corals to climate change with potentially disastrous consequences.”

Genetic diversity is the fuel for species adaptation. One of the main sources of genetic diversity is sexual reproduction—new combinations of genes are created when a sperm fertilizes an egg. However, sexual reproduction by Caribbean corals in the wild is now vanishingly rare. Worse yet, because corals are sessile creatures (fixed in one place), they have a limited ability to gain new genetic diversity through gene flow, the evolutionary force that increases genetic diversity when distant populations come together, each bringing with them their own unique versions of genes.

“To increase genetic diversity in corals, we can use ‘assisted gene flow’ by bringing corals together that are physically distant in the wild, but this is logistically incredibly difficult,” said Baums.

Cryopreservation

Most corals reproduce by broadcasting bundles of eggs and sperm into the sea water in a spectacular spawning event timed with the full moon. The researchers collected these bundles from corals in Florida and Puerto Rico, separated the eggs and sperm, and then quickly froze the sperm cells using a liquid nitrogen cryopreservation technique.

“Because these corals only produce eggs and sperm once per year, frozen sperm collected in Florida and Puerto Rico needed to be cryopreserved in advance and stored for over a year until it could be used for a spawning event in Curaçao,” said Baums.

Some of the sperm were kept frozen at the USDA National Animal Germplasm Program’s gene bank for up to 10 years. The frozen sperm was transported to Curaçao where it was thawed and used to fertilize fresh eggs collected locally. The fertilized eggs developed into larvae that were then transported to Mote Marine Laboratory and The Florida Aquarium in Florida, where they were allowed to develop into adults.

Source/Credit: University of Hawaiʻi

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A source of hope for coral reefs

 

A healthy coral reef in the Phoenix Islands Protected Area in 2018.
Photo credit: Michael Fox

Some coral communities are becoming more heat tolerant as ocean temperatures rise, offering hope for corals in a changing climate.

After a series of marine heatwaves hit the Phoenix Islands Protected Area (PIPA) in the central Pacific Ocean, a new study finds the impact of heat stress on the coral communities lessened over time.

While a 2002-2003 heatwave devastated coral communities in PIPA, the reefs recovered and experienced minimal losses during a similar event in 2009-2010. Then, in 2015-2016, a massive heatwave put twice as much heat stress on the corals, yet the die-off was much less severe than expected, according to new research published in Geophysical Research Letters, AGU’s journal for high-impact reports with immediate implications spanning all Earth and space sciences.

The authors of the new study suspect heat-tolerant offspring from the surviving corals are repopulating the reefs, allowing the community to keep pace with warming seas, at least for the time being.

The new study could help coral reef managers identify coral communities most likely to survive in the warming ocean, improving conservation and restoration outcomes.

“It’s easy to lose faith in coral reefs,” said first author Michael Fox, a postdoctoral scientist and coral reef ecologist at the Woods Hole Oceanographic Institution (WHOI). “But in PIPA, which is protected from local stressors, and where reefs have enough time to recover between heatwaves, the coral populations are doing better than expected.”

Underwater heatwaves

Just like on land, heatwaves underwater are becoming more frequent and intense as the world warms, putting stress on ocean ecosystems. High temperatures hit coral reefs especially hard by causing widespread bleaching events, where corals eject the symbiotic algae in their tissues, further weakening the animals. With continued ocean warming, coral reefs face a dim future.

In the new study, researchers monitored coral communities at four islands within PIPA, an area encompassing over 400,000-square-kilometers of coral reef and deep-sea habitat. The Republic of Kiribati established the reserve in 2008, and the United Nations Educational, Scientific and Cultural Organization (UNESCO) designated PIPA as a World Heritage Site in 2010. “The protected area gives us a rare opportunity to study pristine and isolated coral reef ecosystems, a privilege for which we thank the people of Kiribati,” said co-author Anne Cohen, a marine scientist at WHOI.

The team used daily satellite data and temperature loggers to examine how each heatwave impacted the corals. They ruled out 11 environmental factors that might explain the higher-than-expected survival following the 2009-2010 and 2015-2016 heatwaves, such as greater cloud cover or more gradual warming.

After the 2002-2003 heatwave, the surveyed sites lost more than three-quarters of their coral cover. The reef was beginning to recover when the 2009-2010 heatwave hit, sparking fears of widespread bleaching, but two years later, coral cover had increased by more than 5%. Following the “Super El Niño” in 2015-2016, which raised ocean temperatures by 3 degrees Celsius (5.4 degrees Fahrenheit), the loss of coral cover was 40%— about half of the 2002 losses, despite causing twice the level of thermal stress.

A source of hope for coral reefs

Many of the reef-building species survived the heatwaves. “We’re seeing areas that were devoid of corals after 2002-2003 that are now flourishing with most of the original species,” Fox said.

At other reefs worldwide, sometimes only a handful of especially hardy or fast-growing species recover after a bleaching event. Coral larvae can float long distances on ocean currents, but due to PIPA’s isolation, the researchers hypothesize that local heat-tolerant individuals are repopulating the reefs.

Now that the researchers have shown that some coral communities have the potential to keep up with ocean warming, their next step is to figure out how they are doing it.

The findings are “important for giving us hope for the future of coral reefs, and also for helping to maintain support for protecting reefs, including efforts to reduce local threats, like pollution, sedimentation and overfishing that undermine the reefs’ ability to adapt,” said Lizzie McLeod, the Global Reef Systems Lead at the Nature Conservancy, who was not involved in the study.

She recommends reef conservationists prioritize the conservation of heat-tolerant reefs, because they can act as climate refuges that repopulate other sites decimated by heatwaves.

The study’s authors caution that even these remarkable corals have their limits and reversing climate change remains paramount. As heatwaves become more frequent or intense, even heat-tolerant communities could die out.

“We’re in a race against time, so anything that increases the chances that corals are going to make it is really good news,” said Nancy Knowlton, the Sant Chair in Marine Science Emerita at the Smithsonian National Museum of Natural History, who was not part of the study. “The corals are doing their part,” she said. “We have to do ours.”

Source/Credit: Woods Hole Oceanographic Institution

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Newly developed software unveils relationships between RNA modifications and cancers

Researchers from CSI Singapore have developed a software called ModTect that identifies relationships between RNA modifications and the development of diseases as well as survival outcomes

 In a research breakthrough, a team of researchers from the Cancer Science Institute of Singapore (CSI Singapore) at the National University of Singapore has developed a software that can help reveal the relationships between RNA modifications and the development of diseases and disorders.

Led by Professor Daniel Tenen and Dr Henry Yang, the scientists devised ModTect – a new computational software that can identify RNA modifications using pre-existing sequencing data from clinical cohort studies. With ModTect, the team carried out their own novel pan-cancer study covering 33 different cancer types. They found associations between these RNA modifications and the different survival outcomes of cancer patients.

“This work is one of few studies demonstrating the association of mRNA modification with cancer development. We show that the epitranscriptome was dysregulated in patients across multiple cancer types and was additionally associated with cancer progression and survival outcomes,” explained Dr Henry Yang, Research Associate Professor from CSI Singapore.

"In the past decade, the ability to sequence the Human Genome has transformed the study of normal processes and diseases such as cancer. We anticipate that studies like this one, eventually leading to complete sequencing of RNA and detecting modifications directly in RNA, will also have a major impact on the characterization of disease and lead to novel therapeutic approaches," commented Prof Tenen, Senior Principal Investigator from CSI Singapore.

What are RNA modifications?

While most people are familiar with DNA, RNA plays just as much of a vital role in the human body’s cellular functions. Unlike DNA, which has the double-helix structure that most people are familiar with, RNA is a family of single-stranded molecules that perform various essential biological roles.

For example, messenger RNA (mRNA) conveys genetic information that directs the production of different proteins. Imagine DNA as an expansive library filled with books that carry instructions on how to make different proteins. Each letter in the sequences of words that make up the books’ contents are called nucleotides, which are small molecules that are used to store genetic information. To make sure these instructions are followed, mRNA makes copies of the books and carries them from a cell’s nucleus, where DNA is stored, to the ribosomes. These ribosomes are the “factories” where proteins are synthesized. Without RNA, the valuable genetic instructions stored in our cells would never be used.

Additional types of RNA perform other important functions. Some help catalyze biochemical reactions, just like enzymes, while others regulate gene expression.

Small chemical modifications to RNA can sometimes occur and alter the function and stability of the molecules. The study of these modifications and their effects is called ‘epitranscriptomics’. Research in the past has suggested a link between the development of diseases like Alzheimer’s disease and cancer with certain RNA modifications. However, despite multiple attempts to study these associations in deeper detail, the study of epitranscriptomes has proven to be difficult until this breakthrough by scientists from CSI Singapore.

In large patient cohorts, collecting and processing patient samples is challenging. Detecting RNA modifications often involves technically complex processes, such as treating the samples with chemicals that are difficult to access. These techniques often also require the use of large quantities of sample that are hard to obtain for rarer conditions. Because of this, scientists have been limited in their capacity to establish relationships between specific RNA modifications and various human diseases.

Software makes epitranscriptomics easier

The software that the CSI Singapore team created uses RNA sequences available from other large clinical cohort studies. To detect modifications in these RNA sequences, ModTect looks for mismatch signals and deletion signals. Mismatch signals arise when the experimental enzymes scientists use to turn RNA back into DNA incorporates random nucleotides during sequencing. Deletion signals, on the other hand, are when the enzymes sometimes skip a portion of the sequence. Together, these signals are referred to as misincorporation signals.

Unlike other models, ModTect does not require a database of misincorporation signal profiles corresponding to different types of RNA modifications to identify or classify them. ModTect can even identify new signal profiles that drastically differ from what has been previously recorded.

By applying the software to around 11,000 cancer patient RNA-sequencing datasets, the CSI Singapore team was able to embark on a novel study that investigated the associations between RNA modifications and clinical outcomes in patients. ModTect was able to utilize these large datasets and process them with robust statistical filtering. It unveiled that some types of epitranscriptome were associated with cancer progression and survival outcomes in patients. This finding highlighted the potential use of RNA modifications as biomarkers – molecules that can be used to test for diseases.

Unravelling the mystery of sequence differences that escape detection

As explored before, the transmission of genetic information from DNA in a cell’s nucleus to RNA molecules that carry it to a cell’s ribosomes is a critical process. However, this transmission process is not perfect and leads to differences in RNA-DNA sequences. The sites of these mismatches have been widely documented. However, it is unclear whether these observations are caused by modifications in mRNA and why these sites have escaped detection by Sanger sequencing (one of the most popular methods of DNA sequencing).

The group at CSI Singapore uncovered a potential explanation as to why these RNA modification signals have eluded detection over the years. They explained how some epitranscriptomes impede the use of standard reverse transcriptase (RT), the enzyme that is used to convert RNA into DNA. This enzyme is used by scientists in genome sequencing and its use is one of the most critical steps for experimental success. Hence, RNAs that had these impeding modifications were under-represented in Sanger sequencing techniques.

To combat this, the team used newly developed RT enzymes that have been known for their ability to bypass the effects of these modification sites. This allowed them to observe epitranscriptomes that were originally undetectable with Sanger sequencing.

The discipline of epitranscriptomics is still an emerging and rapidly developing field with around 170 RNA modifications being detected so far. By harnessing ModTect, Prof Tenen and his team were able to provide novel insights into the relationships between human diseases – like cancer – and such RNA modifications. The software will be publicly available on Github for other scientists to use.

The team is hopeful that their contribution will help further research that establishes any potential causal or mechanistic relationships between RNA modifications and tumor formation.

Source/Credit: National University of Singapore

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Nature’s archive reveals Atlantic tempests through time

 

The North Atlantic network of sites that preserve records of hurricanes stretches along the coast from Canada to Central America, but with significant gaps. A new study led by scientists at Rice University shows filling those gaps with data from the mid-Atlantic states will help improve the historical record of storms over the past several thousand years and could aid in predictions of future storms in a time of climate change. Illustration by Elizabeth Wallace

Atlantic hurricanes don’t just come and go. They leave clues to their passage through the landscape that last centuries or more. Rice University scientists are using these natural archives to find signs of storms hundreds of years before satellites allowed us to watch them in real time.

Elizabeth Wallace.
(Credit: Abby Llona)

Postdoctoral fellow Elizabeth Wallace, a paleotempestologist who joined the lab of Rice climate scientist Sylvia Dee this year, is building upon techniques that reveal the frequency of hurricanes in the Atlantic basin over millennia.

The North Atlantic network of sites that preserve records of hurricanes stretches along the coast from Canada to Central America, but with significant gaps. A new study led by scientists at Rice University shows filling those gaps with data from the mid-Atlantic states will help improve the historical record of storms over the past several thousand years and could aid in predictions of future storms in a time of climate change. Illustration by Elizabeth Wallace

Paleoclimate hurricane data (or ‘proxy’ data) is found in archives like tree rings that retain signs of short-term flooding, sediments in blue holes (marine caverns) and coastal ponds that preserve evidence of sand washed inland by storm surges. These natural archives give researchers a rough idea of when and where hurricanes have come ashore.

In a new paper in Geophysical Research Letters, Wallace, Dee and co-author Kerry Emanuel, a climate scientist at the Massachusetts Institute of Technology, take hundreds of thousands of “synthetic” storms spun up from global climate model simulations of the past 1,000 years and examine whether or not they are captured by the vast network of Atlantic paleohurricane proxies.

Reconstructing the past will help scientists understand the ebb and flow of Atlantic hurricanes over time. Previous studies by Wallace and others have demonstrated that a single site capturing past storms cannot be used to reconstruct hurricane climate changes; however, a network of proxies might help refine models of how these storms are likely to be affected by climate change going forward.

Sylvia Dee.
(Credit: Rice University)

“These paleo hurricane proxies allow us to reconstruct storms into the past, and we’re using them to figure out how basin-wide storm activity has changed,” said Wallace, a Virginia native who earned her doctorate at MIT and the Woods Hole Oceanographic Institution last year and connected with Dee when the professor spoke there in 2017.

“If I have a sediment core from Florida, it’s only capturing storms that hit Florida,” she said. “I wanted to see if we can use the full collection of records collected from the Bahamas, the East Coast and the Gulf of Mexico over the past few decades to accurately reconstruct basin-wide storm activity over the last few centuries.”

The synthetic storms they built helped illustrate what Wallace already knew: There’s a bias toward the Caribbean and Gulf of Mexico, and a need for more proxies along the east coasts of North and Central America. The Rice team’s quest going forward will be to refine their climate simulations and add more sites to the networks to better reconstruct past hurricane activity.

“In particular, there aren’t really any sites from the Southeast U.S., places like the Carolinas,” she said. “One of the goals of this work is to highlight where scientists should go to core next.”

Wallace has first-hand experience drilling cores. “During a storm event, you get high winds and waves that take the sand from the beach and essentially just throw it back into a coastal pond,” she said. “Only during storm events do these sand layers get deposited in the pond, and in the sediment cores you can see them interspersed with the fine mud that’s typically there. We can date these sand layers and know when a hurricane struck the site.”

She noted there has not yet been an “intensive” effort to compare sediment and tree ring records. “The tree record is still an uncertain proxy,” Wallace said. “We’re looking for tree ring records with rainfall signatures that correspond to storms going over the past 200 or 300 years that match the sediment records for that same interval.”

Dee said the work is fundamentally different from the paleoclimate models she most often studies. “Here we’re taking climate models and generating hundreds of pseudo-tropical storms,” she said. “We’re ‘playing Gaia’ by making a plausible version of reality and combining it with our knowledge of available proxy sites.

“This tells us how many records from how many places we realistically need to capture a climate signal,” Dee said. “It’s really expensive to go out and drill cores, and this helps give us a way to prioritize where to drill.

“This research is crucial as we accelerate into a climate mean state with ever-warmer Atlantic Ocean temperatures,” she said. “Understanding how these storms have evolved over time provides a baseline against which to evaluate tropical cyclones with and without human impacts on the climate system.”

A Pan Postdoctoral Research Fellowship and Rice Academy Fellowship to Wallace and a Gulf Research Program grant to Dee supported the study. Dee is an assistant professor of Earth, environmental and planetary sciences. Emanuel is the Cecil & Ida Green Professor of Atmospheric Science and co-director of the Lorenz Center at MIT.

Abstract released at: AGU

Source/Credit: Rice University

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Scientists observe cross-immunity against the coronavirus

 

Researchers from Charité – Universitätsmedizin Berlin, the Berlin Institute of Health at Charité (BIH) and the Max Planck Institute for Molecular Genetics (MPIMG) have shown that certain immune cells, which are found in people previously exposed to common cold coronaviruses, enhance the body’s immune response to SARS-CoV-2, both during natural infection and following vaccination. The researchers, whose work has been published in Science, also report that this ‘cross-reactive immunity’ decreases with age. This phenomenon may help to explain why older people are more susceptible to severe disease and why their vaccine-induced immunity is often weaker than that of young people.

Last year, researchers from Charité and the MPIMG made a surprising discovery. They were the first to report that individuals with no prior exposure to SARS-CoV-2 nonetheless had immunological memory cells capable of recognizing this novel virus.

The researchers concluded that these ‘T helper cells’ must have been generated to deal with mostly harmless common cold coronaviruses and that, thanks to the structural similarities between coronaviruses (in particular the characteristic spike protein found on their outer surface), these T helper cells will also attack the novel coronavirus. This ‘cross reactivity’ hypothesis has since been confirmed by a range of studies.

Protective action by cross-reacting T helper cells

Still unclear, however – and the object of intense debate – is the question of whether these immune cells affect the course of subsequent SARS-CoV-2 infections. “Our assumption at the time was that cross-reactive T helper cells have a protective effect, and that prior exposure to endemic (i.e. long-established and widely circulating) coronaviruses therefore reduces the severity of COVID-19 symptoms,” says the study’s (and the previous study’s) first author, Dr. Lucie Loyal, a researcher based at both the Si-M (‘Der Simulierte Mensch – literally ‘The Simulated Human’, a joint research space of Charité and Technische Universität Berlin) and the BIH Center for Regenerative Therapies (BCRT).

She adds: “However, the opposite could have been true. With some viruses, a second infection involving a similar strain can lead to a misdirected immune response and a negative impact on clinical course.” In the current study, the Berlin-based research team presents evidence to support their previous assumptions regarding the existence of a protective effect. According to their data, cross-reactive immunity could be one of several reasons for the variability in disease severity seen with COVID-19 but might also explain differences in vaccine efficacy seen in different age groups.

A universal memory for coronaviruses

For the current study, the researchers recruited individuals with no prior exposure to SARS-CoV-2, testing them at regular intervals to establish whether they had contracted the infection. Out of a total of nearly 800 participants who were recruited from mid-2020 onwards, 17 persons tested positive. The researchers studied the affected individuals’ immune systems in detail. Their analyses showed that the immune response against SARS-CoV-2 also included the mobilization of T helper cells which had been generated in response to endemic common cold viruses.

The researchers also showed that the quality of the immune response against SARS-CoV-2 was linked to the quantity of cross-reactive cells which had been present in the body prior to infection. These cells were particularly effective at recognizing a certain area of the spike protein. In both the endemic viruses and the new coronavirus, this site was characterized by sequence similarities which were particularly well ‘preserved’.

“During infections with the more harmless coronaviruses, the immune system builds up a kind of protective ‘universal coronavirus’ memory,” explains the study’s corresponding author, Dr. Claudia Giesecke-Thiel, Head of the Flow Cytometry Service Group at the MPIMG. “Once exposed to SARS-CoV-2, these memory cells are reactivated and kick-start the response against the new pathogen. This could help accelerate the initial immune response to SARS-CoV-2 and limit viral propagation during the early stages of the infection and is therefore likely to have a positive effect on the course of the disease.”

Taking a more cautionary tone, the researcher adds: “This does not mean that prior exposure to common cold viruses will definitely protect an individual against SARS-CoV-2, nor does it change the course of the pandemic as of now because these underlying mechanisms have been operating all along. It in no way diminishes the importance of getting vaccinated. Our study provides one of several explanations for an observation made since the beginning of the pandemic, namely that the symptoms of SARS-CoV-2 infection can vary greatly between individuals.”

Immune-boosting effect also for vaccination

The researchers’ findings furthermore confirmed that the immunity-enhancing effects of cross-reactive T cells also occur following vaccination with the BioNTech COVID-19 vaccine. Just like natural infection, the vaccine prompts the body to produce the SARS-CoV-2 spike protein (including the well-preserved section of it) and present it to the immune system.

An analysis of the immune responses of 31 healthy individuals before and after vaccination revealed that, while the activation of normal T helper cells took place gradually over the course of two weeks, the activation of cross-reactive T helper cells was extremely rapid, taking place within one week of vaccination. Naturally, this also had a positive effect on the generation of antibodies. Even after the first dose of the vaccine, the body was able to produce antibodies against the preserved section of the spike protein at a rate normally only seen after booster vaccinations.

“Even following vaccination, the body is able to utilize at least some of its immunological memory – provided it has had previous exposure to endemic coronaviruses,” says co-corresponding author Prof. Dr. Andreas Thiel, a Charité researcher based at both the Si-M and the BCRT. He adds: “This might explain the surprisingly rapid and extremely strong protective effect we see after the initial dose of the COVID-19 vaccine, at least in younger individuals.”

Decline with age

In a second part of the study, the researchers analyzed T helper cells in approximately 570 healthy individuals. They were able to show that cross-reactive immunity declines in older adults. In fact, both the number of cross-reactive T cells and the strength of their binding interactions was shown to be lower in older participants than in younger participants. According to the authors, this decline in cross-reactive immunity is caused by normal, age-related changes. “Infection with an endemic coronavirus represents a benefit in younger people, helping them fight off SARS-CoV-2 or develop immunity following vaccination. Sadly, this benefit is less pronounced in older adults,” says Prof. Thiel. He adds: “It is likely that a third (or booster) dose would be able to compensate for this weaker immune response, ensuring that members of this high-risk group have adequate immunity.”

Source/Credit: Max-Planck-Gesellschaft

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