Blocking enzyme could hold the key to preventing, treating severe COVID-19

Amal Amer

The sickest COVID-19 patients develop acute respiratory distress syndrome resulting from the combination of high levels of pro-inflammatory proteins called cytokines, fluid accumulation in air sacs that seeps into lung tissue and blood clots, or thrombosis, caused by damage to cells lining vessel walls. In a series of experiments in infected mice, the research team found that inhibiting caspase 11 reduced the intensity of multiple effects.

Blocking an immune response-related enzyme holds promise in preventing or treating severe COVID-19 symptoms by reducing inflammation, tissue injury and blood clots in the lungs, new research in mice suggests.

Scientists who have long studied this molecule’s functions in bacterial infections traced the development of extensive lung damage in infected mice to heightened levels of the enzyme triggered by the invading SARS-CoV-2 virus.

Versions of this enzyme exist and have similar functions in both mice and humans – they’re called caspase 11 and caspase 4, respectively. After finding that the molecule is an attractive therapeutic target, researchers are exploring compounds that could safely and effectively block its activation.

“The whole idea is if this molecule is not there, the mouse will do better, which means if you target this molecule, then humans should do better,” said co-senior study author Amal Amer, professor of microbial infection and immunity in The Ohio State University College of Medicine.

The research was published online recently in Proceedings of the National Academy of Sciences.

Cuttlefish: Chameleons of the sea

European cuttlefish
Source: City, University of London

Study suggests that European cuttlefish use a more complex strategy than previously thought to camouflage themselves within underwater surroundings.

A new study by City, University of London and others suggests that the European cuttlefish (sepia officinalis) may combine, as necessary, two distinct neural systems that process specific visual features from its local environment, and visual cues relating to its overall background environment to create the body patterns it uses to camouflage itself on the sea floor.

This is in contrast to previous research suggesting that the cognitive (brain) processes involved are much simpler, in that the cuttlefish adopts one of only three major types of body patterns to visually merge with its background. However, that does not explain why the animal possesses about 30 different body pattern components it could use to achieve this.

The study explored whether the cuttlefish uses a cognitive process that is triggered by specific, visual features in its environment and which warrants the number of body pattern components it possesses.

Like their cephalopod relatives the octopus and the squid, cuttlefish are masters at blending in with their environments, which is largely attributable to the way their brains are able to control how pigments in special cells called chromatophores on their skin are displayed across their bodies.

Physicists Announce First Results from Daya Bay’s Final Dataset

Photomultiplier tubes, designed to pick up faint light signals from particle interactions, line the inside of a detector for the Daya Bay Reactor Neutrino experiment.
Credit: Roy Kaltschmidt/Berkeley Lab

Over nearly nine years, the Daya Bay Reactor Neutrino Experiment captured an unprecedented five and a half million interactions from subatomic particles called neutrinos. Now, the international team of physicists of the Daya Bay collaboration has reported the first result from the experiment’s full dataset—the most precise measurement yet of theta13, a key parameter for understanding how neutrinos change their “flavor.” The result, announced today at the Neutrino 2022 conference in Seoul, South Korea, will help physicists explore some of the biggest mysteries surrounding the nature of matter and the universe.

Neutrinos are subatomic particles that are both famously elusive and tremendously abundant. They endlessly bombard every inch of Earth’s surface at nearly the speed of light, but rarely interact with matter. They can travel through a lightyear’s worth of lead without ever disturbing a single atom.

One of the defining characteristics of these ghost-like particles is their ability to oscillate between three distinct “flavors”: muon neutrino, tau neutrino, and electron neutrino. The Daya Bay Reactor Neutrino Experiment was designed to investigate the properties that dictate the probability of those oscillations, or what are known as mixing angles and mass splittings.

Only one of the three mixing angles remained unknown at the time Daya Bay was designed in 2007: theta13. So, Daya Bay was built to measure theta13* with higher sensitivity than any other experiment.

Research Confirms Effectiveness of Oil Dispersants

Marine oil spills are one of the most direct, and harmful, examples of the toll that the extraction of fossil fuels can take on the environment. One of the few tools to mitigate that damage is chemical dispersants that break down oil in the water. However, scientists do not fully understand how well they work. A new study led by Bigelow Laboratory validated their efficacy under real-world conditions in order to better prepare for the next disaster.

“We don’t want to just apply chemicals to the ocean without fully understanding what happens,” said Senior Research Scientist Christoph Aeppli, lead author on the study. “We want to know that dispersants are as effective as they can be to help ecosystem recovery.”

Oil spills impact life at every level of the ocean food web, and emergency response efforts must move quickly to minimize the damage after they occur. Crews could wait until oil washes ashore to clean it up, but its toxic compounds can persist for decades and damage sensitive ecosystems.

Chemical dispersants can be used to address spills at sea by breaking oil into small droplets that get mixed into the water and diluted rapidly. When dispersants are applied, oil typically persists in the water column for much less time than they would on shore even though oil droplets temporarily increase the toxicity in the water. However, adding additional chemicals to the environment has been controversial.

History of Lake Cahuilla

Today, the Salton Sea occupies a fraction of the area once covered by Lake Cahuilla.
Photo: Susanne Clara Bard.

Today, the Salton Sea is an eerie place. Its mirror-like surface belies the toxic stew within. Fish skeletons line its shores and the ruins of a once thriving vacation playground is a reminder of better days.

But long before agricultural runoff bespoiled the Salton Sea, the lakebed it now occupies was home to a much larger body of water known as Lake Cahuilla. The lake was six times the size of the Salton Sea and once covered much of Mexicali, Imperial and Coachella valleys.

“It was a freshwater lake that was about 100 meters deep in its deepest part,” said San Diego State University emeritus professor of geology Tom Rockwell. “It extended from up near Palm Springs southward into Mexico, so it was a very extensive lake.”

Lake Cahuilla went through many cycles of filling and drying out over thousands of years. A new study by Rockwell and his colleagues used radiocarbon dating to determine the timing of the last seven periods of filling. The research sheds light on both the history of human occupation in the area and its seismic past.

Shark antibodies may have the teeth to stop COVID-19

Nurse sharks have a surprisingly effective adaptive immune system that may help shape novel COVID-19 therapies

Fossil evidence suggests sharks first existed 420 million years ago, predating humanity, Mount Everest and even trees. Over the course of time, sharks and other fish with cartilage skeletons developed what is now believed to be the oldest adaptive immune system in the animal kingdom.

According to a recent study published in Nature Communications, these ancient predators and their prehistoric immune systems may also be key to developing effective COVID-19 treatments.

“The shark antibodies neutralized the proteins in ways we weren’t expecting.” — 

Surajit Banerjee, Cornell University/NE-CAT

Professors Aaron LeBeau of the University of Wisconsin and Hideki Aihara of the University of Minnesota used the Advanced Photon Source (APS), a U.S. Department of Energy (DOE) Office of Science user facility at DOE’s Argonne National Laboratory, to look at nurse shark antibodies. With exquisite resolution, the APS’s extremely bright X-ray beams showed that variable new antigen receptors (VNARs), the smallest unit of a shark antibody, can stop SARS-CoV-2, the virus that causes COVID-19 and its variants.

Astronomers identify 116,000 new variable stars

An ASAS-SN telescope helps astronomers discover new stars.
Photo: ASAS-SN

Ohio State University astronomers have identified about 116,000 new variable stars, according to a new paper.

These heavenly bodies were found by The All-Sky Automated Survey for Supernovae (ASAS-SN), a network of 20 telescopes around the world which can observe the entire sky about 50,000 times deeper than the human eye. Researchers from Ohio State have operated the project for nearly a decade.

Now in a paper published on arXiv, an open-access preprint server, researchers describe how they used machine learning techniques to identify and classify variable stars — celestial objects whose brightness waxes and wanes over time, especially if observed from our perspective on Earth.

The changes these stars undergo can reveal important information about their mass, radius, temperature and even their composition. In fact, even our sun is considered a variable star. Surveys like ASAS-SN are an especially important tool for finding systems that can reveal the complexities of stellar processes, said Collin Christy, the lead author of the paper and an ASAS-SN analyst at Ohio State.

“Variable stars are sort of like a stellar laboratory,” he said. “They’re really neat places in the universe where we can study and learn more about how stars actually work and the little intricacies that they all have.”

Great white sharks may have contributed to megalodon extinction

Tooth size comparison between the extinct Early Pliocene Otodus megalodon tooth and a modern great white shark. 
Credit: MPI for Evolutionary Anthropology

The diet of fossil extinct animals can hold clues to their lifestyle, behavior, evolution and ultimately extinction. However, studying an animal’s diet after millions of years is difficult due to the poor preservation of chemical dietary indicators in organic material on these timescales. An international team of scientists led by the Max Planck Institute for Evolutionary Anthropology in Leipzig, Germany, applied a new method to investigate the diet of the largest shark to have ever existed, the iconic Otodus megalodon. This new method investigates the zinc isotope composition of the highly mineralized part of teeth and proves to be particularly helpful to decipher the diet of these extinct animals.

Megatooth sharks like Otodus megalodon, more commonly known as megalodon, lived between 23 and 3.6 million years ago in oceans around the globe and possibly reached as large as 20 meters in length. For comparison, the largest great white sharks today reach a total length of only six meters. Many factors have been discussed to explain the gigantism and extinction of megalodon, with its diet and dietary competition often being thought of as key factors.

Asteroid Institute Uses Revolutionary Cloud-Based Astrodynamics Platform to Discover and Track Asteroids

The Asteroid Institute, a program of B612 Foundation, today announced it is using a groundbreaking computational technique running on its Asteroid Discovery Analysis and Mapping (ADAM) cloud-based astrodynamics platform to discover and track asteroids. The Minor Planet Center has confirmed and added the first 104 of these newly discovered asteroids to its registry, thus opening the door for Asteroid Institute-supported researchers to submit thousands of additional new discoveries.

The ADAM platform is an open-source computational system that runs astrodynamics algorithms using the scalable computational and storage capabilities in Google Compute Engine, Google Cloud Storage, and Google Kubernetes Engine. The novel algorithm used to discover these new asteroids is called THOR (Tracklet-less Heliocentric Orbit Recovery), and it links points of light in different sky images that are consistent with asteroid orbits. Unlike current state-of-the-art algorithms, THOR does not require the telescope to observe the sky in a particular pattern for asteroids to be discoverable. Researchers can now begin systematic explorations of large datasets that were previously not usable for discovering asteroids. THOR recognizes asteroids, and most importantly, calculates their orbits well enough to be recognized by the Minor Planet Center as tracked asteroids.

For its initial demonstration, Joachim Moeyens, THOR co-creator and the Asteroid Institute Graduate Student Fellow at the University of Washington, searched a 30-day window of images from the NOIRLab Source Catalog (NSC), a collection of nearly 68 billion observations taken by the National Optical Astronomy Observatory telescopes between 2012 and 2019. From this Moeyens submitted a small, initial subset of discoveries to the Minor Planet Center for official recognition and validation. Now that the computational discovery technique has been validated, thousands of new discoveries from NSC and other datasets are expected to follow.

The grass may be greener on old mine sites

Researchers at WVU’s Davis College of Agriculture, Natural Resources and Design will use $817,000 in grant funding from the National Institute of Food and Agriculture to study the resiliency of miscanthus, a bioenergy crop that grows well on reclaimed mine land.
Credit: photo/Jenni Kane

West Virginia University researchers are working to better understand how climate change may make an impact on a bioenergy crop that flourishes on reclaimed mining lands.

Previously living materials, including perennial grasses like Miscanthus x giganteus, produce bioenergy. Ember Morrissey, associate professor of environmental microbiology in the Davis College of Agriculture, Natural Resources and Design, is examining the symbiotic relationship between microbes and this type of tall grass to prepare for climate change and decreasing fossil fuel usage.

The research group includes Jeff Skousen, professor of soil science, Louis McDonald, professor of environmental soil chemistry and soil fertility, and Jenni Kane, a doctoral student in plant and soil sciences.

Skousen, an expert in soil reclamation, helped Morrissey establish miscanthus stands on marginal soil for research over the next five years funded with a more than $817,000 grant from the National Institute of Food and Agriculture.

The goal is to determine if fertilization will weaken the relationship between the plant and its microbes and then determine the best way to manage the plant in unpredictable climates.

Making colors out of gold and DNA

In this experiment, the gel is being activated by a red LED before the researchers measure the light it transmits.
Photo: Joonas Ryssy

Folk belief says there’s a pot of gold at the end of the rainbow, but a new technology is turning that idea on its head – using particles of gold to make colors. With further work, the method developed at Aalto University could herald a new display technology.

The technique uses gold nanocylinders suspended in a gel. The gel only transmits certain colors when lit by polarized light, and the color depends on the orientation of the gold nanocylinders. In a clever twist, a collaboration led by Anton Kuzyk’s and Juho Pokki’s research groups used DNA molecules to control the orientation of gold nanocylinders in the gel.

‘DNA isn’t just an information carrier – it can also be a building block. We designed the DNA molecules to have a certain melting temperature, so we could basically program the material,’ says Aalto doctoral candidate Joonas Ryssy, the study’s lead author. When the gel heats past the melting temperature, the DNA molecules loosen their grip and the gold nanocylinders change orientation. When the temperature drops, they tighten up again, and the nanoparticles go back to their original position.

Palms at the Poles: Fossil Plants Reveal Lush Southern Hemisphere Forests in Ancient Hothouse Climate

For decades, paleobotanist David Greenwood has collected fossil plants from Australia – some so well preserved it’s hard to believe they’re millions of years old. These fossils hold details about the ancient world in which they thrived, and Greenwood and a team of researchers including climate modeler and research David Hutchinson, from the University of New South Wales, and UConn Department of Geosciences paleobotanist Tammo Reichgelt, have begun the process of piecing together the evidence to see what more they could learn from the collection. Their findings are published in Paleoceanography & Paleoclimatology.

The fossils date back 55 to 40 million years ago, during the Eocene epoch. At that time, the world was much warmer and wetter, and these hothouse conditions meant there were palms at the North and South Pole and predominantly arid landmasses like Australia were lush and green. Reichgelt and co-authors looked for evidence of differences in precipitation and plant productivity between then and now.

Since different plants thrive under specific conditions, plant fossils can indicate what kinds of environments those plants lived in.

By focusing on the morphology and taxonomic features of 12 different floras, the researchers developed a more detailed view of what the climate and productivity was like in the ancient hothouse world of the Eocene epoch.

Reichgelt explains the morphological method relies on the fact that the leaves of angiosperms — flowering plants — in general have a strategy for responding to climate.

New Artificial Enzyme Breaks Down Tough, Woody Lignin

Researchers Xiao Zhang (L) and Chun-long Chen (R) examine the products of lignin digestion by their novel biomimetic peptoid catalyst.
Photo by Andrea Starr | Pacific Northwest National Laboratory

A new artificial enzyme has shown it can chew through lignin, the tough polymer that helps woody plants hold their shape. Lignin also stores tremendous potential for renewable energy and materials.

Reporting in the journal Nature Communications, a team of researchers from Washington State University and the Department of Energy’s Pacific Northwest National Laboratory showed that their artificial enzyme succeeded in digesting lignin, which has stubbornly resisted previous attempts to develop it into an economically useful energy source.

Lignin, which is the second most abundant renewable carbon source on Earth, mostly goes to waste as a fuel source. When wood is burned for cooking, lignin byproducts help impart that smoky flavor to foods. But burning releases all that carbon to the atmosphere instead of capturing it for other uses.

“Our bio-mimicking enzyme showed promise in degrading real lignin, which is considered to be a breakthrough,” said Xiao Zhang, a corresponding author on the paper and associate professor in WSU’s Gene and Linda Voiland School of Chemical Engineering and Bioengineering. Zhang also holds a joint appointment at PNNL. “We think there is an opportunity to develop a new class of catalysts and to really address the limitations of biological and chemical catalysts.”

Drought, megafires, and flood – citizen scientists reveal impact on river water quality

Upper Macleay River
Source: Southern Cross University

In a few short years Australia’s east coast has experienced drought, blazing bushfires and unprecedented floods, driving discussion about the impacts of climate change. What is less discussed, and also less well understood, are the implications of such extremes for the quality of water in our rivers.

Researchers from Southern Cross University led a unique study published in Water Research with collaboration from dedicated team of citizen scientists to help monitor how these climate extremes impact river water quality.

Professor Scott Johnston, a Landscape Hydrogeochemist from the University’s Faculty of Science and Engineering has overseen this water quality monitoring project in the Macleay River since 2016. The Macleay is a large coastal catchment in Northern New South Wales that stretches across the Great Dividing Range from the tablelands near Armidale to the coast at Kempsey and South West Rocks.

“We collaborated with a trained group of local citizen scientist volunteers who were able to regularly collect river water samples, capturing what took place at a level of detail that is really quite unique,” he said. ‘’Without their hard work on the ground, this study would not have happened and it is a great example of a university and community working closely together to help understand a locally relevant issue.’

Alzheimer’s disease causes cells to overheat and ‘fry like eggs’

Mammalian cell stained with fluorescence polymeric thermometers and falsely-colored based on temperature gradients. 
Credit: Chyi Wei Chung

The researchers, from the University of Cambridge, used sensors small and sensitive enough to detect temperature changes inside individual cells, and found that as amyloid-beta misfolds and clumps together, it causes cells to overheat.

In an experiment using human cell lines, the researchers found the heat released by amyloid-beta aggregation could potentially cause other, healthy amyloid-beta to aggregate, causing more and more aggregates to form.

In the same series of experiments, the researchers also showed that amyloid-beta aggregation can be stopped, and the cell temperature lowered, with the addition of a drug compound. The experiments also suggest that the compound has potential as a therapeutic for Alzheimer’s disease, although extensive tests and clinical trials would first be required.

The researchers say their assay could be used as a diagnostic tool for Alzheimer’s disease, or to screen potential drug candidates. The results are reported in the Journal of the American Chemical Society.