How Omicron escapes from antibodies

Image: CDC; Christine Daniloff, MIT

A new study from MIT suggests that the dozens of mutations in the spike protein of the Omicron variant help it to evade all four of the classes of antibodies that can target the SARS-CoV-2 virus that causes Covid-19.

This includes antibodies generated by vaccinated or previously infected people, as well as most of the monoclonal antibody treatments that have been developed, says Ram Sasisekharan, the Alfred H. Caspary Professor of Biological Engineering and Health Sciences and Technology (HST) at MIT.

Using a computational approach that allowed them to determine how mutated amino acids of the viral spike protein influence nearby amino acids, the researchers were able to get a multidimensional view of how the virus evades antibodies. According to Sasisekharan, the traditional approach of only examining changes in the virus’ genetic sequence reduces the complexity of the spike protein’s three-dimensional surface and doesn’t describe the multidimensional complexity of the protein surfaces that antibodies are attempting to bind to.

“It is important to get a more comprehensive picture of the many mutations seen in Omicron, especially in the context of the spike protein, given that the spike protein is vital for the virus’s function, and all the major vaccines are based on that protein,” he says. “There is a need for tools or approaches that can rapidly determine the impact of mutations in new virus variants of concern, especially for SARS-CoV-2.”

Sasisekharan is the senior author of the study, which appears this week in Cell Reports Medicine. The lead author of the paper is MIT HST graduate student Nathaniel Miller. Technical associate Thomas Clark and research scientist Rahul Raman are also authors of the paper.

Even though Omicron is able to evade most antibodies to some degree, vaccines still offer protection, Sasisekharan says.

World-record lightning “megaflashes” detected using space-based technology

Satellite image of the record lightning flash over Uruguay and Argentina on June 18, 2020, which lasted 17.102 seconds.

A researcher at Los Alamos National Laboratory has detected two world-record lightning “megaflashes.” The longest-distance flash was detected in the southern United States on April 29, 2020 and spanned more than 477 miles from Mississippi to Texas. The longest-duration lightning strike was detected over Uruguay on June 18, 2020 and lasted 17.1 seconds.

“We are now at a place where we have excellent lightning measurements, which allows us to discover surprising new aspects of its behavior,” said lead author Michael Peterson, of the Space and Remote Sensing group at Los Alamos. “Now that we have a robust record of these massive flashes, we can better understand how they occur and the impact that they have.”

These megaflashes are incredibly rare events. In order to record one from the ground, or from an aircraft or satellite in a low orbit, the sensor has to be exactly in the right place at the right time, which is very unlikely.

Scientists discover link between high blood pressure and diabetes

The long-standing enigma of why so many patients suffering with high blood pressure (known as hypertension) also have diabetes (high blood sugar) has finally been cracked by an international team led by the universities of Bristol, UK, and Auckland, New Zealand.

The important new discovery has shown that a small protein cell glucagon-like peptide-1 (GLP-1) couples the body’s control of blood sugar and blood pressure.

Professor Julian Paton, a senior author, and Director of Manaaki Mãnawa - The Centre for Heart Research at the University of Auckland, said: "We've known for a long time that hypertension and diabetes are inextricably linked and have finally discovered the reason, which will now inform new treatment strategies."

The research, published online ahead of print in Circulation Research today, involved contributions from collaborating scientists in Brazil, Germany, Lithuania, and Serbia, as well as the UK and New Zealand.

LP-1 is released from the wall of the gut after eating and acts to stimulate insulin from the pancreas to control blood sugar levels. This was known but what has now been unearthed is that GLP-1 also stimulates a small sensory organ called the carotid body located in the neck.

The University of Bristol group used an unbiased, high-throughput genomics technique called RNA sequencing to read all the messages of the expressed genes in the carotid body in rats with and without high blood pressure. This led to the finding that the receptor that senses GLP-1 is located in the carotid body, but less so in hypertensive rats.

Hepatitis E virus defies alcoholic hand disinfectants

The hepatitis E virus (HEV) can cause serious inflammation of the liver and is the most common cause of acute virus-mediated hepatitis worldwide. The infection can be prevented by suitable hygiene measures. Scientists from TWINCORE, Center for Experimental and Clinical Infection Research, the Hannover Medical School (MHH) and the Ruhr University Bochum (RUB) have examined the effectiveness of various common hand disinfectants against HEV together with partners from industry. They could show that most formulations do not completely inactivate the virus. They publish these results in the Journal of Hepatology.

Pork infection

In Germany and Europe, HEV has its natural reservoir in pigs. The infection can pass from the animals to humans, one speaks here of a zoonosis. This is often done by meat products that are not fully heated or raw, such as Mett. In tropical regions of the world, contaminated water leads to infections with sometimes larger outbreaks. "Some of these infections may have been prevented by the right hygiene measures," says Dr. Patrick Behrendt, doctor in the clinic for gastroenterology, hepatology and endocrinology at MHH and head of the junior research group "Translational Virology" at TWINCORE. This includes correct hygienic hand disinfection, especially in everyday clinical practice in dealing with hepatitis E patients and infected animals.

Together with the team of Prof. Dr. Eike Steinmann, head of the Department of Molecular and Medical Virology at RUB, examined Behrendt whether common hand disinfectants can render the virus harmless. "We tested the effects of the alcohols ethanol and propanol, both individually and in the mixing ratios recommended by the WHO, as well as commercial hand disinfectants," says Steinmann. “However, only one product that contained another component was effective."

New study finds some flowers unchanged for 100 million years

Flower preserved in amber
Credit: The Open University

An international research team has discovered 100-million-year-old fossil flowers preserved in amber, showing that some flowers found living today in South Africa have remained unchanged since the time of the dinosaurs.

The flowers, discovered by experts from The Open University, Qingdao University, and others, are nearly identical to those of modern Phylica species, which are part of the Cape Fynbos flora that is exposed to frequent wildfires.

The fossils were found alongside long-extinct burned plants, pointing to wildfires being an important aspect of early flower evolution.

The sudden appearance of flowering plants as fossils in middle Cretaceous time was described by Charles Darwin as an “abominable mystery” and usually, flower fossils are rare, not well preserved and come from an extinct group of species.

However, this study, published in Nature Plants, found an exception – the research team found flowers, trapped in fossil ambers, that are almost identical to plants living today near Cape Town, South Africa.

Robert A. Spicer, Emeritus Professor at The Open University, described the historical context of the flowers and what the findings can tell us about the plant evolution:

“These exquisitely preserved flowers, fruits, leaves and pollen from 100 million years ago provide a snapshot of an important time in the evolution of flowering plants, showing that early flowers were not primitive as many people suppose, but were already superbly adapted to survive the frequent wildfires that ravaged the warm ‘greenhouse’ world of the Cretaceous.

Number of Earth’s tree species estimated to be 14% higher than currently known, with some 9,200 species yet to be discovered

Coniferous mixed forest, Val Saisera, Italian Julian Alps, Italy.
Image credit: Dario Di Gallo, Regional Forest Service of Friuli Venezia Giulia, Italy

A new study involving more than 100 scientists from across the globe and the largest forest database yet assembled estimates that there are about 73,000 tree species on Earth, including about 9,200 species yet to be discovered.

The global estimate is about 14% higher than the current number of known tree species. Most of the undiscovered species are likely to be rare, with very low populations and limited spatial distribution, the study shows.

That makes the undiscovered species especially vulnerable to human-caused disruptions such as deforestation and climate change, according to the study authors, who say the new findings will help prioritize forest conservation efforts.

“These results highlight the vulnerability of global forest biodiversity to anthropogenic changes, particularly land use and climate, because the survival of rare taxa is disproportionately threatened by these pressures,” said University of Michigan forest ecologist Peter Reich, one of two senior authors of a paper scheduled for publication Jan. 31 in Proceedings of the National Academy of Sciences.

Low Volcanic Temperature Ushered in Global Cooling and the Thriving of Dinosaurs

Researchers in Japan, Sweden, and the US have unearthed evidence that low volcanic temperatures led to the fourth mass extinction, enabling dinosaurs to flourish during the Jurassic period.

Large volcanic eruptions create climatic fluctuations, ushering in evolutionary changes. Yet it is the volcanic temperature of the eruption that determines whether the climate cools or warms.

Since the emergence of early animals, five mass extinctions have taken place. The fourth mass extinction occurred at the end of the Triassic Period - roughly 201 million years ago. This mass extinction saw many marine and land animals go extinct, especially large-body, crocodilian-line reptiles known as pseudosuchia. Approximately 60-70% of animal species disappeared. As a result, small bodied dinosaurs were able to grow and prosper.

Scientists think the fourth mass extinction was triggered by the eruptions in the Central Atlantic Magmatic Province - one of the largest regions of volcanic rock. But the correlation between the eruption and mass extinction has not yet been clarified.

Understanding coral reef connectivity important to focus conservation efforts

Coral reef in Fiji.
Photo credit: Joao Paulo Krajewski

Local fisheries and their associated biodiversity benefit from the transfer of larvae between reefs, with some benefitting more than others, prompting recommendations to protect larval connectivity among coral reefs. A team of international researchers, led in part by the Hawaiʻi Institute of Marine Biology (HIMB) within the University of Hawaiʻi at Mānoa, emphasize that coral reef connectivity is crucial to supporting the benefits coral reefs provide. Their study is published in Science.

Researchers identified significant gaps and opportunities for positioning marine protected areas (MPAs) and other effective area-based conservation measures (OECMs) strategically on coral reefs.

The findings indicate fundamental differences in the relative importance of coral reefs’ connectivity characteristics and their role in maintaining biodiversity and supporting local fisheries. That’s according to the study’s lead author, Luisa Fontoura, a postdoctoral researcher from Macquarie University’s School of Natural Sciences in Australia and recently-graduated doctoral student and UH Mānoa faculty Elizabeth Madin.

2D materials could be used to simulate brain synapses in computers

Credit: KTH Royal Institute of Technology

With the introduction of a new component material, researchers at KTH take another step toward computers that mimic the human brain.

Researchers from KTH Royal Institute of Technology in Stockholm and from Stanford University have fabricated a material for components that enable the commercial viability of computers which mimic the human brain.

Electrochemical random access (ECRAM) memory components made with 2D titanium carbide showed outstanding potential for complementing classical transistor technology, and contributing toward commercialization of powerful computers that are modeled after the brain’s neural network. Such neuromorphic computers can be thousands of times more energy efficient than today’s computers.

These advances in computing are possible because of some fundamental differences from the classic computing architecture in use today, and the ECRAM, a component that acts as a sort of synaptic cell in an artificial neural network, says KTH Associate Professor Max Hamedi.

“Instead of transistors that are either on or off, and the need for information to be carried back and forth between the processor and memory—these new computers rely on components that can have multiple states, and perform in-memory computation,” Hamedi says.

Quantum leap on film

Jumping electrons: Using a combination of scanning tunneling microscopy and laser spectroscopy with attosecond pulses, Max Planck researchers have filmed electrons in PTCDA molecules arranged next to each other. The position of two molecules are made visible by graphical models. One electron at a time switches back and forth between a higher-energy state and a lower-energy state. The blue coloring stands for a low electron density and the red for a high one. The electron is initially in the energetically higher state. This can be recognized by the relatively high proportion with low electron density (blue). Excited by a laser, it then jumps back and forth between the higher-energy and lower-energy states. The lower-energy state can be recognized by the generally more even distribution of electron density (green, yellow, and orange). After about 1.4 femtoseconds (three images), the electron once again reaches the higher-energy state.
Credit:  Manish Garg / MPI for Solid State Research

An ultra-fast microscope combines atomic spatial and temporal resolution and thus enables unprecedented insights into the dynamics of electrons in molecules

In order to better understand (and possibly control) fast chemical reactions, it is necessary to study the behavior of electrons as precisely as possible – in both space and time. However, up to now, microscopy methods have delivered only either spatially or temporally sharp images. By cleverly combining established techniques of tunneling microscopy and laser spectroscopy, a team led by Klaus Kern, Director at the Max Planck Institute for Solid State Research in Stuttgart, has now overcome these obstacles. Using their atomic quantum microscope, they can make the movement of electrons in individual molecules visible.

It is essential not only for understanding biological processes (e.g. plant photosynthesis) to map the electron dynamics in molecules but also for many technical applications such as the development of solar cells or new types of electronic components. Until now, imaging methods have sometimes delivered images that are difficult to reproduce – or even contradictory. This is because they cannot map the fast electrons directly but rather must resort to techniques that can only reconstruct the behavior of the electrons.