ORNL-led team designs molecule to disrupt SARS-CoV-2 infection

Oak Ridge National Laboratory led a team of scientists to design a molecule that disrupts the infection mechanism of the SARS-CoV-2 coronavirus and could be used to develop new treatments for COVID-19 and future virus outbreaks.
Video Credit: Michelle Lehman/ORNL, U.S. Dept. of Energy

A team of scientists led by the Department of Energy’s Oak Ridge National Laboratory designed a molecule that disrupts the infection mechanism of the SARS-CoV-2 coronavirus and could be used to develop new treatments for COVID-19 and other viral diseases.

The molecule targets a lesser-studied enzyme in COVID-19 research, PLpro, that helps the coronavirus multiply and hampers the host body’s immune response. The molecule, called a covalent inhibitor, is effective as an antiviral treatment because it forms a strong chemical bond with its intended protein target.

“We’re attacking the virus from a different front, which is a good strategy in infectious disease research,” said Jerry Parks, who led the project and leads the Molecular Biophysics group at ORNL.

The research, detailed in Nature Communications, turned a previously identified noncovalent inhibitor of PLpro into a covalent one with higher potency, Parks said. Using mammalian cells, the team showed that the inhibitor molecule limits replication of the original SARS-CoV-2 virus strain as well as the Delta and Omicron variants.

Extinction of steam locomotives derails assumptions about biological evolution

The Union Pacific Big Boy Steam Engine (one of the largest steam engines ever built and still functioning) visited Lawrence on Sept. 2, 2021.
Photo Credit: Bruce Lieberman

When the Kinks’ Ray Davies penned the tune “Last of the Steam-Powered Trains,” the vanishing locomotives stood as nostalgic symbols of a simpler English life. But for a paleontologist at the University of Kansas, the replacement of steam-powered trains with diesel and electric engines, as well as cars and trucks, might be a model of how some species in the fossil record died out.

Bruce Lieberman, professor of ecology & evolutionary biology and senior curator of invertebrate paleontology at the KU Biodiversity Institute & Natural History Museum, sought to use steam-engine history to test the merits of “competitive exclusion,” a long-held idea in paleontology that species can drive other species to extinction through competition.

Working with former KU postdoctoral researcher Luke Strotz, now of Northwest University in Xi’an, China, Lieberman found the fossil record largely lacks the detailed data verifying competitive exclusion found in the history of steam engines: “It's really hard to actually see any evidence that competition does play a big role in evolution,” Lieberman said.

Their findings have just been published in the paper “The end of the line: competitive exclusion and the extinction of historical entities2” in the peer-reviewed journal Royal Society Open Science.

Tur­bu­lence: Decades-old the­ory gets a major remake

Ivana Stiperski and the students from the Field Course in Alpine Meteorology setting up the instruments at the “Hochhäuser” i-Box station in the Inn Valley.
Photo Credit: Tobias Posch

Turbulence plays an essential role in weather and climate, and correctly representing its effects in numerical models is crucial for accurate weather forecasts and climate projections. However, the theory describing the effect of turbulence has not changed since its conception in 1950s, despite the fact that it is not representative for the majority of the Earth’s land surface, especially over mountains and polar regions. The Innsbruck meteorologist Ivana Stiperski has now extended the turbulence theory to complex atmospheric conditions. The researcher thus paves the way for the first generalized turbulence theory over complex terrain.

Turbulence is the most important exchange mechanism between the Earth's surface and the overlying atmosphere. However, this mechanism remains one of the last great puzzles of classical physics and mathematics. Ivana Stiperski, head of the research group "Atmospheric Turbulence" at the Department of Atmospheric and Cryospheric Sciences at the University of Innsbruck, has dedicated her work to the study of turbulence over mountains, and since 2020 her team is working on the topic within the framework of an ERC Consolidator Grant. "Turbulence affects phenomena as diverse as climate, storm systems, air pollution and glacier melt. Accurate weather forecasts and climate predictions therefore require a precise description of turbulence, and over the complex terrain of mountainous regions this is particularly difficult as very little is known about how complex terrain modifies turbulence, and no major advance has happened over the past 70 years", Stiperski explains. Until now, the understanding of atmospheric turbulence and how it is included in weather and climate models has been based on the so-called similarity theory, more specifically the "Monin-Obukhov similarity theory " first postulated in 1954. This decades-old theory of turbulence, however, assumes that the Earth’s surface is flat and horizontally homogeneous (i.e., has uniform characteristics in the horizontal, such as for example infinite grasslands or corn fields), and therefore it is not representative for the majority of the Earth’s land surface. This incorrect representation of turbulence adds uncertainty to weather prediction and climate projections.

Wild animals stop the spread of socially transmitted misinformation

For wild animals, false alarms are the most widespread form of misinformation.
Photo Credit: Kaylee Rose Fahimipour

Despite the benefits of learning about the world through social ties, social connections also provide a conduit for misinformation that impedes effective decision-making.

For wild animals, false alarms are the most widespread form of misinformation. For example, when an individual animal in a group makes the decision to produce an alarm signal or initiate an escape maneuver in the absence of a real threat. This initial action produces sensory stimuli that can be perceived by others in the group as an indication of danger, resulting in a cascade of erroneous escape responses that can spread contagiously.

Behavioral and neurophysiological studies suggest that relatively simple behavioral strategies control decision-making in many of these settings. Yet, it is unknown whether these strategies somehow account for the possibility of exposure to misinformation.

How whale shark rhodopsin evolved to see, in the deep blue sea!

Whale shark
Photo Credit: Mitsumasa Koyanagi, OMU

A new study reveals that the photoreceptor rhodopsin of whale sharks (Rhincodon typus), pictured here, evolved to improve sight for the low-light low-temperature deep-sea environment in a unique way.

A research group including Professors Mitsumasa Koyanagi and Akihisa Terakita of the Osaka Metropolitan University Graduate School of Science has investigated both the genetic information and structure of the photoreceptor rhodopsin, responsible for detecting dim light, of whale sharks to investigate how they can see in the dim light at extreme depths. The research group compared the whale sharks to zebra sharks, which are considered their closest relative, and brown-banded bamboo sharks, which are in the same group: the order orectolobiformes—commonly known as carpet sharks.

“This research used genetic information and molecular biological techniques to achieve stunning results—without harming whale sharks’ or their biology. Our research approach is to use these techniques to provide clues that reveal the mysteries of how these organisms live,” explained Professor Koyanagi. “The beautiful part is that it even works for species where information is limited, such as large or wild animals that are difficult to observe or follow in their natural habitat.”

Coronavirus causes chaos in infected cells’ RNA

Illustration Credit: Fusion Medical Animation

Coronavirus disease (COVID-19) hijacks parts of infected cells' vital RNA machinery, thereby blocking important functions in the cells. These damaging changes in the RNA can likely be reversed, potentially leading to new drugs against COVID-19, University of Gothenburg researchers show.

Genetic material in the body's cells consists of DNA, which serves as long-term storage of genetic information. RNA carries this encoded information to the cells for transcription and translation. These processes enable them to make proteins, which perform most intracellular tasks. The cells' RNA is modifiable to allow correct transfer of the DNA information to the proteins. In recent years, scientific understanding of the complexity and importance of these RNA modifications has grown.

Drastic impact

It has been shown that RNA modifications take place in various viruses, but exactly how the viruses affect the RNA modification processes when they infect cells is unknown. This study reports that SARS-CoV-2 infection disrupts the RNA modifications, and the extent of these RNA modification changes surprised the researchers.

One of the modifications affected by SARS-CoV-2, known as m6A (a multifaceted regulator of gene expression), is highly important for RNA’s basic functions, including transportation of data to the protein-making parts of the cell, and transcription and translation into amino acids there.

“We were surprised at the extent and drastic scale of m6A RNA modification loss in SARS-CoV-2 infection. We also found that the coronavirus variants have differing effects on m6A levels,” says Tanmoy Mondal, researcher at Sahlgrenska Academy, University of Gothenburg, who led the project.

Preserving the stars: light pollution and what you can do about it

Astrophysicist Ms Kirsten Banks explains what we can do to reverse the impact of "light glow".
Photo Credit: UNSW Sydney.

An astrophysicist from UNSW Sydney explains why it’s so important that we can all look up and see the stars. 

Astronomer Carl Sagan famously said that there were more stars in the universe than grains of sand on earth.  

It has been estimated that there are over 100 billion stars in the Milky Way galaxy. While there is a limit to how many stars we can see from earth with the naked eye, that number is dramatically reducing due to light pollution. 

“We should be able to see around 2500 stars with the naked eye on any night, and we can see about 125 of them at best in Sydney,” says astrophysicist, proud Wiradjuri woman and UNSW PhD candidate Ms. Kirsten Banks.

In fact, in a recent study published in Science, data collected by citizen scientists around the world found light pollution is increasing at a rate that is equivalent to the brightness of the sky doubling every eight years.  

This latest research continues to expose the extent to which we’re losing the darkness of our night sky. Not being able to look up and see the stars will have significant cultural impacts, but there are steps we can all be taking to reduce the effect of light pollution.

Turtle and crocodile species with unique characteristics are more likely to go extinct

A Mugger Crocodile (Crocodylus palustris). In Pakistan, this species is still illegally hunted for its skin.
Image Credit: Bishnu Sarangi

New research led by the University of Oxford has revealed that the most endangered turtle and crocodile species are those that are most unique. Their loss could have widespread impacts on the ecosystems they live in since they carry out critical processes important for many other species. The results have been published in Nature Communications.

"When it comes to the conservation of turtles and crocodiles, we are dealing with a critical scenario. Furthermore, our actions are affecting unevenly more so those species that are characterized by unique life strategies. Once they are gone, these life strategies will be gone too, with no other species being able to provide a back-up." 

Professor Rob Salguero-Gómez, Department of Biology, University of Oxford

Turtles and crocodiles are two of the world's most endangered animal groups, with approximately half of the species globally threatened (International Union for Conservation of Nature, IUCN). Greater understanding of which species are most threatened and why is urgently needed to inform conservation efforts to save them.

In a new study led by researchers at the Department of Biology, University of Oxford, an international team examined the greatest risks to wild populations of turtles and crocodiles worldwide. The results demonstrate that the most endangered turtles and crocodile species are those that have evolved unique life strategies. These species typically carry out highly specific roles within their ecosystems that are unlikely to be taken up by other species if they disappear.

Separated at last

In the new method, laser pulses of different power (green) are combined in such a way that single excitation (blue), double excitation (red) and triple excitation (yellow) can be distinguished, for example, in biological light-harvesting complexes.
Illustration Credit: Julian Lüttig / Universität Würzburg

Scientists at the Universities of Würzburg and Ottawa have solved the decades-old problem of distinguishing between single and multiple light excitations. They present their new method in the journal Nature.

The construction of the first laser in 1960 ushered in commercial applications with light that have become an integral part of our everyday lives. At the same time, this development opened up the scientific field of laser spectroscopy – a technique that is central to the analysis of materials and the study of fundamental physical phenomena.

Despite all the successes, however, research teams have struggled since the 1970s with the problem that a laser shining on a sample can excite it not just once, but several times per experiment. In this case, the measurement results of the single excitation and the multiple excitations overlap and usually cannot be separated, making it difficult to understand the material.

Climate change threatens lemurs on Madagascar

A female grey mouse lemur (Microcebus murinus) carrying an infant.
Photo Credit: Manfred Eberle

They are small, have a high reproductive output and live in the forests of Madagascar. During the 5-month rainy season, offspring are born and a fat pad is created to survive the cool dry season when food is scarce. But what happens when the rainy season becomes drier and the dry season warmer? Can mouse lemurs adapt to climate change thanks to their high reproductive output? Researchers from the German Primate Center – Leibniz Institute for Primate Research, together with colleagues from the University of Zurich, have analyzed long-term data from Madagascar and found that climate change is destabilizing mouse lemur populations and increasing their risk of extinction. The fact that climate change is leading to greater fluctuations in population density and thus increases extinction risk in a fast-paced, ecological generalist is an alarming warning signal for potential biodiversity losses in the tropics.

Effects of climate change have mostly been studied in large, long-lived species with low reproductive output. Small mammals with high reproductive rates can usually adapt well to changing environmental conditions, so they have been studied little in the context of climate change. Claudia Fichtel and Peter Kappeler from the German Primate Center – Leibniz Institute for Primate Research (DPZ) have been researching lemurs on Madagascar for many years and have thus built up a unique data set to fill this knowledge gap.