COVID-19 virus spike protein flexibility improved by human cell's own modifications

University of Illinois researchers created atomic-level models of the spike protein that plays a key role in COVID-19 infection and immunity, revealing how the protein bends and moves as it seeks to engage receptors. 
Credit: Tianle Chen

When the coronavirus causing COVID-19 infects human cells, the cell’s protein-processing machinery makes modifications to the spike protein that render it more flexible and mobile, which could increase its ability to infect other cells and to evade antibodies, a new study from the University of Illinois Urbana-Champaign found.

The researchers created an atomic-level computational model of the spike protein and ran multiple simulations to examine the protein’s dynamics and how the cell’s modifications affected those dynamics. This is the first study to present such a detailed picture of the protein that plays a key role in COVID-19 infection and immunity, the researchers said.

Biochemistry professor Emad Tajkhorshid, postdoctoral researcher Karan Kapoor and graduate student Tianle Chen published their findings in the journal PNAS.

“The dynamics of a spike are very important – how much it moves and how flexible it is to search for and bind to receptors on the host cell,” said Tajkhorshid, who also is a member of the Beckman Institute for Advanced Science and Technology. “In order to have a realistic representation, you have to look at the protein at the atomic level. We hope that the results of our simulations can be used for developing new treatments. Instead of using one static structure of the protein to search for drug-binding pockets, we want to reproduce its movements and use all of the relevant shapes it adopts to provide a more complete platform for screening drug candidates instead of just one structure.”

Why natural gas is not a bridge technology

The expansion of the natural gas infrastructure poses a risk to the energy transition, since natural gas is not a bridge technology towards a 100 percent renewable energy system within the meaning of the Paris climate agreement. This is the result of a study by an interdisciplinary German research team. July 2022 in the journal Nature Energy. The researchers examine the natural gas question from five perspectives and provide the gas with a similarly poor climate balance sheet as coal or oil. They recommend politics and science to revise the current assumptions about natural gas.

The study was led by Prof. Dr. Claudia Kemfert from the German Institute for Economic Research (DIW) and the Leuphana University of Lüneburg in collaboration with Franziska Hoffart from the Ruhr University Bochum, Fabian Präger from the Technical University of Berlin and Isabell Braunger and Hanna Brauers from the European University Flensburg.

Energy crisis is only one side of the problem

In the wake of the Russian war of aggression, the government in Germany faces the challenge of reducing Russia's energy dependency and continuing to ensure an affordable and secure energy supply that is in line with climate targets. Efforts are currently underway to balance Russian natural gas, the delivery of which is throttled and unsafe, by building new gas trading relationships and new infrastructure. Claudia Kemfert, head of the study, explains: “Fossil natural gas is neither clean nor safe. The too long adherence to fossil natural gas has led Germany into an energy crisis, from which now only decisive action for consistent decarbonization can lead to a full supply of renewable energies”.

Astronomers Identified the Nature of Instability in the Accretion Disk of the Galaxy NGC 4258

The galaxy NGC 4258 is 22.8 million light-years from Earth.
Photo Credit: NASA

An international group of researchers, including Andrey Sobolev, a leading researcher at the Kourovka Astronomical Observatory of the Ural Federal University, for the first time examined the details of the distribution of maser emissions in the accretion It was found that in this disk acts magneto-rotational instability. Scientists reported the discovery in the journal Nature Astronomy.

"The discovery of a disk around this galaxy was reported by Miyoshi and Greenhill back in 1995 in articles in Nature and in The Astrophysical Journal. That was the first time we knew there was a disk. But now, with the RadioAstron's ultra-high angular resolution, we have been able to ascertain for the first time the details of the distribution of the maser emission spots. The regularity in their maser locations is explained by the fact that there is a magneto-rotational instability in the accretion disk," says Andrey Sobolev.

The instabilities determine the evolution of disks. We can use them to know whether the disk is stationary or whether everything in it is changing rather rapidly. In other words, the instabilities help determine the physical status or physical state of the disk: how it is formed, what happens in it, and predict whether it will change over time. Therefore, to understand the processes that occur in the accretion disk, scientists need to understand what instabilities are operating there, and the detection of the magneto-rotational instability is extremely important. At the same time, scientists are not going to put an end to the research of the unique object around the supermassive black hole. According to Sobolev, now it is the turn of theorists to explain the unique data obtained at the cosmic interferometer - the largest device created by mankind. This interferometer was created as part of the RadioAstron project, in which Russian scientists play a leading role.

Gut bacteria potential key to IBD and colon cancer prevention

Jakob Begun  ATH - Associate Professor
Mater Research Institute-UQ Faculty of Medicine
Source: University of Queensland

Researchers have isolated five strains of gut bacteria that could pave the way for new inflammatory bowel disease treatments and potentially help prevent some forms of bowel cancer.

The study by University of Queensland and Mater researchers identified gut bacterial strains that suppress inappropriate gut inflammation and debilitating inflammatory bowel disease (IBD) symptoms.

IBD is a chronic condition characterized by relapsing gut inflammation believed to be caused by an abnormal gut bacterial composition which produces an immune response in genetically susceptible people resulting in severe symptoms.

University of Queensland researcher and Inflammatory Bowel Disease Research Group Leader, Associate Professor Jake Begun, said his team isolated bacteria found in the healthy gut and identified several species that produced a range of anti-inflammatory substances.

“While the gut microbiome is made up of trillions of bacteria that have co-evolved with humans over time, our lab tests identified five strains that were able to suppress inflammation in blood and tissue samples from IBD patients,” Dr Begun said.

“Furthermore, one of these healthy gut bacterial strains produced anti-inflammatory substances that were able to reduce disease severity in a pre-clinical model by inhibiting one of the master molecular regulators of inflammation called NF-kB, without causing any side-effects.”

Mater Research and UQ PhD candidate Rabina Giri said the research found good bacterial strains inhibited the pro-inflammatory enzyme NF-kB by about half.

Shedding light on comet Chury’s unexpected chemical complexity

Data from comet “Chury”, collected while the comet passed the point of its orbit closest to the Sun, shows a plethora of surprising molecules sublimating from expelled dust particles. On average, this complex organic material resembles that present in meteorites and Saturn’s ring rain, indicating a shared presolar origin.
Credit: University of Bern

A team of researchers led by the University of Bern has for the first time identified an unexpected richness of complex organic molecules at a comet. This was achieved thanks to the analysis of data collected during ESA’s Rosetta mission at comet 67P/Churyumov-Gerasimenko, also known as Chury. Delivered to the early Earth by impacting comets, these organics may have helped to kick-start carbon-based life as we know it.

Comets are fossils from ancient times and from the depths of our Solar System, and they are relics from the formation of the sun, planets, and moons. A team led by chemist Dr. Nora Hänni of the Physics Institute of the University of Bern, Department of Space Research and Planetary Sciences, has now succeeded for the first time in identifying a whole series of complex organic molecules at a comet as they report in a study published in the prestigious journal Nature Communications.

Dr. Nora Hänni, Physics Institute, Space Research and Planetary Sciences (WP), University of Bern
Credit: Courtesy of Nora Hänni

These Energy-Packed Batteries Work Well in Extreme Cold and Heat

Study first author Guorui Cai, a nanoengineering postdoctoral researcher at UC San Diego, prepares a battery pouch cell for testing at subfreezing temperature.
Credit: David Baillot/UC San Diego Jacobs School of Engineering

Engineers at the University of California San Diego have developed lithium-ion batteries that perform well at freezing cold and scorching hot temperatures, while packing a lot of energy. The researchers accomplished this feat by developing an electrolyte that is not only versatile and robust throughout a wide temperature range, but also compatible with a high energy anode and cathode.

The temperature-resilient batteries are described in a paper published the week of July 4 in Proceedings of the National Academy of Sciences (PNAS). (As of this posting the paper is not on PNAS)

Such batteries could allow electric vehicles in cold climates to travel farther on a single charge; they could also reduce the need for cooling systems to keep the vehicles’ battery packs from overheating in hot climates, said Zheng Chen, a professor of nanoengineering at the UC San Diego Jacobs School of Engineering and senior author of the study.

“You need high temperature operation in areas where the ambient temperature can reach triple digits and the roads get even hotter. In electric vehicles, the battery packs are typically under the floor, close to these hot roads,” explained Chen, who is also a faculty member of the UC San Diego Sustainable Power and Energy Center. “Also, batteries warm up just from having a current run through during operation. If the batteries cannot tolerate this warmup at high temperature, their performance will quickly degrade.”

Nitrogen footprint: high pollution and loss of resources due to manure

In Germany, manure is usually applied to arable or grassland areas without pretreatment. The nitrogen released has a negative impact on the environment.
Credit: Markus Breig, KIT

Factory farming for meat production harms the environment. In addition to the directly emitted methane, the spreading of liquid manure releases climate-damaging nitrogen compounds such as ammonia and laughing gas into the atmosphere. In addition, the groundwater is contaminated with nitrate via the liquid phase. Researchers at the Karlsruhe Institute of Technology (KIT) have now examined how the manure that is produced in livestock farming and is often used as fertilizer affects the nitrogen footprint. They have shown that the nitrogen pollution from manure from beef production is three or eight times higher than for manure from pork and poultry meat production.

Large quantities of nitrogenous fertilizers and animal feed are used in agriculture. A significant part of the nitrogen used is released into the environment unused, for example by washing out nitrate from arable soils or by ammonia emissions from animal husbandry. “It is known that meat production has a very negative impact on the global nitrogen balance. The Nitrogen footprint calculator So far, however, it has not shown what a large proportion of the amount of manure that is generated in it,” says Prantik Samanta from the Engler Bunte Institute - Water Chemistry and Water Technology at KIT. “At the same time, these amounts of nitrogen mean an enormous loss of resources. Because recovering nitrogen is very expensive in terms of energy. "The doctoral student and first author of the study has now examined together with colleagues how much nitrogen about manure in beef, pork and poultry meat production pollutes the environment and is lost as a raw material. In addition, they calculated how much energy would be needed to process the manure and recover nitrogen. Again, this could be made available specifically as fertilizer.

Study explores coevolution of mammals and their lice

Elephant shrews, also called jumping shrews or sengis, are small insectivorous mammals native to Africa. The elephant shrew louse was among the earliest diverging lineages of mammalian lice.
Credit: Joey Makalintal, CC BY 2.0

According to a new study, the first louse to take up residence on a mammalian host likely started out as a parasite of birds. That host-jumping event tens of millions of years ago began the long association between mammals and lice, setting the stage for their coevolution and offering more opportunities for the lice to spread to other mammals.

The first louse to take up residence on a mammalian host likely started out as a parasite of birds, a new study finds. Pictured: A bird louse of the genus Rhopaloceras. 
Credit: Stephany Virrueta Herrera

Reported in the journal Nature Ecology and Evolution, the study compared the genomes and family trees of lice and their mammalian hosts. The effort revealed that the two trees share a lot of parallel branches and twigs. Those branching points – where one group of mammals began diverging into new forms – often were echoed in the genomes of the lice that parasitized those mammals, the researchers reported.

Nature restoration as a climate solution not enough to reduce peak global temperatures

The research found the process of restoring degraded natural ecosystems is crucial, but any climate benefits are dwarfed by the scale of fossil fuel emissions.
Source: University of Melbourne

Nature restoration cannot be scaled up quickly enough to compensate for fossil fuel emissions, new research led by the University of Melbourne has found.

Published today in One Earth, the research found that nature restoration, the process of restoring degraded natural ecosystems, is crucial but any climate benefits are dwarfed by the scale of ongoing fossil fuel emissions.

Lead author Dr Kate Dooley said nature restoration can marginally lower peak warming but should not be seen as a substitute for reducing fossil fuel emissions.

“Any form of land-based carbon dioxide removal takes decades to be realized, meaning the benefits from nature restoration could take generations to make a notable reduction in global temperatures,” Dr Dooley said.

“If we are to meet the goals of the Paris Agreement then relying on nature restoration and land management options are not the complete solution. We need policies that respect and understand the most crucial factor to mitigating rising temperature, which is to categorically move away from fossil fuels.”

The Higgs particle turns ten

A collision event in the Atlas detector: Higgs boson coupling to top quark 
Credit: ATLAS/CERN

Exactly ten years ago, the Atlas and CMS experiments announced a resounding success: Little less than three years after the launch of the Large Hadron Collider (LHC) at Cern, the last missing piece in the Standard Model of particle physics had been found: The Higgs boson, a kind of messenger of the Higgs field that in turn gives mass to all matter particles. To mark the Higgs birthday physicists, among them two researchers of the Max Planck Institute for Physics, sum up what they found out about the Higgs boson so far and look into the future, which insights might to be gained, yet.

July 4, 2012, was all about the Higgs boson: The particle physics community rejoiced at its success, and there was hardly a newspaper or news program that did not report on the spectacular discovery. Predicted by the theorists Peter Higgs, Robert Brout and François Englert as early as the 1960s, it took almost 50 years until the appropriate "search engine" was ready: the particle accelerator LHC with the experiments Atlas and CMS. Proton-proton collisions take place there, and physicists have successfully searched the debris for traces of the predicted Higgs particle.

With the Higgs boson, particle physics completed its Standard Model: Twelve elementary matter particles, four exchange particles and, as the keystone, the Higgs boson - the only particle without spin. This particle is the manifestation of the Higgs quantum field which fills the universe like a syrup, "sticking" to the other particles as mass.