Category: Chemistry

A common amino acid, glycine, can deliver a “slow-down” signal to the brain, likely contributing to major depression, anxiety and other mood disorders in some people, scientists at the Wertheim UF Scripps Institute for Biomedical Innovation & Technology have found.

The discovery, outlined Thursday in the journal Science, improves understanding of the biological causes of major depression and could accelerate efforts to develop new, faster-acting medications for such hard-to-treat mood disorders, said neuroscientist Kirill Martemyanov, Ph.D., corresponding author of the study.

“Most medications for people with depression take weeks before they kick in, if they do at all. New and better options are really needed,” said Martemyanov, who chairs the neuroscience department at the institute in Jupiter.

Major depression is among the world’s most urgent health needs. Its numbers have surged in recent years, especially among young adults. As depression’s disability, suicide numbers and medical expenses have climbed, a study by the U.S. Centers for Disease Control and Prevention in 2021 put its economic burden at $326 billion annually in the United States.

Martemyanov said he and his team of students and postdoctoral researchers have spent many years working toward this discovery. They didn’t set out to find a cause, much less a possible treatment route for depression. Instead, they asked a basic question: How do sensors on brain cells receive and transmit signals into the cells? Therein lay the key to understanding vision, pain, memory, behavior and possibly much more, Martemyanov suspected.

“It’s amazing how basic science goes. Fifteen years ago we discovered a binding partner for proteins we were interested in, which led us to this new receptor,” Martemyanov said. “We’ve been unspooling this for all this time.”

In 2018 the Martemyanov team found the new receptor was involved in stress-induced depression. If mice lacked the gene for the receptor, called GPR158, they proved surprisingly resilient to chronic stress.

That offered strong evidence that GPR158 could be therapeutic target, he said. But what sent the signal?

A breakthrough came in 2021, when his team solved the structure of GPR158. What they saw surprised them. The GPR158 receptor looked like a microscopic clamp with a compartment—akin to something they had seen in bacteria, not human cells.

“We were barking up the completely wrong tree before we saw the structure,” Martemyanov said. “We said, ‘Wow, that’s an amino acid receptor. There are only 20, so we screened them right away and only one fit perfectly. That was it. It was glycine.”

That wasn’t the only odd thing. The signaling molecule was not an activator in the cells, but an inhibitor. The business end of GPR158 connected to a partnering molecule that hit the brakes rather than the accelerator when bound to glycine.

“Usually receptors like GPR158, known as G protein Coupled Receptors, bind G proteins. This receptor was binding an RGS protein, which is a protein that has the opposite effect of activation,” said Thibaut Laboute, Ph.D., a postdoctoral researcher from Martemyanov’s group and first author of the study.

Scientists have been cataloging the role of cell receptors and their signaling partners for decades. Those that still don’t have known signalers, such as GPR158, have been dubbed “orphan receptors.”

The finding means that GPR158 is no longer an orphan receptor, Laboute said. Instead, the team renamed it mGlyR, short for “metabotropic glycine receptor.”

“An orphan receptor is a challenge. You want to figure out how it works,” Laboute said. “What makes me really excited about this discovery is that it may be important for people’s lives. That’s what gets me up in the morning.”

Laboute and Martemyanov are listed as inventors on a patent application describing methods to study GPR158 activity. Martemyanov is a cofounder of Blueshield Therapeutics, a startup company pursuing GPR158 as a drug target.

Glycine itself is sold as a nutritional supplement billed as improving mood. It is a basic building block of proteins and affects many different cell types, sometimes in complex ways. In some cells, it sends slow-down signals, while in other cell types, it sends excitatory signals. Some studies have linked glycine to the growth of invasive prostate cancer.

More research is needed to understand how the body maintains the right balance of mGlyR receptors and how brain cell activity is affected, he said. He intends to keep at it.

“We are in desperate need of new depression treatments,” Martemyanov said. “If we can target this with something specific, it makes sense that it could help. We are working on it now.”

More information: Thibaut Laboute et al, Orphan receptor GPR158 serves as a metabotropic glycine receptor: mGlyR, Science (2023). DOI: 10.1126/science.add7150. www.science.org/doi/10.1126/science.add7150

Journal information: Science 

Provided by University of Florida 

A breakthrough in synthesis strategy enables the facile formulation of inorganic membranes that are not just energy-efficient but also highly customizable, potentially revolutionizing the way many industries operate for greater sustainability.

Inorganic membranes can be thought of as kitchen sieves. Similar to how sieves separate smaller particles from larger ones, inorganic membranes, typically made of ceramics or metals, selectively separate molecules based on their size and properties.

In a ground-breaking achievement, a team of researchers from the College of Design and Engineering (CDE) at the National University of Singapore, led by Professor Ho Ghim Wei from the Department of Electrical and Computer Engineering, has developed a revolutionary technique for producing ultrathin inorganic membranes. These freestanding membranes can function without any supporting substrate—a significant advancement in membrane technology. The team’s findings were published in the scientific journal Nature on March 29, 2023.

Highly customizable and simple to produce, the inorganic membranes—underpinned by a universal, facile synthesis strategy—have the potential to benefit applications beyond filtration and separation. From energy conversion to catalysis and sensing, the membranes’ versatility could transform various sectors and industries that depend on membrane technology. By promoting efficiency and sustainability in industrial processes, the NUS scientists’ pioneering research has unveiled new possibilities for overcoming energy challenges in the face of climate change.

Membranes reimagined

Conventional membrane technologies used in purification and separation processes are known to be energy-intensive and therefore expensive, often entailing a combination of pressure, heat, and sometimes chemicals to function effectively. Moreover, the membranes must be regenerated, while the filtered components usually require further treatment after separation, leading to additional energy demands and costs.

Such limitations of traditional membrane technologies served as the impetus for postdoctoral research fellow Dr. Zhang Chen in Prof Ho’s team to develop a new synthesis strategy for highly efficient inorganic membranes. Dr. Zhang’s method involves taming chaotic, free-floating, inorganic building-blocks in a liquid environment, coaxing them to self-assemble into the desired membrane. This tunable process provides an effective means to tailor the membrane’s thickness and pore characteristics for specific applications, achieving maximum energy efficiency.

“Our study has also allowed us to take a fresh approach to rethink how inorganic membranes are traditionally developed,” added Dr. Zhang.

The NUS scientists have presented a synthesis template that other researchers can utilize for their work, which could spur the discovery of more novel membranes with a wider compositional range in a scalable and cost-effective manner.

From a structural perspective, the membranes they produced have more geometric diversity than conventional ones, providing more flexibility and options when designing membrane structures.

Additionally, the study also explores membrane functionality, where highly selective 2D barriers are used to control energy flow across the membrane. This feature could influence how the membrane functions—allowing ions to be filtered based on their charge, different forms of energy such as thermal, electrical, or light to be harnessed, or specific molecules to be selectively concentrated. Such flexibility is highly desirable in various energy-related applications, including fuel cells and solar energy conversion.

“Our new technique has the potential to transform industries that heavily rely on membranes for their operation, particularly those related to energy or the environment,” said Prof Ho. “The ability to create freestanding inorganic membranes that are highly selective opens up numerous exciting possibilities for applications in advanced spatial dynamic separation, catalysis, sensors, memories, and ionic conductors, all of which represent unprecedented developments.”

Formulating a greener future

With an emphasis on efficiency and customization, the researchers’ innovation plays a key role in NUS’ sustainability initiatives, greatly reducing the energy consumption of membrane-related processes worldwide and cutting the carbon footprint of various industries as a result.

Driven by the potential of the breakthrough, Prof Ho plans to lead an interdisciplinary team of scientists in a multi-faceted research program to advance membrane technology to the next level. “By exploring the vast range of membrane compositions and coupling them with various forms of energy, we hope to unlock new applications and make further strides towards a more sustainable future,” shared Prof Ho.

The team is also looking to develop automated manufacturing tools to streamline the production process of inorganic membranes, ultimately making their technology more accessible on a larger scale.

More information: Chen Zhang et al, Mechanistic formulation of inorganic membranes at the air–liquid interface, Nature (2023). DOI: 10.1038/s41586-023-05809-y

Journal information: Nature 

Provided by National University of Singapore 

Photocatalysis is the use of light to accelerate the rate of a reaction in the presence of a photocatalyst. The catalyst plays a crucial role in this process—it absorbs the light being shined onto it and makes it available in ways that can help accelerate the chemical reaction and also enhance it. These catalysts are used for a variety of light-dependent reactions ranging from the production of paper to the conversion of carbon dioxide to fuel.

Given these applications, the development of ideal photocatalysts is important. An ideal photocatalyst is one that uses a single transition metal that performs both visible light absorption and chemical transformation. Currently, visible light-driven single transition metal catalysts are limited to only one mechanism of operation, known as the radical mechanism, or have a low light-harvesting ability, making them heavily dependent on certain substrates. Thus, there is a need for an ideal single transition metal catalyst that solves these problems.

A team of researchers from Tokyo Institute of Technology (Tokyo Tech), led by Assistant Professor Yuki Nagashima, have reported a novel visible light-driven single transition metal catalyst that solves these issues. Their findings are published in Nature Synthesis. Dr. Nagashima explains, “We envisioned unprecedented rhodium (Rh)-based photocatalysts—spiro-fluorene-indenoindenyl (SFI)-Rh(I) complexes—that combine high light harvesting abilities with broad applicability.”

The team found that extending the molecules around the central Rh atom—called the ligand—is necessary to increase the light harvesting abilities of these complexes, but also makes them less stable. Thus, the team designed SFI-Rh(I) complexes using a non-fused extension strategy, extending the molecules around the ligand without compromising the stability of the resultant catalyst.

In fact, their extension strategy made the catalyst stable against protonation and helped in increasing its light-harvesting ability, thus reducing its substrate dependence. The catalyst was also designed to be able to perform using multiple mechanisms, beyond the radical mechanism used by previous catalysts.

“The careful design of our catalyst enabled it to have many advantages compared to previously described catalysts, while making it suitable for complex reactions. The SFI-Rh(I) complexes can easily extend the scope of typical Rh-catalyzed reactions using blue light LED irradiation at room temperature. This opens many avenues for future applications of these catalysts, as well as photocatalytic reactions in general,” says Nagashima.

“We believe that this catalyst has the potential to be a versatile light-driven catalyst that can break through the ground-state limitations in various photoreactions.”

More information: Yuki Nagashima, Design, synthesis and visible-light-induced non-radical reactions of dual-functional Rh catalysts, Nature Synthesis (2023). DOI: 10.1038/s44160-023-00268-9. www.nature.com/articles/s44160-023-00268-9

Journal information: Nature Synthesis 

Provided by Tokyo Institute of Technology 

Osaka Metropolitan University scientists have developed a process using artificial photosynthesis to successfully convert more than 60% of waste acetone into 3-hydroxybutyrate, a material used to manufacture biodegradable plastic. The results were obtained using low-concentration CO₂, equivalent to exhaust gas, and powered by light equivalent to sunlight for 24 hours.

The researchers expect that this innovative way of producing biodegradable plastic could not only reduce CO₂ emissions but also provide a way of reusing laboratory and industrial waste acetone. Their findings have been published in the journal Green Chemistry.

Poly-3-hydroxybutyrate—a biodegradable plastic—is a strong water-resistant polyester often used in packaging materials, made from 3-hydroxybutyrate as a precursor. In previous studies, a research team led by Professor Yutaka Amao from the Research Center for Artificial Photosynthesis at Osaka Metropolitan University found that 3-hydroxybutyrate can be synthesized from CO₂ and acetone with high efficiency, but this was only demonstrated at higher concentrations of CO₂ or sodium bicarbonate.

This new study aimed to reuse waste acetone from permanent marker ink and low concentrations of CO₂—equivalent to exhaust gas from power plants, chemical plants, or steel factories. Acetone is a relatively inexpensive and reasonably harmless chemical used in many different laboratory settings, either for reactions or as a cleaning agent, which produces waste acetone. The acetone and CO₂ acted as raw materials to synthesize 3-hydroxybutyrate using artificial photosynthesis, powered by light equivalent to sunlight.

“We focused our attention on the importance of using CO₂ created by exhaust gas from thermal power plants and other sources to demonstrate the practical application of artificial photosynthesis,” explained Professor Amao.

After 24 hours, more than 60% of acetone had been successfully converted to 3-hydroxybutyrate. “In the future, we aim to develop artificial photosynthesis technology further, so that it can use acetone from liquid waste and as well as exhaust gas from the laboratory as raw materials,” stated Professor Amao.

More information: Yu Kita et al, Visible-light-driven 3-hydroxybutyrate production from acetone and low concentrations of CO2 with a system of hybridized photocatalytic NADH regeneration and multi-biocatalysts, Green Chemistry (2023). DOI: 10.1039/D3GC00247K

Journal information: Green Chemistry 

Provided by Osaka Metropolitan University 

Researchers at the University of São Paulo (USP) in Brazil have developed a kraft paper-based electrochemical sensor that can detect traces of pesticides in fruit and vegetables in real time when coupled to an electronic device. In an apple or cabbage, for example, it can detect carbendazim, a fungicide widely used in Brazil despite being banned.

The results are reported in an article published in the journal Food Chemistry.

“To find out whether a food sample contains traces of pesticides by conventional methods, you must grind up the sample and submit it to time-consuming chemical processes before any such substances can be detected. Wearable sensors like the one we developed for continuous monitoring of pesticides in agriculture and the food industry eliminate the need for these complex processes. Inspection is much easier, cheaper and reliable for a supermarket, restaurant or importer, for example,” said Osvaldo Novais de Oliveira Junior, penultimate author of the article and a professor at IFSC-USP.

The new device is highly sensitive and resembles the glucometers used by diabetics to measure blood sugar, except that the results of food scanning for pesticides are displayed on a smartphone. “In the tests we performed, its sensitivity was similar to the conventional method’s. Plus, it’s fast and inexpensive,” said José Luiz Bott Neto, corresponding author of the article and a postdoctoral fellow at IFSC-USP.

How it works

The device consists basically of a paper substrate modified with carbon ink and submitted to electrochemical treatment in an acid medium to activate carboxyl groups and make detection possible, Bott Neto explained.

“We use the silkscreen process to transfer carbon-conducting ink to a strip of kraft paper, thereby creating a device based on electrochemistry. It has three carbon electrodes and is immersed in an acidic solution to activate the carboxyl groups. In other words, oxygen atoms are added to the structure of the carbon electrode. When it comes into contact with a sample contaminated with carbendazim, the sensor induces an electrochemical oxidation reaction that permits detection of the fungicide. The quantity of carbendazim is measured via electrical current,” he said.

In developing the device, the researchers evaluated the stability and structure of the paper substrate. “The properties of the paper itself were an important part of our research,” said Thiago Serafim Martins, first author of the article and a postdoctoral fellow at IFSC-USP.

Best option

The researchers analyzed kraft paper and parchment, finding both types of paper to be stable enough to serve as a substrate for the sensor. However, the porousness of kraft paper conferred more sensitivity on the sensor and the carboxyl groups formed during electrochemical activation, Martins explained, adding that paper-based electrodes could be used in many applications.

“There are commercial electrodes made of plastic or ceramic material. We successfully developed electrochemical sensors based on paper, a much more malleable material and therefore potentially useful in many areas, not just on farms or in supermarkets, but also in healthcare, for example,” he said.

More information: Thiago S. Martins et al, Optimized paper-based electrochemical sensors treated in acidic media to detect carbendazim on the skin of apple and cabbage, Food Chemistry (2023). DOI: 10.1016/j.foodchem.2023.135429

Journal information: Food Chemistry 

Provided by FAPESP 

A self-propagating chemical reaction can transform a liquid monomer into a solid polymer, and the interaction between the propagating front and the reaction’s natural convection leads to patterns in the resulting solid polymeric material. New University of Illinois Urbana-Champaign work has shown how the coupling between natural convection and frontal polymerization leads to those observed patterns.

This research was led by a unique team of researchers: Materials Science and Engineering professor Nancy Sottos, Aerospace Engineering professor Philippe Geubelle, and Mechanical Science and Engineering professor Leonardo Chamorro. A paper describing this research was recently published in Physical Review Letters.

Thermoset polymers and composite materials are used in a wide range of industries, but producing such materials requires their being cured at high temperatures in a slow and highly energy intensive process. Frontal polymerization to cure the materials is an attractive alternative approach that is significantly faster and more energy efficient.

In frontal polymerization, a self-propagating chemical front converts a liquid monomer into a solid polymer through a reaction that generates a significant amount of heat. Monomers are a simple class of molecular “building blocks” that can react to form larger molecules that are polymers. All of the energy needed to create the polymer is contained within the monomer itself, and to harness that energy, only a small stimulus is needed to kick off the reaction.

Because of instabilities, that self-propagating front doesn’t always move uniformly. Although it is ideal for the front to move smoothly and at a constant speed for applications like composite manufacturing and 3D printing, Geubelle says, “We’re actually very interested in these instabilities because they allow us to generate patterns in the material. That’s very exciting, because for some materials, these instabilities can lead to very different properties for the material.”

Geubelle explains that the team’s goal was “to understand, experimentally and computationally, the interaction between the front that is propagating in the monomer bath and the convection that takes place ahead of it, and how the interaction between the two can lead to patterns in the material.”

To visualize and characterize the polymerization front and the recirculation ahead of the front, the team had to design a clever mold that would allow them to make observations through both the top and the side. They constructed and used a glass mold that allowed for the observation of the front from the top and for a laser beam to enter from the side.

They then used particle image velocimetry (PIV) to characterize the velocity field. To use PIV, they needed to seed the fluid with small “tracer” particles that would follow the flow and would be tracked by a camera and illuminated by a laser sheet to visualize the patterns in the material. Chamorro says that particle selection was one of the challenges of this work. The team tried various kinds of particles before settling on silver-coated glass particles.

They were able to show that as the front propagates and transforms the liquid monomer into the solid polymer, the energy released generates convection. Convection is a process where heat is transferred by the movement of a heated fluid. Like water in the ocean, when a fluid is heated, it expands, and due to buoyancy, the hotter fluid rises because it is less dense, and colder fluid replaces it by sinking to the bottom because it is more dense. This process continues, creating a recirculating flow.

The polymerization process gives off a lot of heat, resulting in temperatures over 350° F. That heat generated during the transformation goes to the top of the surface. The researchers showed that this was a buoyancy-driven process, and that the recirculation associated with the heat of the reaction, along with the effect of gravity, leads to the formation of the patterning observed in the material and to the impact on the polymerization front. Thanks to the recirculation, the front tends to be inclined rather than perfectly vertical. That inclined front can result in a different speed or cooling effect and even a different patterning effect.

Sottos says the experiments revealed that the recirculation not only creates patterns inside the material that affects the material’s properties, but “it also creates surface patterns on the top of the material as well, because the monomer is getting pushed by the recirculating flow.”

The revealed mechanisms of the interaction between the polymerization front and the induced natural convection, and the resulting patterning, represent a deepened understanding of frontal polymerization that may be helpful in the future manufacture of polymeric materials.

Other authors on this work include Yuan Gao (postdoc, Beckman Institute and Aerospace Engineering); Justine Paul (graduate student, Beckman Institute and Material Science and Engineering); Manxin Chen (undergraduate student, Beckman Institute and Aerospace Engineering); and Liu Hong (graduate student, Mechanical Science and Engineering).

More information: Y. Gao et al, Buoyancy-Induced Convection Driven by Frontal Polymerization, Physical Review Letters (2023). DOI: 10.1103/PhysRevLett.130.028101

Journal information: Physical Review Letters 

Provided by University of Illinois Grainger College of Engineering 

The Haber-Bosch (HB) process is one of the most important industrial chemical reactions. It combines nitrogen and hydrogen gases in the presence of an iron-based catalyst at high temperatures and pressures to produce ammonia fertilizer which helps provide food for over five billion people.

Over the decades, researchers have tried to bring down the reaction temperature of the HB process to increase the ammonia yield while reducing energy consumption. To this end, they have recently developed new catalysts based on other transition metals, such as ruthenium, cobalt, and nickel, which exhibit much higher catalytic activity than iron.

However, these catalysts preferentially adsorb hydrogen atoms onto their surface at low temperatures of 100–150^oC, which reduces nitrogen adsorption and thus hampers ammonia production. This phenomenon, known as hydrogen poisoning, poses an obstacle to the low-temperature HB process.

In this light, researchers led by Professor Michikazu Hara of the Laboratory for Materials and Structures at Tokyo Institute of Technology (Tokyo Tech), have refocused on iron-based catalysts and modified them to produce ammonia at 100^oC. Their work is all set to be published in the Journal of the American Chemical Society.

Prof. Hara explains the motivation behind the research. “Hydrogen poisoning is not strong for iron-based catalysts. Therefore, they may be used for the low-temperature HB process but only when combined with an appropriate promoter that increases their catalytic activity.” In this work, the researchers prepared metallic iron (Fe) nanoparticles on calcium hydride (CaH₂) particles, with a mixture of barium oxide (BaO) and barium hydride (BaH₂) deposited on them.

A set of experiments revealed that the iron nanoparticles interact strongly with the hydride ions of both hydrides. As a result, hydrogen atoms move from the hydrides to the nanoparticles and get desorbed as hydrogen gas, leaving behind electrons. The hydrides donate these electrons to the iron nanoparticles. It facilitates the breaking of nitrogen gas into atoms, resulting in enhanced catalytic activity for ammonia production even at low temperatures.

The BaH₂–BaO/Fe/CaH₂ catalyst exhibited a turnover frequency of 0.23 s^-1 at 100^oC and 12.3 s^-1 at 300^oC under a moderate pressure of 0.9 MPa. These values, orders of magnitude higher than those for catalysts based on other transition metals, result from the ability of iron to prevent hydrogen poisoning by desorbing the adsorbed hydrogen atoms as hydrogen gas at low temperatures.

Discussing the future potential of their work, Prof. Hara observes, “The BaH₂–BaO/Fe/CaH₂ catalyst facilitates low-temperature HB process, which consumes less energy. As such, it can reduce the use of fossil fuels and potentially lower global carbon emissions. In addition, iron is abundant and inexpensive, which makes the HB process more sustainable.”

More information: Michikazu Hara et al, Low temperature ammonia synthesis on iron catalyst with an electron donor, Journal of the American Chemical Society (2023). DOI: 10.1021/jacs.2c13015

Journal information: Journal of the American Chemical Society 

Provided by Tokyo Institute of Technology 

Manganese oxides are natural reactive minerals and widely spread in aquatic and terrestrial environments, affecting the fate of metals (such as As³⁺ and Cd²⁺) and organic pollutants (such as phenols and diclofenac) through adsorption and oxidation in sewage treatment. Usually, the manganese (III/IV) oxides in the environment are thought to be formed by the oxidation of dissolved Mn(II) through abiotic or biotic processes.

Oxidation of aqueous Mn(II) by dissolved oxygen is thermodynamically favored, but the kinetic is slow due to the high energy barrier of the reaction from dissolved Mn(II) to Mn(III/IV) oxides. The presence of microorganisms accelerates the oxidation rate, which is 4–5 orders of magnitude faster than the rate of abiotic chemical oxidation, therefore is considered as the initial source of manganese oxides in the environment.

Bacteria capable of catalyzing the oxidation of dissolved Mn(II) ions to undissolved Mn(III/IV) oxides are usually called manganese-oxidizing bacteria. The bacterial oxidation of Mn(II) ions are divided into direct and indirect ways, and the process catalyzed by enzymes on the surface of microorganisms is called direct oxidation. For indirect pathways, some bacteria can change their surrounding environmental conditions for Mn(II) oxidation (e.g., the pH and Eh).

Roseobacter clade has been demonstrated to oxidize Mn(II) by producing extracellular reactive oxygen species in recent studies. Do other bacteria clades have similar Mn(II) oxidation processes with Roseobacter? Is the Mn(II) oxidation closely relative to the physiological process of bacteria?

To answer these questions, Prof. Feng Zhao from Chinese Academy of Sciences and his team members explored the microbial manganese oxidation process under visible light by using coastal surface seawater microorganisms. The relationship between the transformation of soluble Mn(II) into insoluble Mn(III/IV) oxides by microorganisms and physiological role was analyzed. This study is published in Frontiers of Environmental Science & Engineering in 2023.

In this study, the research team found visible light greatly promotes the oxidation rate of Mn(II), and the average rate reaches 64 μmol/(L·d). The generated manganese oxides were then conducive to Mn(II) oxidation, thus the rapid manganese oxidation was the result of the combined action of biotic and abiotic, and biological function accounts for 88 % ± 4 %.

Extracellular superoxide produced by microorganisms induced by visible light is the decisive factor for the rapid manganese oxidation in our study. But the production of these superoxides does not require the presence of Mn(II) ions, the Mn(II) oxidation process was more like an unintentional side reaction, which did not affect the growth of microorganisms.

More than 70 % of heterotrophic microorganisms in nature are capable of producing superoxide, based on the oxidizing properties of free radicals, all these bacteria can participate in the geochemical cycle of manganese. What’s more, the superoxide oxidation pathway might be a significant natural source of manganese oxide.

This study revealed an essential pathway for bacterial manganese oxidation. Heterotrophic bacteria produce superoxide under visible light irradiation and oxidize Mn(II) ions in the surrounding environment, which is the main source of manganese oxides. The biogenerated Mn(III/IV) oxides can also oxidize Mn(II) ions indirectly through abiotic reactions under light illumination.

Many bacteria in the environment that produce superoxide actively or passively may also oxidize Mn(II) in this way, suggesting that the manganese oxidation pathway through superoxide is a common behavior in the environment. In light of the oxidation properties and semiconductor properties of manganese oxides, this research will provide new ideas for the treatment of environmental pollution.

More information: Fan Yang et al, Visible light induces bacteria to produce superoxide for manganese oxidation, Frontiers of Environmental Science & Engineering (2022). DOI: 10.1007/s11783-023-1619-y

Provided by Higher Education Press

Just as a tight core is a component of good physical fitness for humans, helping to stabilize our bodies, mutations that tightened the core of the SARS-CoV-2 spike protein in new variants may have increased the virus’s fitness.

New research led by Penn State reveals that the stem region of the spike protein became progressively tighter over time, and the team thinks this likely improved the virus’s ability to transmit through nasal droplets and infect host cells once in the body. The team said the stem region of the protein that emerged in the most recent omicron variants is as rigid as it can get, which could mean that newer vaccines may be effective for longer than the ones that targeted the original variant.

“We wanted to see how the spike protein morphed structurally as it evolved from the original wild-type strain of the virus, through the alpha, delta and most recently omicron variants,” said Ganesh Anand, associate professor of chemistry and of biochemistry and molecular biology, Penn State.

“We found that the spike protein was initially more flexible at the stem region, which is where the spike protein is bundled together, but over time, mutations caused the protein to become progressively tighter and more rigid, and we think it’s now as rigid as it can get. This is important because it means that vaccines that are developed to target the current variant with these rigid spike proteins are likely to be effective for much longer than previous vaccines against the more flexible wild-type strain.”

To study how the spike protein changed with each of the new variants, the team studied the virus in vitro (in a test tube) using a technique called amide hydrogen/deuterium exchange mass spectrometry.

Anand explained that the SARS-CoV-2 spike protein is composed of three chain molecules called monomers that are bound together to form a trimer. The spike protein is made up of two subunits, an S1 and S2 subunit. The S1 subunit contains a receptor binding domain while the S2 subunit contains the stem region responsible for bundling the trimer.

“It is analogous to a tree, with the stem forming the trunk and the receptor binding domain forming the branches,” said Anand.

The team’s results, which published in the journal eLife, revealed that the spike protein stem first became more rigid with the D614G mutation, which is common to all SARS-CoV-2 variants. The stem became progressively more twisted with the emergence of new mutations in subsequent variants, and the omicron BA.1 variant showed the largest magnitude increase in stabilization relative to preceding variants.

Why would the virus benefit from a tighter core?

“We did not study the virus in patients, so we cannot determine if the changes we observed in the spike protein directly affected the newer variants such as omicron’s ability to transmit more readily; however, we can say that the changes likely made the virus more fit, which could translate to better transmission,” said Anand.

“A tighter core could likely make the virus more stable in nasal droplets and faster at binding to and entering host cells. So, for example, what initially took about 11 days to develop an infection after exposure now takes only about four days.”

Anand noted that one of the reasons the vaccines have not been able to fully neutralize the virus is because they were generated against the spike protein of the original wild-type variant.

“The latest bivalent booster—which targets newer variants—helps, but people who never got this booster aren’t receiving this more targeted protection,” he said. “Future vaccines that focus specifically on omicron are likely to be effective for longer.”

Finally, Anand said that the spike protein has now become so tightly twisted that it is unlikely to structurally change further at the stem region.

“There are limits to how much it can tighten,” he said. “I think that we can have some cautious optimism, in that we’re not going to continuously have variants emerging, at least tightening is not going to be a mechanism.”

Other Penn State authors on the paper include chemistry graduate students Sean Braet, Theresa Buckley and Varun Venkatakrishnan. Kim-Marie Dam, postdoctoral research fellow, and Pamela Bjorkman, assistant professor of biology and biological engineering, Caltech, also are authors.

More information: Sean M Braet et al, Timeline of changes in spike conformational dynamics in emergent SARS-CoV-2 variants reveal progressive stabilization of trimer stalk with altered NTD dynamics, eLife (2023). DOI: 10.7554/eLife.82584

Journal information: eLife 

Provided by Pennsylvania State University