Penn State scientists have discovered a new mechanism by which bacteria can select between different rare earth elements, using the ability of a bacterial protein to bind to another unit of itself, or “dimerize,” when it is bound to certain rare earths, but prefer to remain a single unit, or “monomer,” when bound to others.

By figuring out how this molecular handshake works at the atomic level, the researchers have found a way to separate these similar metals from one another quickly, efficiently, and under normal room temperature conditions. This strategy could lead to more efficient, greener mining and recycling practices for the entire tech sector, the researchers state.

“Biology manages to differentiate rare earths from all the other metals out there — and now, we can see how it even differentiates between the rare earths it finds useful and the ones it doesn’t,” said Joseph Cotruvo Jr., associate professor of chemistry at Penn State and lead author on a paper about the discovery published today (May 31) in the journal Nature. “We’re showing how we can adapt these approaches for rare earth recovery and separation.”

Rare earth elements, which include the lanthanide metals, are in fact relatively abundant, Cotruvo explained, but they are what mineralogists call “dispersed,” meaning they’re mostly scattered throughout the planet in low concentrations.

“If you can harvest rare earths from devices that we already have, then we may not be so reliant on mining it in the first place,” Cotruvo said. However, he added that regardless of source, the challenge of separating one rare earth from another to get a pure substance remains.

“Whether you are mining the metals from rock or from devices, you are still going to need to perform the separation. Our method, in theory, is applicable for any way in which rare earths are harvested,” he said.

All the same — and completely different

In simple terms, rare earths are 15 elements on the periodic table — the lanthanides, with atomic numbers 57 to 71 — and two other elements with similar properties that are often grouped with them. The metals behave similarly chemically, have similar sizes, and, for those reasons, they often are found together in the Earth’s crust. However, each one has distinct applications in technologies.

Conventional rare earth separation practices require using large amounts of toxic chemicals like kerosene and phosphonates, similar to chemicals that are commonly used in insecticides, herbicides and flame retardants, Cotruvo explained. The separation process requires dozens or even hundreds of steps, using these highly toxic chemicals, to achieve high-purity individual rare earth oxides.

“There is getting them out of the rock, which is one part of the problem, but one for which many solutions exist,” Cotruvo said. “But you run into a second problem once they are out, because you need to separate multiple rare earths from one another. This is the biggest and most interesting challenge, discriminating between the individual rare earths, because they are so alike. We’ve taken a natural protein, which we call lanmodulin or LanM, and engineered it to do just that.”

Learning from nature

Cotruvo and his lab turned to nature to find an alternative to the conventional solvent-based separation process, because biology has already been harvesting and harnessing the power of rare earths for millennia, especially in a class of bacteria called “methylotrophs” that often are found on plant leaves and in soil and water and play an important role in how carbon moves through the environment.

Six years ago, the lab isolated lanmodulin from one of these bacteria, and showed that it was unmatched — over 100 million times better — in its ability to bind lanthanides over common metals like calcium. Through subsequent work they showed that it was able to purify rare earths as a group from dozens of other metals in mixtures that were too complex for traditional rare earth extraction methods. However, the protein was less good at discriminating between the individual rare earths.

Cotruvo explained that for the new study detailed in Nature, the team identified hundreds of other natural proteins that looked roughly like the first lanmodulin but homed in on one that was different enough — 70% different — that they suspected it would have some distinct properties. This protein is found naturally in a bacterium (Hansschlegelia quercus) isolated from English oak buds.

The researchers found that the lanmodulin from this bacterium exhibited strong capabilities to differentiate between rare earths. Their studies indicated that this differentiation came from an ability of the protein to dimerize and perform a kind of handshake. When the protein binds one of the lighter lanthanides, like neodymium, the handshake (dimer) is strong. By contrast, when the protein binds to a heavier lanthanide, like dysprosium, the handshake is much weaker, such that the protein favors the monomer form.

“This was surprising because these metals are very similar in size,” Cotruvo said. “This protein has the ability to differentiate at a scale that is unimaginable to most of us — a few trillionths of a meter, a difference that is less than a tenth of the diameter of an atom.”

Fine-tuning rare earth separations

To visualize the process at such a small scale, the researchers teamed up with Amie Boal, Penn State professor of chemistry, biochemistry and molecular biology, who is a co-author on the paper. Boal’s lab specializes in a technique called X-ray crystallography, which allows for high-resolution molecular imaging.

The researchers determined that the protein’s ability to dimerize dependent on the lanthanide to which it was bound came down to a single amino acid — 1% of the whole protein — that occupied a different position with lanthanum (which, like neodymium, is a light lanthanide) than with dysprosium.

Because this amino acid is part of a network of interconnected amino acids at the interface with the other monomer, this shift altered how the two protein units interacted. When an amino acid that is a key player in this network was removed, the protein was much less sensitive to rare earth identity and size. The findings revealed a new, natural principle for fine-tuning rare earth separations, based on propagation of miniscule differences at the rare earth binding site to the dimer interface.

Using this knowledge, their collaborators at Lawrence Livermore National Laboratory showed that the protein could be tethered to small beads in a column, and that it could separate the most important components of permanent magnets, neodymium and dysprosium, in a single step, at room temperature and without any organic solvents.

“While we are by no means the first scientists to recognize that metal-sensitive dimerization could be a way of separating very similar metals, mostly with synthetic molecules,” Cotruvo said, “this is the first time that this phenomenon has been observed in nature with the lanthanides. This is basic science with applied outcomes. We’re revealing what nature is doing and it’s teaching us what we can do better as chemists.”

Cotruvo believes that the concept of binding rare earths at a molecular interface, such that dimerization is dependent on the exact size of the metal ion, can be a powerful approach for accomplishing challenging separations.

“This is the tip of the iceberg,” he said. “With further optimization of this phenomenon, the toughest problem of all — efficient separation of rare earths that are right next to each other on the periodic table — may be within reach.”

A patent application was filed by Penn State based on this work and the team is currently scaling up operations, fine-tuning and streamlining the protein with the goal of commercializing the process.

Other Penn State co-authors are Joseph Mattocks, Jonathan Jung, Chi-Yun Lin, Neela Yennawar, Emily Featherston and Timothy Hamilton. Ziye Dong, Christina Kang-Yun and Dan Park of the Lawrence Livermore National Laboratory also co-authored the paper.

The work was funded by the U.S. Department of Energy, the National Science Foundation, the National Institutes of Health, the Jane Coffin Childs Memorial Fund for Medical Research, and the Critical Materials Institute, an Energy Innovation Hub funded by the DOE, Office of Energy Efficiency and Renewable Energy, Advanced Materials and Manufacturing Technologies Office. Part of the work was performed under the auspices of the DOE by Lawrence Livermore National Laboratory.

Since its discovery by Roentgen in 1895, X-rays have been used everywhere, from medical examinations to security screenings in airports. Even Curiosity, NASA’s Mars rover, is equipped with an X-ray device to examine the materials composition of the rocks in Mars. An important usage of X-rays in science is to identify the type of materials in a sample. Over the years, the quantity of materials in a sample required for X-ray detection has been greatly reduced thanks to the development of synchrotron X-rays sources and new instruments. To date, the smallest amount one can X-ray a sample is in attogram, that is about 10,000 atoms or more. This is due to the X-ray signal produced by an atom being extremely weak so that the conventional X-ray detectors cannot be used to detect it. According to Hla, it is a long-standing dream of scientists to X-ray just one atom, which is now being realized by the research team led by him.

“Atoms can be routinely imaged with scanning probe microscopes, but without X-rays one cannot tell what they are made of. We can now detect exactly the type of a particular atom, one atom-at-a-time, and can simultaneously measure its chemical state,” explained Hla, who is also the director of the Nanoscale and Quantum Phenomena Institute at Ohio University. “Once we are able to do that, we can trace the materials down to ultimate limit of just one atom. This will have a great impact on environmental and medical sciences and maybe even find a cure that can have a huge impact for humankind. This discovery will transform the world.”

Their paper, published in the scientific journal Nature on May 31, 2023, and gracing the cover of the print version of the scientific journal on June 1, 2023, details how Hla and several other physicists and chemists, including Ph.D. students at OHIO, used a purpose-built synchrotron X-ray instrument at the XTIP beamline of Advanced Photon Source and the Center for Nanoscale Materials at Argonne National Laboratory.

For demonstration, the team chose an iron atom and a terbium atom, both inserted in respective molecular hosts. To detect X-ray signal of one atom, the research team supplemented conventional detectors in X-rays with a specialized detector made of a sharp metal tip positioned at extreme proximity to the sample to collect X-ray excited electrons — a technique known as synchrotron X-ray scanning tunneling microscopy or SX-STM. X-ray spectroscopy in SX-STM is triggered by photoabsorption of core level electrons, which constitutes elemental fingerprints and is effective in identifying the elemental type of the materials directly.

According to Hla, the spectrums are like fingerprints, each one being unique and able to detect exactly what it is.

“The technique used, and concept proven in this study, broke new ground in X-ray science and nanoscale studies,” said Tolulope Michael Ajayi, who is the first author of the paper and doing this work as part of his Ph.D. thesis. “More so, using X-rays to detect and characterize individual atoms could revolutionize research and give birth to new technologies in areas such as quantum information and the detection of trace elements in environmental and medical research, to name a few. This achievement also opens the road for advanced materials science instrumentation.”

For the last 12 years, Hla has been involved in the development of an SX-STM instrument and its measurement methods together with Volker Rose, a scientist at the Advanced Photon Source at Argonne National Laboratory.

“I have been able to successfully supervise four OHIO graduate students for their Ph.D. theses related to SX-STM method development over a 12-year period. We have come a long way to achieve the detection of a single atom X-ray signature,” Hla said.

Hla’s study is focused on nano and quantum sciences with a particular emphasis on understanding materials’ chemical and physical properties at the fundamental level — on an individual atom basis. In addition to achieving X-ray signature of one atom, the team’s key goal was to use this technique to investigate the environmental effect on a single rare-earth atom.

“We have detected the chemical states of individual atoms as well,” Hla explained. “By comparing the chemical states of an iron atom and a terbium atom inside respective molecular hosts, we find that the terbium atom, a rare-earth metal, is rather isolated and does not change its chemical state while the iron atom strongly interacts with its surrounding.”

Many rare-earth materials are used in everyday devices, such as cell phones, computers and televisions, to name a few, and are extremely important in creating and advancing technology. Through this discovery, scientists can now identify not only the type of element but its chemical state as well, which will allow them to better manipulate the atoms inside different materials hosts to meet the ever-changing needs in various fields. Moreover, they have also developed a new method called “X-ray excited resonance tunneling or X-ERT” that allows them to detect how orbitals of a single molecule orient on a material surface using synchrotron X-rays.

“This achievement connects synchrotron X-rays with quantum tunneling process to detect X-ray signature of an individual atom and opens many exciting research directions including the research on quantum and spin (magnetic) properties of just one atom using synchrotron X-rays,” Hla said.

In addition to Ajayi, several other OHIO graduate students including current Ph.D. students Sineth Premarathna in Physics and Xinyue Cheng in Chemistry, as well as Ph.D. in Physics alumni Sanjoy Sarkar, Shaoze Wang, Kyaw Zin Latt, Tomas Rojas, and Anh T. Ngo, currently an Associate Professor of Chemical Engineering at the University of Illinois-Chicago, were involved in this research. College of Arts and Sciences Roenigk Chair and Professor of Chemistry Eric Masson designed and synthesized the rare earth molecule used in this study.

Going forward, Hla and his research team will continue to use X-rays to detect properties of just one atom and find ways to further revolutionize their applications for use in gathering critical materials research and more.

Described as “groundbreaking” by a team of researchers at UC San Diego’s Scripps Institution of Oceanography, this previously unknown process accounts for between 7% to 25% of all the oxygen produced and carbon fixed in the ocean. When also considering photosynthesis occuring on land, researchers estimated that this mechanism could be responsible for generating up to 12% of the oxygen on the entire planet.

Scientists have long recognized the significance of phytoplankton — microscopic organisms that drift in aquatic environments — due to their ability to photosynthesize. These tiny oceanic algae form the base of the aquatic food web and are estimated to produce around 50% of the oxygen on Earth.

The new study, published May 31 in the journal Current Biology, identifies how a proton pumping enzyme (known as VHA) aids in global oxygen production and carbon fixation from phytoplankton.

“This study represents a breakthrough in our understanding of marine phytoplankton,” said lead author Daniel Yee, who conducted the research while a PhD student at Scripps Oceanography and currently serves as a joint postdoctoral researcher at the European Molecular Biology Laboratory and University of Grenoble Alpes in France. “Over millions of years of evolution, these small cells in the ocean carry out minute chemical reactions, in particular to produce this mechanism that enhances photosynthesis, that shaped the trajectory of life on this planet.”

Working closely with Scripps physiologist Martín Tresguerres, one of his co-advisors, and other collaborators at Scripps and the Lawrence Livermore National Laboratory, Yee unraveled the complex inner workings of a specific group of phytoplankton known as diatoms, which are single-celled algae famous for their ornamental cell walls made of silica.

Understanding the “proton pump” enzyme

Previous research in the Tresguerres Lab has worked to identify how VHA is used by a variety of organisms in processes critical to life in the oceans. This enzyme is found in nearly all forms of life, from humans to single-celled algae, and its basic role is to modify the pH level of the surrounding environment.

“We imagine proteins as Lego blocks,” explained Tresguerres, a study co-author. “The proteins always do the same thing, but depending on what other proteins they are paired with, they can achieve a vastly different function.”

In humans, the enzyme aids kidneys in regulating blood and urine functions. Giant clams use the enzyme to dissolve coral reefs, where they secrete an acid that bores holes in the reef to take shelter. Corals use the enzyme to promote photosynthesis by their symbiotic algae, while deep-sea worms known as Osedax use it to dissolve the bones of marine mammals, such as whales, so they can consume them. The enzyme is also present in the gills of sharks and rays, where it is part of a mechanism that regulates blood chemistry. And in fish eyes, the proton pump helps deliver oxygen that enhances vision.

Looking at this previous research, Yee wondered how the VHA enzyme was being used in phytoplankton. He set out to answer this question by combining high-tech microscopy techniques in the Tresguerres Lab and genetic tools developed in the lab of the late Scripps scientist Mark Hildebrand, who was a leading expert on diatoms and one of Yee’s co-advisors.

Using these tools, he was able to label the proton pump with a fluorescent green tag and precisely locate it around chloroplasts, which are known as “organelles” or specialized structures within diatom cells. The chloroplasts of diatoms are surrounded by an additional membrane compared to other algae, enveloping the space where carbon dioxide and light energy are converted into organic compounds and released as oxygen.

“We were able to generate these images that are showing the protein of interest and where it is inside of a cell with many membranes,” said Yee. “In combination with detailed experiments to quantify photosynthesis, we found that this protein is actually promoting photosynthesis by delivering more carbon dioxide, which is what the chloroplast uses to produce more complex carbon molecules, like sugars, while also producing more oxygen as a by-product.”

Connection to evolution

Once the underlying mechanism was established, the team was able to connect it to multiple aspects of evolution. Diatoms were derived from a symbiotic event between a protozoan and an algae around 250 million years ago that culminated into the fusing of the two organisms into one, known as symbiogenesis. The authors highlight that the process of one cell consuming another, known as phagocytosis, is widespread in nature. Phagocytosis relies on the proton pump to digest the cell that acts as the food source. However, in the case of diatoms, something special occurred in which the cell that was eaten didn’t get fully digested.

“Instead of one cell digesting the other, the acidification driven by the proton pump of the predator ended up promoting photosynthesis by the ingested prey,” said Tresguerres. “Over evolutionary time, these two separate organisms fused into one, for what we now call diatoms.”

Not all algae have this mechanism, so the authors think that this proton pump has given diatoms an advantage in photosynthesis. They also note that when diatoms originated 250 million years ago, there was a big increase in oxygen in the atmosphere, and the newly discovered mechanism in algae might have played a role in that.

The majority of fossil fuels extracted from the ground are believed to have originated from the transformation of biomass that sank to the ocean floor, including diatoms, over millions of years, resulting in the formation of oil reserves. The researchers are hopeful that their study can provide inspiration for biotechnological approaches to improve photosynthesis, carbon sequestration, and biodiesel production. Additionally, they think it will contribute to a better understanding of global biogeochemical cycles, ecological interactions, and the impacts of environmental fluctuations, such as climate change.

“This is one of the most exciting studies in the field of symbiosis in the past decades and it will have a large impact on future research worldwide,” said Tresguerres.

Additional co-authors include Raffaela Abbriano, Bethany Shimasaki, Maria Vernet, Greg Mitchell, and the late Mark Hildebrand of Scripps Oceanography; Ty Samo, Xavier Mayali, and Peter Weber of the Lawrence Livermore National Laboratory; and Johan Decelle of University of Grenoble Alpes.

The authors did not receive any funding for this study. Yee’s doctoral studies at Scripps Oceanography were supported by the Scripps Fellowship, the NIH training grant, and the Ralph Lewin Graduate Fellowship. Funds by UC San Diego’s Arthur M. and Kate E. Tode Research Endowment in Marine Biological Sciences supported the purchase of a microscope that was essential for the research.

Influenza viruses represent a major risk to human and animal health. Their potential for mutation makes them particularly elusive. ”We already knew that the influenza A virus binds to sugar structures on the cell surface, then rolls along the cell surface until it finds a suitable entry point into the host cell. However, we did not know which proteins on the host cell surface marked this entry point, and how they favoured the entry of the virus,” explains Mirco Schmolke, Associate Professor in the Department of Microbiology and Molecular Medicine and in the Geneva Centre for Inflammation Research (GCIR) at the UNIGE Faculty of Medicine, who led this work.

A receptor as a key to infection

The scientists first identified cell surface proteins present in the vicinity of the viral haemagglutinin, the protein used by the influenza A virus to enter the cell. One of these proteins stood out: transferrin receptor 1. This acts as a revolving door transporting iron molecules into the cell, which are essential for many physiological functions.

”The influenza virus takes advantage of the continuous recycling of the transferrin receptor 1 to enter the cell and infect it,” explains Béryl Mazel-Sanchez, a former post-doctoral researcher in Mirco Schmolke’s laboratory and first author of this work. ”To confirm our discovery, we genetically engineered human lung cells to remove the transferrin receptor 1, or on the contrary to overexpress it. By deleting it in cells normally susceptible to infection, we prevented influenza A from entering. Conversely, by overexpressing it in cells normally resistant to infection, we made them easier to infect”.

Inhibiting this mechanism

The research team then succeeded in reproducing this mechanism by inhibiting the transferrinreceptor 1 using a chemical molecule. ”We tested it successfully on human lung cells, on human lung tissue samples and on mice with several viral strains,” says Béryl Mazel-Sanchez. ”In the presence of this inhibitor, the virus replicated much less. However, in view of its potentially oncogenic characteristics, this product cannot be used to treat humans.” On the other hand, anti-cancer therapies based on the inhibition of the transferrin receptor are under development and could also be interesting in this context.

”Our discovery was made possible thanks to the excellent collaboration within the Faculty of Medicine as well as with the University Hospitals of Geneva (HUG) and the Swiss Institute of Bioinformatics (SIB),” the authors add. In addition to the transferrin receptor 1, scientists have identified some 30 other proteins whose role in the influenza A entry process remains to be deciphered. It is indeed likely that the virus uses a combination involving other receptors. ”Although we are still far from a clinical application, blocking the transferrin receptor 1 could become a promising strategy for treating influenza virus infections in humans and potentially in animals.”

In a set of experiments, individual plant cells responded to the touch of a very fine glass rod by sending slow waves of calcium signals to other plant cells, and when that pressure was released, they sent much more rapid waves. While scientists have known that plants can respond to touch, this study shows that plant cells send different signals when touch is initiated and ended.

“It is quite surprising how finely sensitive plants cells are — that they can discriminate when something is touching them. They sense the pressure, and when it is released, they sense the drop in pressure,” said Michael Knoblauch, WSU biological sciences professor and senior author of the study in the journal Nature Plants. “It’s surprising that plants can do this in a very different way than animals, without nerve cells and at a really fine level.”

Knoblauch and his colleagues conducted a set of 84 experiments on 12 plants using thale cress and tobacco plants that had been specially bred to include calcium sensors, a relatively new technology. After placing pieces of these plants under a microscope, they applied a slight touch to individual plant cells with a micro-cantilever, essentially a tiny glass rod about the size of a human hair. They saw many complex responses depending on the force and duration of the touch, but the difference between the touch and its removal was clear.

Within 30 seconds of the applied touch to a cell, the researchers saw slow waves of calcium ions, called cytosolic calcium, travelling from that cell through the adjacent plant cells, lasting about three to five minutes. Removal of the touch showed an almost instant set of more rapid waves that dissipated within a minute.

The authors believe these waves are likely due to the change in pressure inside the cell. Unlike animal cells with permeable membranes, plant cells also have strong cellular walls that cannot be easily breached, so just a light touch will temporarily increase pressure in a plant cell.

The researchers tested the pressure theory mechanically by inserting a tiny glass capillary pressure probe into a plant cell. Increasing and decreasing pressure inside the cell resulted in similar calcium waves elicited by the start and stop of a touch.

“Humans and animals sense touch through sensory cells. The mechanism in plants appears to be via this increase or decrease of the internal cell pressure,” said Knoblauch. “And it doesn’t matter which cell it is. We humans may need nerve cells, but in plants, any cell on the surface can do this.”

Previous research has shown that when a pest like a caterpillar bites a plant leaf, it can initiate the plant’s defensive responses such as the release of chemicals that make leaves less tasty or even toxic to the pest. An earlier study also revealed that brushing a plant triggers calcium waves that activate different genes.

The current study was able to differentiate the calcium waves between touch and letting go, but how exactly the plant’s genes respond to those signals remains to be seen. With new technologies like the calcium sensors used in this study, scientists can start to untangle that mystery, Knoblauch said.

“In future studies, we have to trigger the signal in a different way than has been done before to know what signal, if touch or letting go, triggers downstream events,” he said.

This study was supported by grants from the National Science Foundation. The international team included researchers from the Technical University of Denmark; Ludwig Maximilian Universitaet Muenchen and Westfaelische Wilhelms-Universitaet Muenster in Germany; and University of Wisconsin-Madison as well as WSU.

Walk-in freezers and refrigerated trucks generally maintain their set temperatures, but accidents can happen. Wireless sensors can monitor the temperature of individual products, but these devices produce a lot of electronic waste. Recently, researchers have suggested using materials that act as visual indicators to provide this information with less waste. Yet some current options using colorful reactions or dyes produce hues that can fade. Or they only track above-freezing temperatures, which isn’t useful for some COVID-19 vaccines that can actually start breaking down below freezing — above -4 or -94 degrees Fahrenheit. So, Yadong Yin, Xuemin Du and colleagues wanted to develop a better color-changing material with tunable melting to track a wide range of temperatures.

The researchers used structural colors, instead of dyes, for their indicator system. The team made glycerol-coated silicon dioxide nanoparticles, which appeared bright green or red when they clustered together into microcrystals in water. Next, they created liquids with variable melting points by mixing different proportions of polyethylene glycol or ethylene glycol and water. When these two parts were put together, they could produce an irreversible color loss when the temperature-triggered solution melted and the microcrystals broke apart. The materials could be customized to track temperature exposures from -94 to +99 degrees Fahrenheit that lasted from a few minutes to multiple days. In other experiments, the two-part indicator systems were packaged into flexible round vial labels and a QR code. These systems were very sensitive and successfully indicated when the materials got too warm. The researchers say that structural color-changing materials hold promise for the diverse scenarios encountered in medical cold supply chains.

The authors acknowledge funding from the National Natural Science Foundation of China, the National Key R&D Program of China, the Youth Innovation Promotion Association of Chinese Academy of Sciences, the Guangdong Regional Joint Fund-Key Project, the Chinese Academy of Sciences Key Laboratory of Health Informatics, the Shenzhen Institutes of Advanced Technology and the Fundamental Research Program of Shenzhen.