Conservation ecologist Rebecca Brunner, a Ph.D. candidate at the University of California, Berkeley, has discovered that the glass frog Sachatamia orejuela can be added to the list of species that make use of visual cues in response to their acoustic environments. This is the first time a member of the glass frog family (Centrolenidae) has been observed using visual communication in this manner.

“A handful of other frog species around the world use visual signaling, in addition to high-pitched calls, to communicate in really loud environments,” Brunner said. “What’s interesting is that these species are not closely related to each other, which means that these behaviors likely evolved independently, but in response to similar environments — a concept called convergent evolution.”

Sachatamia orejuela glass frogs are native to the rainforests of Ecuador and Colombia. They are especially unique because they are almost exclusively found on rocks and boulders within the spray zones of waterfalls, where rushing water and slippery surfaces offer some protection against predators, and their green-gray color and semi-transparent skin make them nearly impossible to spot. As a result, little is known about this species’ mating and breeding behavior.

Brunner, who studies the bioacoustics of different ecological environments, was chest-deep in an Ecuadorean rainforest stream recording the call of a Sachatamia orejuela when she first observed this visual signaling behavior. As soon as she saw the frog repeatedly raising its front and back legs, Brunner climbed a slippery rock face and balanced on one foot to get video footage of the behavior.

“I was already over the moon because I had finally found a calling male after months of searching. Before our publication, there was no official record of this species’ call, and basic information like that is really important for conservation,” Brunner said. “But then I saw it start doing these little waves, and I knew that I was observing something even more special.”

While she filmed, the frog continued to wave its hands and feet and bob its head. She also observed another male Sachatamia orejuela glassfrog a few meters away performing the same actions.

“This is a really exhilarating discovery because it’s a perfect example of how an environment’s soundscape can influence the species that live there. We’ve found that Sachatamia orejuela has an extremely high-pitched call, which helps it communicate above the lower-pitched white noise of waterfalls. And then to discover that it also waves its hands and feet to increase its chances of being noticed — that’s a behavior I’ve always loved reading about in textbooks, so it is beyond thrilling to be able to share another amazing example with the world,” said Brunner.

Though the COVID-19 pandemic has put a pause on Brunner’s fieldwork, she hopes to return to Ecuador soon to continue her research, which links bioacoustics and conservation.

“One of the best things about fieldwork is that nature is always full of surprises — you never know what discoveries you may happen upon,” Brunner said. “I hope our findings can serve as a reminder that we share this planet with incredible biodiversity. Conserving ecosystems that support species like Sachatamia orejuela is important not only for our well-being, but also for our sense of wonder.”

Video: https://www.youtube.com/watch?v=U6prmVIyxXI&feature=emb_logo

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Materials provided by University of California – Berkeley. Original written by Kara Manke. Note: Content may be edited for style and length.

The researchers are the first to observe metallic lines in a perovskite crystal. Perovskites abound in the Earth’s center, and barium stannate (BaSnO3) is one such crystal. However, it has not been studied extensively for metallic properties because of the prevalence of more conductive materials on the planet like metals or semiconductors. The finding was made using advanced transmission electron microscopy (TEM), a technique that can form images with magnifications of up to 10 million.

The research is published in Science Advances.

“The conductive nature and preferential direction of these metallic line defects mean we can make a material that is transparent like glass and at the same time very nicely directionally conductive like a metal,” said Mkhoyan, a TEM expert and the Ray D. and Mary T. Johnson/Mayon Plastics Chair in the Department of Chemical Engineering and Materials Science at the University of Minnesota’s College of Science and Engineering. “This gives us the best of two worlds. We can make windows or new types of touch screens transparent and at the same time conductive. This is very exciting.”

Defects, or imperfections, are common in crystals — and line defects (the most common among them is the dislocation) are a row of atoms that deviate from the normal order. Because dislocations have the same composition of elements as the host crystal, the changes in electronic band structure at the dislocation core, due to symmetry-reduction and strain, are often only slightly different than that of the host. The researchers needed to look outside the dislocations to find the metallic line defect, where defect composition and resulting atomic structure are vastly different.

“We easily spotted these line defects in the high-resolution scanning transmission electron microscopy images of these BaSnO3 thin films because of their unique atomic configuration and we only saw them in the plan view,” said Hwanhui Yun, a graduate student in the Department of Chemical Engineering and Materials Science and a lead author of the study.

For this study, BaSnO3 films were grown by molecular beam epitaxy (MBE) — a technique to fabricate high-quality crystals — in a lab at the University of Minnesota Twin Cities. Metallic line defects observed in these BaSnO3 films propagate along film growth direction, which means researchers can potentially control how or where line defects appear — and potentially engineer them as needed in touchscreens, smart windows, and other future technologies that demand a combination of transparency and conductivity.

“We had to be creative to grow high-quality BaSnO3 thin films using MBE. It was exciting when these new line defects came into light in the microscope,” said Bharat Jalan, associate professor and Shell Chair in the Department of Chemical Engineering and Materials Science, who heads up the lab that grows a variety of perovskite oxide films by MBE.

Perovskite crystals (ABX3) contain three elements in the unit cell. This gives it freedom for structural alterations such as composition and crystal symmetry, and the ability to host a variety of defects. Because of different coordination and bonding angles of the atoms in the line defect core, new electronic states are introduced and the electronic band structure is modified locally in such a dramatic way that it turns the line defect into metal.

“It was fascinating how theory and experiment agreed with each other here,” said Turan Birol, assistant professor in the Department of Chemical Engineering and Materials Science and an expert in density functional theory (DFT). “We could verify the experimental observations of the atomic structure and electronic properties of this line defect with first principles DFT calculations.”

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Materials provided by University of Minnesota. Note: Content may be edited for style and length.

To assist these efforts, researchers at the University of Wisconsin School of Medicine and Public Health and UW Health have developed a tool (https://www.hipxchange.org/COVIDvaccine) that incorporates a person’s age and socioeconomic status to prioritize vaccine distribution among people who otherwise share similar risks due to their jobs. The tool helps identify those who are at greater risk of severe complications or death from COVID-19.

UW Health has implemented the prioritization algorithm to equitably provide limited doses to frontline health care workers. Other organizations can also access the freely available tool to guide their own vaccine distribution plans.

While the UW-Madison tool was designed with the first phase of eligible recipients in mind, it could be used as vaccine distribution expands to larger populations. As the eligible population increases, the gap between initial supply and demand could grow, making such prioritization tools even more helpful.

“Knowing we’re going to have limited vaccine for some time, we wanted to develop an algorithm to equitably distribute vaccinations within these risk groups,” says Grace Flood, the director of clinical analytics and reporting in the Office of Population Health at UW Health, who helped lead development of the tool along with the Health Innovation Program within SMPH.

In addition to age, the algorithm uses the Social Vulnerability Index to measure a person’s susceptibility to severe COVID-19 based on where they live. The Centers for Disease Control and Prevention developed the SVI metric to help emergency responders identify which neighborhoods and towns will require the most support following natural disasters or public health emergencies.

The SVI incorporates 15 measures in four categories: socioeconomic status, housing composition and disability, minority status and language, and housing and transportation. Race and ethnicity have been closely correlated with higher COVID-19-related hospitalizations and mortality.

Flood and her team incorporated the SVI in accordance with a report by the National Academies of Sciences, Engineering and Medicine that recommended using the index to fairly distribute vaccines. Because Wisconsin publishes data about COVID-19 deaths at the census-tract level, “we were able to determine the relationship for risk of mortality between age and SVI,” says Flood. This relationship allowed the researchers to verify that age and SVI combined provide an accurate estimate of an individual’s risk.

Since age and SVI are readily available pieces of information about an individual and each contributes to COVID-19 risk, an algorithm that incorporates both elements may serve as one of the best ways to distribute vaccines until supply catches up to demand, says Flood.

The researchers have published their algorithm (https://deepblue.lib.umich.edu/handle/2027.42/163774) in the Annals of Family Medicine COVID-19 collection and made it available for download on the project’s website.

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Materials provided by University of Wisconsin-Madison. Original written by Eric Hamilton. Note: Content may be edited for style and length.

Scientists know that microbiota — the trillions of beneficial microbes living harmoniously inside our gut — can protect people from bacterial infections, but little is known about how they provide protection. Scientists are studying the microbiota with an eye to finding or enhancing natural treatments to replace antibiotics, which harm microbiota and become less effective as bacteria develop drug resistance.

The scientists observed that microbiota that had experienced prior infection and transferred to germ-free mice helped prevent infection with Kpn. They identified a class of bacteria — Deltaproteobacteria — involved in fighting these infections, and further analysis led them to identify taurine as the trigger for Deltaproteobacteria activity.

Taurine helps the body digest fats and oils and is found naturally in bile acids in the gut. The poisonous gas hydrogen sulfide is a byproduct of taurine. The scientists believe that low levels of taurine allow pathogens to colonize the gut, but high levels produce enough hydrogen sulfide to prevent colonization. During the study, the researchers realized that a single mild infection is sufficient to prepare the microbiota to resist subsequent infection, and that the liver and gallbladder — which synthesize and store bile acids containing taurine — can develop long-term infection protection.

The study found that taurine given to mice as a supplement in drinking water also prepared the microbiota to prevent infection. However, when mice drank water containing bismuth subsalicylate — a common over-the-counter drug used to treat diarrhea and upset stomach — infection protection waned because bismuth inhibits hydrogen sulfide production.

Scientists from NIH’s National Institute of Allergy and Infectious Diseases led the project in collaboration with researchers from the National Institute of General Medical Sciences; the National Cancer Institute; the National Institute of Diabetes and Digestive and Kidney Diseases; and the National Human Genome Research Institute.

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Stanford University material scientists led by Jennifer Dionne have done just that by using light and advanced fabrication and characterization techniques to endow catalysts with new abilities.

In a proof-of-concept experiment, rods of palladium that were approximately 1/200th the width of a human hair served as catalysts. The researchers placed these nanorods above gold nanobars that focused and “sculpted” the light around the catalyst. This sculpted light changed the regions on the nanorods where chemical reactions — which release hydrogen — took place. This work, published Jan. 14 in Science, could be an early step toward more efficient catalysts, new forms of catalytic transformations and potentially even catalysts capable of sustaining more than one reaction at once.

“This research is an important step in realizing catalysts that are optimized from the atomic-scale to the reactor-scale,” said Dionne, associate professor of materials science and engineering who is senior author of the paper. “The aim is to understand how, with the appropriate shape and composition, we can maximize the reactive area of the catalyst and control which reactions are occurring.”

A mini lab

Simply being able to observe this reaction required an exceptional microscope, capable of imaging an active chemical process on an extremely small scale. “It’s difficult to observe how catalysts change under reaction conditions because the nanoparticles are extremely small,” said Katherine Sytwu, a former graduate student in the Dionne lab and lead author of the paper. “The atomic-scale features of a catalyst generally dictate where a transformation happens, and so it’s crucial to distinguish what’s happening within the small nanoparticle.”

For this particular reaction — and the later experiments on controlling the catalyst — the microscope also had to be compatible with the introduction of gas and light into the sample.

To accomplish all of this, the researchers used an environmental transmission electron microscope at the Stanford Nano-Shared Facilities with a special attachment, previously developed by the Dionne lab, to introduce light. As their name suggests, transmission electron microscopes use electrons to image samples, which allows for a higher level of magnification than a classic optical microscope, and the environmental feature of this microscope means that gas can be added into what is otherwise an airless environment.

“You basically have a mini lab where you can do experiments and visualize what’s happening at a near-atomic level,” said Sytwu.

Under certain temperature and pressure conditions, hydrogen-rich palladium will release its hydrogen atoms. In order to see how light would affect this standard catalytic transformation, the researchers customized a gold nanobar — designed using equipment at the Stanford Nano-Shared Facilities and the Stanford Nanofabrication Facility — to sit below the palladium and act as an antenna, collecting the incoming light and funneling it to the nearby catalyst.

“First we needed to understand how these materials transform naturally. Then, we started to think about how we could modify and actually control how these nanoparticles change,” said Sytwu.

Without light, the most reactive points of the dehydrogenation are the two tips of the nanorod. The reaction then travels through the nanorod, popping out hydrogen along the way. With light, however, the researchers were able to manipulate this reaction so that it traveled from the middle outward or from one tip to the other. Based on the location of the gold nanobar and the illumination conditions, the researchers managed to produce a variety of alternative hotspots.

Bond breaking and breakthroughs

This work is one of the rare instances showing that it is possible to tweak how catalysts behave even after they are made. It opens up significant potential for increasing efficiency at the single-catalyst level. A single catalyst could play the role of many, using light to perform several of the same reactions across its surface or potentially increase the number of sites for reactions. Light control may also help scientists avoid unwanted, extraneous reactions that sometimes occur alongside desired ones. Dionne’s most aspirational goal is to someday develop efficient catalysts capable of breaking down plastic at a molecular level and transforming it back to its source material for recycling.

Dionne emphasized that this work, and whatever comes next, would not be possible without the shared facilities and resources available at Stanford. (These researchers also used the Stanford Research Computing Center to do their data analysis.) Most labs cannot afford to have this advanced equipment on their own, so sharing it increases access and expert support.

“What we can learn about the world and how we can enable the next big breakthrough is so critically enabled by shared research platforms,” said Dionne, who is also senior associate vice provost for research platforms/shared facilities. “These spaces not only offer critical tools, but a really amazing community of researchers.”

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Materials provided by Stanford University. Original written by Taylor Kubota. Note: Content may be edited for style and length.

“RNA folding is a dynamic process that is fundamental for life,” said Northwestern’s Julius B. Lucks, who led the study. “RNA is a really important piece of diagnostic and therapeutic design. The more we know about RNA folding and complexities, the better we can design treatments.”

Using data from RNA-folding experiments, the researchers generated the first-ever data-driven movies of how RNA folds as it is made by cellular machinery. By watching their videos of this folding occur, the researchers discovered that RNA often folds in surprising, perhaps unintuitive ways, such as tying itself into knots — and then immediately untying itself to reach its final structure.

“Folding takes place in your body more than 10 quadrillion times a second,” Lucks said. “It happens every single time a gene is expressed in a cell, yet we know so little about it. Our movies allow us to finally watch folding happen for the first time.”

The research will be published Jan. 15 in the journal Molecular Cell.

Lucks is an associate professor of chemical and biological engineering at Northwestern’s McCormick School of Engineering and a member of Northwestern’s Center for Synthetic Biology. He co-led the work with Alan Chen, an associate professor of chemistry at the University of Albany.

Although videos of RNA folding do exist, the computer models that generate them are full of approximations and assumptions. Lucks’ team has developed a technology platform that captures data about RNA folding as the RNA is being made. His group then uses computational tools to mine and organize the data, revealing points where the RNA folds and what happens after it folds. Angela Yu, a former student of Lucks, inputted this data into computer models to generate accurate videos of the folding process.

“The information that we give the algorithms helps the computer models correct themselves,” Lucks said. “The model makes accurate simulations that are consistent with the data.”

Lucks and his collaborators used this strategy to model the folding of an RNA called SRP, an ancient RNA found in all kingdoms of life. The molecule is well-known for its signature hairpin shape. When watching the videos, the researchers discovered that the molecule ties itself into a knot and unties itself very quickly. Then it suddenly flips into the correct hairpin-like structure using an elegant folding pathway called toehold mediated strand displacement.

“To the best of our knowledge, this has never been seen in nature,” Lucks said. “We think the RNA has evolved to untie itself from knots because if knots persist, it can render the RNA nonfunctional. The structure is so essential to life that it had to evolve to find a way to get out of a knot.”

The study, “Computationally reconstructing cotranscriptional RNA folding pathways from experimental data reveals rearrangement of non-native folding intermediates,” was supported by the National Institutes of Health (award numbers T32GM083937, 1DP2GM110838 and GM120582), the National Science Foundation (award numbers MCB1651877 and 1914567) and the Searle Funds at The Chicago Community Trust.

Video: https://www.youtube.com/watch?v=2XTi9LG9NnU&feature=emb_logo

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Materials provided by Northwestern University. Original written by Amanda Morris. Note: Content may be edited for style and length.