Tuesday, May 16, 2023

New study reveals widespread presence of environmental DNA in the sky, including allergens and pathogens


Peer-Reviewed Publication

PEERJ

Kimberly L. Metris 

IMAGE: AUTHOR KIMBERLY L. METRIS view more 

CREDIT: CREDIT: KIMBERLY L. METRIS

Recently published in PeerJ Life and Environment, researchers successfully use aircraft surveys with novel instrumentation to capture airborne nucleic acids and probe biodiversity in the atmosphere, uncovering surprising findings.

[Clemson, May 2023] - A groundbreaking research article titled "Aircraft Surveys for Air eDNA: Probing Biodiversity in the Sky" unveils a revolutionary approach to studying genetic material in the atmosphere. Scientists have developed a durable and sterilizable probe and supporting system to capture air environmental nucleic acids (eDNA) with full-flow filtration and a high-integrity chamber.

Using this innovative probe, the research team aerially mapped environmental DNA by employing a standardized and scalable flight pattern using light aircraft. The aim of the study was to collect bioaerosols, which are aerosolized biological matter, from a range of organisms at various altitudes above major emissions sources, and sequence them for identification.

This work began with an idea to explore, recounts Dr. Kimberly Metris, a faculty member at Clemson University and lead investigator. “I’m a molecular ecologist who works on diverse wild species, from bacteria to bluehead chub to African buffalo. I also fly airplanes, and one summer while I was flying skydivers I had a lot of time to think while climbing to jump run altitude. Meteorologically speaking, the conditions were great—10 statute miles visibility, rather calm winds, a rather nice day at the office—but this was during a Saharan dust storm and there was particulate matter visible outside, everywhere. An odd feeling, but it gets the wheels spinning.” What precisely is in the air that we can’t see, biologically speaking? This is what she and her coauthor set out to explore. “And now we are pushing the boundaries of what we thought we knew about the sky. The sky is not a limit, it is a treasure trove!”

The findings of the study are extraordinary. Through the use of their sampling probe and high throughput metagenomic sequencing, the researchers discovered the widespread presence of prokaryotic and eukaryotic eDNA in the atmosphere, reaching thousands of meters into the planetary boundary layer in the southeastern US. Notably, the study detected chicken, cow, and human eDNA at all altitudes flown, including an astonishing 8,500 feet above the ground. 

The researchers identified various common plant-based allergens from grasses, weeds, and trees, as well as from species not typically reported in the air, such as garlic, revealing a diverse array of airborne genetic material.

They also discovered pathogenic bacteria and bacteria previously unknown to be present in the atmosphere but found in other extreme environments such as deep-sea sediment.

The sterilizable and reusable sampling probe employed in the study proved to be reliable, limiting sample loss and contamination while filtering genetic material directly from the air. This groundbreaking work enables the mapping of genetic material from potentially all species using aircraft or other flight or stationary methods and connects aerobiome profiles to ground level processes, providing valuable insight into the presence and diversity of genetic material found in the air we breathe.

The implications of this research are far-reaching, with applications in biodiversity, wildlife ecology, biodefense, and pathogen and allergen monitoring. The study's high-throughput amplicon sequencing of DNA from bacteria, vertebrates, and plants demonstrates that bioaerosols can originate from natural processes, such as wind-induced pollination in fields and forests, and human-mediated activities, namely production agriculture, wastewater treatment, and industry practices including hospital waste decontamination.

Airborne DNA profiles detected in the atmosphere reflect surface emissions, allergens, and potential ice and cloud condensation nuclei. The effectiveness of aerosolization is believed to influence the air DNA profiles detected at altitude, suggesting the incorporation of indices of lift and air mass characteristics for standardizing air eDNA surveys. Additionally, the researchers recommend standardized reporting of real-time, empirical flow rates, total air volumes, and sampler type(s) used, as they have crucially different operating airflow requirements.

Biological material in the form of eDNA/RNA can be lifted, carried, and deposited elsewhere by atmospheric mixing, lifting, and buoyancy, potentially leading to biological consequences such as gene flow and hybridization processes. The atmosphere is powerful and essential to life--The discovery of airborne vertebrate-derived eDNA floating thousands of meters from its origin at Earth’s surface suggests that the atmosphere contains biodiverse material, and has implications for biomonitoring and disease surveillance. Scientists can gain insight into the presence, abundance, and distribution of species in an area, providing valuable evidence for identifying individuals or tracing their movements, or monitoring production agriculture from the atmosphere. 

This groundbreaking study paves the way for a deeper understanding of airborne genetic material and its implications for various fields of study. By unlocking the secrets of the sky, scientists are gaining new insights into our environment, the air we breathe, and intricate connections among biodiversity on Earth.

For more information or to access the full research article: 

Métris KL, Métris J. Aircraft surveys for air eDNA: probing biodiversity in the sky. PeerJ. 2023 Apr 14;11:e15171. doi: 10.7717/peerj.15171. PMID: 37077310; PMCID: PMC10108859.  https://peerj.com/articles/15171/ 

See the Video Abstract:   https://youtu.be/9lNVLedumsA

Summer Flight Metris

Kimberly L. Metris & Husband/Co-Author Jérémy Métris

Kimberly L. Metris

CREDIT

Credit: Kimberly L. Metris

Tetris reveals how people respond to unfair AI

Peer-Reviewed Publication

CORNELL UNIVERSITY

ITHACA, N.Y. – A Cornell University-led experiment in which two people play a modified version of Tetris revealed that players who get fewer turns perceived the other player as less likable, regardless of whether a person or an algorithm allocated the turns.

Most studies on algorithmic fairness focus on the algorithm or the decision itself, but researchers sought to explore the relationships among the people affected by the decisions.

“We are starting to see a lot of situations in which AI makes decisions on how resources should be distributed among people,” said Malte Jung, associate professor of information science, whose group conducted the study. “We want to understand how that influences the way people perceive one another and behave towards each other. We see more and more evidence that machines mess with the way we interact with each other.”

In an earlier study, a robot chose which person to give a block to and studied the reactions of each individual to the machine’s allocation decisions.

“We noticed that every time the robot seemed to prefer one person, the other one got upset,” said Jung. “We wanted to study this further, because we thought that, as machines making decisions becomes more a part of the world – whether it be a robot or an algorithm – how does that make a person feel?”

Using open-source software, Houston Claure – the study’s first author and postdoctoral researcher at Yale University – developed a two-player version of Tetris, in which players manipulate falling geometric blocks in order to stack them without leaving gaps before the blocks pile to the top of the screen. Claure’s version, Co-Tetris, allows two people (one at a time) to work together to complete each round.

An “allocator” – either human or AI, which was conveyed to the players – determines which player takes each turn. Jung and Claure devised their experiment so that players would have either 90% of the turns (the “more” condition), 10% (“less”) or 50% (“equal”).

The researchers found, predictably, that those who received fewer turns were acutely aware that their partner got significantly more. But they were surprised to find that feelings about it were largely the same regardless of whether a human or an AI was doing the allocating.

The effect of these decisions is what the researchers have termed “machine allocation behavior” – similar to the established phenomenon of “resource allocation behavior,” the observable behavior people exhibit based on allocation decisions. Jung said machine allocation behavior is “the concept that there is this unique behavior that results from a machine making a decision about how something gets allocated.”

The researchers also found that fairness didn’t automatically lead to better game play and performance. In fact, equal allocation of turns led, on average, to a worse score than unequal allocation.

“If a strong player receives most of the blocks,” Claure said, “the team is going to do better. And if one person gets 90%, eventually they’ll get better at it than if two average players split the blocks.”

The Social Consequences of Machine Allocation Behavior: Fairness, Interpersonal Perceptions and Performance,” published in Computers in Human Behavior.

For additional information, see this Cornell Chronicle story

Cornell University has dedicated television and audio studios available for media interviews.

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Chemists unravel reaction mechanism for clean energy catalyst

Pulse radiolysis experiments at Brookhaven Lab revealed rapid reactivity that has never been observed before

Peer-Reviewed Publication

DOE/BROOKHAVEN NATIONAL LABORATOry

Pulse Radiolysis Lab 

IMAGE: DMITRY POLYANSKY (LEFT) AND DAVID GRILLS IN THE PULSE RADIOLYSIS LAB WHERE THE RESEARCH WAS CONDUCTED. HERE, GRILLS PROGRAMS A SYRINGE PUMP THAT DELIVERS THE CATALYST TO THE RADIOLYSIS CELL. POLYANSKY ADJUSTS THE RADIOLYSIS CELL INSIDE A WHITE INSULATED COMPARTMENT. view more 

CREDIT: BROOKHAVEN NATIONAL LABORATORY

UPTON, NY—Hydrogen, the simplest element on Earth, is a clean fuel that could revolutionize the energy industry. Accessing hydrogen, however, is not a simple or clean process at all. Pure hydrogen is extremely rare in nature, and practical methods to produce it currently rely on fossil fuels. But if scientists find the right chemical catalyst, one that can split the hydrogen and oxygen in water molecules apart, pure hydrogen could be produced from renewable energy sources such as solar power.

Now, scientists are one step closer to finding that catalyst. Chemists at the University of Kansas and the U.S. Department of Energy’s (DOE) Brookhaven National Laboratory have unraveled the entire reaction mechanism for a key class of water-splitting catalysts. Their work was published today in Proceedings of the National Academy of Sciences (PNAS).

“It’s very rare that you can get a complete understanding of a full catalytic cycle,” said Brookhaven chemist Dmitry Polyansky, a co-author of the paper. “These reactions go through many steps, some of which are very fast and cannot be easily observed.”

Rapid intermediate steps make it difficult for scientists to decipher exactly where, when, and how the most important parts of a catalytic reaction occur—and therefore, if the catalyst is suitable for large-scale applications.

At the University of Kansas, associate professor James Blakemore was researching possible candidates when he noticed something unusual about one catalyst in particular. This catalyst, called a pentamethylcyclopentadienyl rhodium complex, or Cp*Rh complex, was demonstrating reactivity in an area where molecules are usually stable.

“Metal complexes—molecules that contain a metal center surrounded by an organic scaffold—are important for their ability to catalyze otherwise difficult reactions,” said Blakemore, who is also a co-author of the paper. “Typically, reactivity happens directly at the metal center, but in our system of interest, the ligand scaffold appeared to directly take part in the chemistry.”

So, what exactly was reacting with the ligand? Was the team really observing an active step in the reaction mechanism or just an undesirable side reaction? How stable were the intermediate products that were produced? To answer questions like these, Blakemore collaborated with chemists at Brookhaven Lab to use a specialized research technique called pulse radiolysis.

Pulse radiolysis harnesses the power of particle accelerators to isolate rapid, hard-to-observe steps within a catalytic cycle. Brookhaven’s Accelerator Center for Energy Research (ACER) is one of only two locations in the United States where this technique can be conducted, thanks to the Lab’s advanced particle accelerator complex.

“We accelerate electrons, which carry significant energy, to very high velocities,” said Brookhaven chemist David Grills, another co-author of the paper. “When these electrons pass through the chemical solution we’re studying, they ionize the solvent molecules, generating charged species that are intercepted by the catalyst molecules, which rapidly alter in structure. We then use time-resolved spectroscopy tools to monitor the chemical reactivity after this rapid change occurs.”

Spectroscopic studies provide spectral data, which can be thought of as the fingerprints of a molecule’s structure. By comparing these signatures to known structures, scientists can decipher physical and electronic changes within the short-lived intermediate products of catalytic reactions.

“Pulse radiolysis allows us to single out one step and look at it on a very short timescale,” Polyansky said. “The instrumentation we used can resolve events at one millionth to one billionth of a second.”

By combining pulse radiolysis and time-resolved spectroscopy with more common electrochemistry and stopped-flow techniques, the team was able to decipher every step of the complex catalytic cycle, including the details of the unusual reactivity occurring at the ligand scaffold.

“One of the most remarkable features of this catalytic cycle was direct involvement of the ligands,” Grills said. “Often, this area of the molecule is just a spectator, but we observed reactivity within the ligands that had not yet been proven for this class of compounds. We were able to show that a hydride group, an intermediate product of the reaction, jumped onto the Cp* ligand. This proved that the Cp* ligand was an active part of the reaction mechanism.”

Capturing these precise chemical details will make it significantly easier for scientists to design more efficient, stable, and cost-effective catalysts for producing pure hydrogen.

The researchers also hope their findings will provide clues for deciphering reaction mechanisms for other classes of catalysts.

“In chemistry, findings like ours can often be generalized and applied to optimize other systems, but obtaining critical details on rapid reactivity, like we have done here, is a key step,” Blakemore said. “We hope other research groups will take our insights and build on them, perhaps by using ligand-promoted reactivity to build better catalysts.”

This study is just one set of experiments among a large body of clean energy work that scientists at the University of Kansas and Brookhaven Lab are conducting.

“We’re building the fundamental chemical knowledge that will, one day, help scientists design the optimal catalyst for producing pure hydrogen,” Polyansky said.

This work was supported by the National Science Foundation and the DOE Office of Science.

Brookhaven National Laboratory is supported by the Office of Science of the U.S. Department of Energy. The Office of Science is the single largest supporter of basic research in the physical sciences in the United States and is working to address some of the most pressing challenges of our time. For more information, visit science.energy.gov.

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