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Air Quality

New Computer Language Unlocks Hidden Pollutants in Environmental Data

Biologists and chemists have a new programming language to uncover previously unknown environmental pollutants at breakneck speed — without requiring them to code.

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New Computer Language Unlocks Hidden Pollutants in Environmental Data

In a breakthrough for environmental science, researchers at UC Riverside have developed a programming language called Mass Query Language (MassQL) that enables biologists and chemists to quickly identify previously unknown pollutants in massive chemical datasets. This innovative tool has already helped scientists discover toxic compounds hidden in plain sight.

The power of MassQL lies in its ability to function like a search engine for mass spectrometry data, which is akin to a chemical fingerprint. By making it easier to search these vast datasets, the language allows researchers to find patterns that would otherwise require advanced programming skills. This has significant implications for environmental science, as scientists can now quickly identify pollutants in water, air, and other samples.

Developed by Mingxun Wang, an assistant professor of computer science at UC Riverside, MassQL was created to empower chemists and biologists without extensive coding experience to mine their data exactly how they want. This user-friendly approach has the potential to revolutionize environmental research, enabling scientists to quickly identify pollutants and develop strategies for removal.

One notable example of MassQL’s effectiveness is its use by Nina Zhao, a UCR postdoctoral student now at UC San Diego. She employed the language to sift through the entire world’s mass spectrometry data on water samples, searching for organophosphate esters – compounds commonly found in flame retardants. The results were staggering: MassQL pulled out thousands of measurements, including some chemicals that have not been previously described or catalogued.

These findings highlight the importance of MassQL in environmental science. By providing a powerful tool for identifying pollutants, researchers can now develop strategies to address these toxic compounds and protect human and animal health.

MassQL’s development was made possible by a collaborative effort involving over 70 scientists from various fields. This consensus-driven approach ensured that the language would be useful across multiple disciplines and real-life situations.

The potential applications of MassQL are vast, ranging from detecting fatty acids as markers of alcohol poisoning to identifying new drugs to combat antibiotic resistance. The research team has demonstrated the effectiveness of the language in a variety of scenarios, including finding forever chemicals on playgrounds.

As Wang notes, “I wanted to create one language that could handle multiple kinds of queries. And now we have. I’m excited to hear about the discoveries that could come from this.”

With MassQL, researchers can now quickly identify pollutants and develop strategies for removal, paving the way for a cleaner, healthier environment for all.

Air Quality

“Visualizing the Rotten Egg: Scientists Use Cryo-EM to Reveal the 3D Structure of Sulfite Reductase”

Most people have witnessed — or rather smelled — when a protein enzyme called sulfite reductase works its magic. This enzyme catalyzes the chemical reduction of sulfite to hydrogen sulfide. Hydrogen sulfide is the rotten egg smell that can occur when organic matter decays and is frequently associated with sewage treatment facilities and landfills. But scientists have not been able to capture a visual image of the enzyme’s structure until now, thus limiting their full understanding of how it works.

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The ability to visualize complex chemical reactions has long been a holy grail for scientists. For one particularly pungent protein enzyme called sulfite reductase, this dream has finally become a reality, thanks to the work of Florida State University Professor Elizabeth Stroupe and her former doctoral student Behrouz Ghazi Esfahani.

Sulfite reductase is an enzyme that catalyzes the reduction of sulfite to hydrogen sulfide, which is infamous for its “rotten egg” smell. This reaction occurs in various natural environments, from fruit and vegetable decomposition to sewage treatment facilities and landfills. However, despite its importance, scientists had been unable to capture a clear visual image of the enzyme’s structure – until now.

Using an advanced technique called cryo-electron microscopy (cryo-EM), Stroupe and Ghazi Esfahani were able to visualize the 3D structure of sulfite reductase in unprecedented detail. Cryo-EM allows scientists to capture images of chemical reactions as they occur, providing the necessary data to reconstruct the complex molecular structures.

The resulting image is a striking representation of the protein’s intricate arrangement of atoms and electron transfer mechanisms. Stroupe describes it as an “octopus with four yo-yos” due to its flexibility and dynamic nature.

This breakthrough has significant implications for scientists, particularly in understanding how to control or manipulate chemical reactions – a process crucial for drug manufacturers and industry. As Ghazi Esfahani notes, the research also has environmental implications, such as understanding how bacteria use sulfur as an energy source.

While this achievement marks a major step forward in understanding sulfite reductase, there are still unanswered questions about its function as part of larger protein assemblies and how similar enzymes work in other organisms – like the pathogen that causes tuberculosis. Stroupe’s lab is continuing to explore these mysteries, shedding more light on the intricate chemistry of sulfur metabolism.

In conclusion, the ability to visualize complex chemical reactions has finally been achieved for sulfite reductase, thanks to the innovative use of cryo-EM by Stroupe and Ghazi Esfahani. This breakthrough opens doors to new understanding and manipulation of chemical reactions – with far-reaching implications for science, industry, and the environment.

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Air Pollution

Uncovering the Hidden Dangers of Wildfire Smoke

With wildfires increasing in frequency, severity, and size in the Western U.S., researchers are determined to better understand how smoke impacts air quality, public health, and even the weather. As fires burn, they release enormous amounts of aerosols — the vaporized remains of burning trees and homes that enter the atmosphere and the air we breathe. Now, a new study dissects these aerosols and gases to pinpoint their potential effects on our health as well as the planet’s short and long-term weather.

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Wildfires have become an increasing threat in the Western United States, with devastating effects on both public health and the environment. As these fires rage, they release enormous amounts of aerosols into the atmosphere, which can travel far and wide, impacting air quality and human health. A recent study, published in Environmental Science: Atmospheres, has shed light on the alarming consequences of wildfire smoke on air quality and the planet’s short-term weather.

The research, led by scientists Siying Lu and Andrey Khlystov from the Desert Research Institute (DRI), monitored air quality in Reno, Nevada over a 19-month period between 2017 and 2020. During this time, more than 106 wildfires impacted the city’s air, with smoke accounting for up to 65% of PM2.5 concentrations and 26% of carbon monoxide levels.

The findings reveal that fine aerosols (PM2.5), which can travel deep into lungs, increased significantly during smoky days. These particles are produced when trees and homes burn, releasing soot and other pollutants into the air. The data also showed that larger aerosols can promote cloud formation and duration by acting as nuclei for water vapor to condense around.

Furthermore, the study found higher concentrations of carbon monoxide present in Reno’s air during smoky days. This gas can reduce the ability of blood to carry oxygen to the brain and other organs. In contrast, levels of nitrogen oxides and ozone remained relatively stable during both smoky and average days.

The research team used a combination of equipment on DRI’s roof and data from a downtown Reno EPA air monitoring station to collect hourly concentrations of PM2.5, ozone, carbon monoxide, and other air pollutants. They also employed satellite images and fire location information from NASA and NOAA to verify when air pollution was caused by wildfire smoke.

The implications of this study are far-reaching. The findings suggest that wildfires can have a significant impact on local air quality, with potential effects on public health and the environment. As wildfires continue to increase in frequency and severity, it is essential to understand their impact on air quality and develop strategies to mitigate these effects.

In conclusion, the study highlights the importance of monitoring air quality during smoky days and provides valuable insights into the consequences of wildfire smoke on human health and the planet’s short-term weather. As we continue to face the challenges posed by wildfires, it is crucial that we prioritize air quality research and public health messaging to ensure a safer and healthier environment for all.

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Air Pollution

Revolutionizing Air Pollution Combat with Rapid Simulations

A pioneering method to simulate how microscopic particles move through the air could boost efforts to combat air pollution, a study suggests.

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Rapid simulations of toxic particles could aid air pollution fight by providing more precise ways of monitoring air quality and predicting how these harmful substances move through the air. Researchers have developed a new computer modeling approach that significantly improves the accuracy and efficiency of simulating nanoparticles’ behavior in the air.

These tiny particles, found in exhaust fumes, wildfire smoke, and other airborne pollutants, are linked to serious health conditions such as stroke, heart disease, and cancer. Predicting how they move is notoriously difficult, making it challenging to develop effective strategies for mitigating their impact.

The new method allows researchers to calculate a key factor governing how particles travel – known as the drag force – up to 4,000 times faster than existing techniques. This breakthrough was made possible by creating a mathematical solution based on how air disturbances caused by nanoparticles fade with distance.

By applying this approach to simulations, researchers can zoom in much closer to particles without compromising accuracy. This differs from current methods, which involve simulating vast regions of surrounding air to mimic undisturbed airflow and require far more computing power.

The new approach could help better predict how these particles will behave inside the body, potentially aiding the development of improved air pollution monitoring tools. It could also inform the design of nanoparticle-based technologies, such as lab-made particles for targeted drug delivery.

The study, published in the Journal of Computational Physics, was supported by the Engineering and Physical Sciences Research Council (EPSRC). Lead author Dr Giorgos Tatsios, from the University of Edinburgh’s School of Engineering, said: “Our method allows us to simulate their behavior in complex flows far more efficiently, which is crucial for understanding where they go and how to mitigate their effects.”

Professor Duncan Lockerby, from the University of Warwick’s School of Engineering, added: “This approach could unlock new levels of accuracy in modeling how toxic particles move through the air – from city streets to human lungs – as well as how they behave in advanced sensors and cleanroom environments.”

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