Month: December 2024

Two 2 Tango

December 9, 2024

TWO 2 Tango

October 25, 2024

​​Chemistry faculty & graduate student duos prove that two minds are better than one.

 

Unraveling Bacterial Genomes

At the University of Utah's Department of Chemistry, faculty member Aaron Puri and graduate student Delaney Beals are pioneering research to decode bacterial genomes by understanding their natural environments. Their project, which began with Puri's pilot experiments during his postdoctoral fellowship, focuses on linking methanotroph phenotypes to genotypes using a spatially resolved model ecosystem.

Graduate student Delaney Beals and faculty member Aaron Puri

Puri, who started his research group in 2019, brings a diverse and impressive background to the project. With triple bachelor's degrees from the University of Chicago, a PhD in chemical and systems biology from Stanford University, and postdoctoral research at the University of Washington, Puri's expertise spans chemical tools for host-pathogen interactions and genetic tools for methane-oxidizing bacteria. Now a faculty member in the Henry Eyring Center for Cell & Genome Science, his work centers on the biological chemistry of bacteria that grow on one-carbon compounds like methane and methanol.

Beals, a fifth-year PhD candidate, contributes vital expertise in the chemical ecology of methane-oxidizing bacterial communities. Originally from North Carolina with a bachelor's from UNC Asheville, Beals was drawn to Puri's lab due to its focus on bacterially derived natural products. "By studying how a particular microbe behaves in the natural environment versus in the lab,” she explains, “we can better understand the ecological context in which various compounds are produced, and thus improve efforts to capitalize on a naturally occurring process."

Their research aims to uncover how bacteria use natural products to interact with each other and the environment. Puri elucidates the challenge: "We live in a time where we have virtually unlimited access to bacterial DNA (genome) sequences. But we have a hard time making sense of the vast majority of this information in the lab." To address this, the team grows bacteria in conditions closer to their natural environment, which has revealed exciting insights. Puri notes, "We can use relatively simple materials to uncover new bacterial behaviors in the lab in a reproducible manner."

The Puri-Beals collaboration has yielded significant findings, showing that bacterial behavior varies depending on their location within the model ecosystem. This research has potential applications in alternative energy, agriculture, and health by optimizing the use of microbes for various purposes. Their work not only advances our understanding of bacterial genetics but also paves the way for practical applications with far-reaching societal impacts.

As Puri emphasizes, "This work underscores that it is critical to think about the environment the bacterium of interest came from to understand what the genes in bacterial DNA are doing, since that is where they evolved." This approach promises to enhance our ability to harness microbes as sources for new natural products and to optimize their use in diverse applications.

Decoding Human Milk Oligosaccharides

In the aftermath of the 2022-2023 infant formula shortage, the research of Professor Gabe Nagy and graduate student Sanaz Habibi (they/their) has taken on newfound significance. Their project, focused on characterizing human milk oligosaccharides (HMOs), addresses crucial sugars in human milk that play a vital role in infant development.

Gabe Nagy and graduate student Sanaz Habibi

The complexity of HMOs presents a significant challenge, with potentially over 200 different compounds, yet authentic references are currently available for only about 30 of them. Nagy and Habibi are at the forefront of developing new analytical techniques to enhance HMO characterization, which could have profound implications for improving infant formula and understanding infant nutrition.

Habibi, who joined Nagy's lab in 2021, brings expertise in analytical chemistry and instrumentation from their undergraduate studies at Virginia Commonwealth University. Their research utilizes high-resolution cyclic ion mobility spectrometry-mass spectrometry (cIMS-MS) to analyze HMOs. Habibi explains their journey: "I became very interested in the cIMS-MS instrument that was being used in his lab, despite having little to no background in IMS or MS. I realized that Gabe's lab was the best fit for me to learn a different type of separation technique and increase my knowledge of mass spectrometry for studying an important class of carbohydrates."

Further elaborating on their innovative approach Nagy says, "We aim to develop advanced methods using ion mobility separations and mass spectrometry. These methods aim to decipher the structures of all possible HMOs, addressing the gap in understanding caused by the lack of comprehensive reference materials." This work involves constructing collision cross section databases, which provide numerical descriptions of the size, shape, and charge of ions—crucial for accurately identifying both known and unknown HMOs in real human milk samples.

The team's work is particularly timely, as Nagy points out: "The world of sugar analysis has lagged behind other fields by 10-20 years, and we believe that our lab could develop new tools in order to bridge this gap." The duo’s research not only contributes to solving immediate challenges in infant nutrition but also has broader implications for analytical chemistry.

Nagy and Habibi are optimistic about the wider applicability of their tools and methods. They envision their advancements being adopted by laboratories worldwide across various molecule classes. Habibi emphasizes the potential of their work "to enhance the comprehensive profiling of human milk using our developed methods."

This pioneering research has the potential to empower other disciplines such as biology and medicine by providing access to advanced analytical tools. As infant nutrition continues to be a critical area of study, the work of Nagy and Habibi stands at the forefront of efforts to improve our understanding and application of human milk components in infant formula and beyond.

By Julia McNulty and David Pace

2024 Clarivate’s Most Cited

December 9, 2024

Bill Anderegg, Highly Cited Researcher 2024

December 9, 2024
Above: William Anderegg at the One-U Responsible AI inaugural symposium in September. Courtesy of @The U.

Highly Cited Researchers have demonstrated significant and broad influence in their field(s) of research.

William Anderegg, associate professor in the School of Biological Sciences and director of the Wilkes Center for Climate Science and Policy has again been selected as one of Clarivate's Highly Cited Researchers for 2024. Each researcher selected has authored multiple Highly Cited Papers™ which rank in the top 1% by citations for their field(s) and publication year in the Web of Science™ over the past decade.

Citation activity, however, is not the sole selection indicator. This list, based on citation activity is then refined using qualitative analysis and expert judgment as the global analytics company observes for evidence of community-wide recognition from an international and wide-ranging network of citing authors.

Of the world’s population of scientists and social scientists, Highly Cited Researchers are 1 in 1,000.

“As the need for high-quality data from rigorously selected sources is becoming ever more important,"  says David Pendlebury, Head of Research Analysis at the Institute for Scientific Information at Clarivate, "we have adapted and responded to technological advances and shifts in the publishing landscape. Just as we have applied stringent standards and transparent selection criteria to identify trusted journals in the Web of Science™, we continue to refine our evaluation and selection policies for our annual Highly Cited Researchers™ program to address the challenges of an increasingly complex and polluted scholarly record.”

According to the Clarivate's website, "The Highly Cited Researchers 2024 list identifies and celebrates individuals who have demonstrated significant and broad influence in their fields of research. Through rigorous selection criteria and comprehensive analysis, we recognize researchers whose exceptional and community-wide contributions shape the future of science, technology and academia globally."

"This program also emphasizes our commitment to research integrity. Our evaluation and selection process continues to evolve with filters to address hyper-authorship, excessive self-citation, anomalous citation patterns and more, ensuring that recognized researchers meet the benchmarks we require for this program."

Exploring the "global landscape of top-tier research talent," they continue, "provides us with insights on global research and innovation trends."

This year Clarivate™ awarded 6,886 Highly Cited Researcher designations to 6,636 individuals. Some researchers have been recognized in more than one Essential Science Indicators™ (ESI) field, resulting in more designations than individual awardees. This analysis, which includes the distribution of designations across nations and institutions, reflects the impact of these 6,886 appearances, distributed across fields, in accordance with the size of each.

While the sole researcher from the College of Science this year to be honored with the designation, Anderegg, one of three at the University of Utah, was the only one at the U to appear in two categories, Plant & Animal Science and Environment & Ecology.

This table summarizes the number of researcher designations by field of research and the cross-field category.

One-U Responsible AI

William-Anderegg

Anderegg is also the executive committee member who leads the One-U Responsible AI’s environmental working group. The group’s members bring their diverse expertise to establish ethical policy, explore AI’s impact on society and the environment, and develop responsible methods for using AI to improve climate research.

“Our goal of this working group is to put together a vision and a mission about responsibly developing and using AI to address human environmental challenges across scales to promote resilience and foster sustainable development,” said Anderegg at the group's inaugural symposium this past September. “AI could have an enormous negative impact on the environment itself. There are direct impacts for the cost of running AI—the power and water needed to run the massive data centers, and the greenhouse gas emissions that result. Then there are indirect challenges—misinformation, polarization, and increasing demands on the power grid. At the same time, there are another set of opportunities in using AI to tackle the marginal problems in forecasting and grid rewarding systems.”

The working group’s vision is to utilize AI to bolster our resilience to climate change with collaboration, training, technology, and ethical governance.

“The University of Utah is set to engage in these two focal areas of developing sustainable AI—how we use AI in a manner that minimizes environmental impact and maximizes long-term sustainability? Then, how do we harness AI for environmental resilience challenges?” Anderegg noted.

This is the second year in a row that Anderegg has made the Highly Cited Researcher list. With his mentor, biology professor emeritus John Sperry, the two were honored in the 2023 cohort. The two of them worked closely together, publishing multiple papers over the course of about six years in the areas of plant hydrology and forest stress. Their research is an auspicious example of how, in the tradition of peer-reviewed research, scientists routinely stand on the shoulders of others to move forward human understanding.

You can link to selected publications by Bill Anderegg here. 

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AI: The Promise and Peril for the Planet

December 4, 2024

AI: The Promise and Peril for the Planet

Dec 04, 2024
Above: The AI image was generated using DALL·E.

For the past few decades, we have lived in the “Digital Age.” Now, we are stepping into a new one — the Age of AI.

While artificial intelligence (AI) has existed in primitive forms since the 1950s, it has now advanced to a readily accessible and ubiquitous state. Browser-based programs like ChatGPT are well-known, but they represent only a small portion of the scope, demands, capabilities and consequences of AI.

At its inaugural symposium last September at the University of Utah, the One-U Responsible AI Initiative invited over two hundred attendees, including researchers, university faculty, government officials, and industry leaders, to discuss the role and responsible usage of AI. Three key issues were addressed at the first panel of the symposium; the environmental impacts of AI, the dangers of AI-generated misinformation, and the application of AI for wildfire forecasting, an issue that poses challenges for the West’s electrical grid.

Resilience and sustainability

William Anderegg, director of the U-based Wilkes Center for Climate Science & Policy, is the executive committee member who leads the One-U RAI’s environmental working group. The group’s members bring their diverse expertise to establish ethical policy, explore AI’s impact on society and the environment, and develop responsible methods for using AI to improve climate research.

The working group’s vision is to utilize AI to bolster our resilience to climate change with collaboration, training, technology, and ethical governance.

AI for wildfire forecasting

Researchers, including Derek Mallia, research assistant professor of atmospheric sciences, have also utilized AI to forecast wildfires and its hazardous smoke.

“When you think of extreme weather, you think of hurricanes, tornadoes and so on. But one of the biggest causes of mortality is actually poor air quality,” said Mallia. “Wildfires cause a degradation in air quality during the summer, and these effects are becoming more widespread. We’re not just seeing smoke across the western U.S., but also in areas that traditionally don’t see a lot of wildfire smoke—parts of NewYork, for example.”

Read the full article by Ethan Hood in @TheU.

The intersection of science and aesthetics

December 4, 2024

The intersection of science and aesthetics

Dec 04, 2024

The work of recent chemistry graduate Uziel Gonzalez BS ‘24 was featured in the September 24 publication of C & E News feature “Chemistry in Pictures.” 

Uziel Gonzalez (BS ‘24)

Tom Richmond said for the C & E News “While purifying tert-butylmalononitrile, a useful starting material for the synthesis of organic electronic materials, University of Utah chemistry undergraduate Uziel Gonzalez discovered the molecule had made beautiful, fernlike crystals via room temperature sublimation. Though not suitable for structure determination by X-ray diffraction, which was the original goal, the crystals in the resulting 6 x 4 mm microscope image were suitable for framing. The acidic C–H bond of the malononitrile provides a useful handle to make new carbon-carbon bonds with highly fluorinated aromatics. 

Uziel Gonzalez is one of the 2024 Laya F. Kesner Award recipient. When he received the award, Professor Thomas Richmond noted, “Uziel was an outstanding student in Inorganic Chemistry, has been involved with the ACS student affiliate's group and even managed to make some new fluorocarbon molecules in my lab. Ultimately, he would like a career as an FBI Agent."  

The feature “showcases the beauty of chemistry, chemical engineering and related sciences” to the 150,000 readers of C&E News and beyond.  As noted in the article, an elegant leaf-like structure was formed upon sublimation of a volatile organic compound.  Although not suitable for crystallography, it was suitable for framing. 

This story was originally posted on @chem.utah.edu  where you can see other stunning images from Uziel Gonzalez 's collection.

The surprising role of CO₂ in cellular health

December 2, 2024

The surprising role of CO₂ in cellular health

Dec 02, 2024

The cells in our bodies are like bustling cities, running on an iron-powered system that uses hydrogen peroxide (H₂O₂) not just for cleaning up messes but also for sending critical signals.

Normally, this works fine, but under stress, such as inflammation or a burst of energy use, oxidative stress damages cells at the genetic level.

This is because iron and H₂O₂ react in what’s known as the Fenton reaction, producing hydroxyl radicals, destructive molecules that attack DNA and RNA indiscriminately. But there’s a catch. In the presence of carbon dioxide — that pesky gas disrupting global climate systems — our cells gain a secret weapon in the form of bicarbonate which helps keep pH levels balanced.

A team of University of Utah chemists has discovered that bicarbonate doesn’t just act as a pH buffer but also alters the Fenton reaction itself in cells. Instead of producing chaotic hydroxyl radicals, the reaction instead makes carbonate radicals, which affect DNA in a far less harmful way, according to Cynthia Burrows, a distinguished professor of chemistry and senior author of a study published this week in PNAS.

“So many diseases, so many conditions have oxidative stress as a component of disease. That would include many cancers, effectively all age-related diseases, a lot of neurological diseases,” Burrows said. “We’re trying to understand cells’ fundamental chemistry under oxidative stress. We have learned something about the protective effect of CO₂ that I think is really profound.”

Co-authors include Aaron Fleming, a research associate professor, and doctoral candidate Justin Dingman, both members of the Burrows Laboratory.

“Just like opening up a can of beer. You release the CO₂ when you take your cells out of the incubator. It’s like doing experiments with a day-old glass of beer. It’s pretty flat. It has lost the CO₂, its bicarbonate buffer,” Burrows said. “You no longer have the protection of CO₂ to modulate the iron-hydrogen peroxide reaction.”

She believes bicarbonate needs to be added to ensure reliable results from such experiments.

Read the full article by Brian Maffly in @TheU.

Exploring the Vulnerabilities of Endangered Birds

December 2, 2024

Exploring the Vulnerabilities of Endangered Birds

Dec 02, 2024
Above: Kyle Kittelberger( a graduate student in the School of Biological Sciences) at a bird banding station in northeastern Turkey holding a steppe buzzard. Courtesy Kyle Kittelberger.

Looking to inform the conservation of critically endangered bird species, University of Utah biologists completed an analysis identifying traits that correlate with all 216 bird extinctions since 1500.

Species most likely to go extinct sooner were endemic to islands, lacked the ability to fly, had larger bodies and sharply angled wings, and occupied ecologically specific niches, according to research published this month.

While some of these findings mirror previous research on extinct birds, they are the first to correlate bird traits with the timing of extinctions, said lead author Kyle Kittelberger, a graduate student in the School of Biological Sciences.

“I’ve been very interested in extinctions and understanding the species that we’ve lost and trying to get a sense of how we can use the past to better inform the present and future,” said Kittelberger, who is completing his dissertation on how the bodies and wings of certain species of migratory songbirds have changed in response to climate change.

Connecting bird traits with species extinction

His team’s analysis tapped into BirdBase, a dataset of ecological traits for the world’s 11,600+ bird species compiled by U biology professor Çağan Şekercioğlu and the Biodiversity and Conservation Ecology Lab at the U. The team simultaneously analyzed a broad range of biogeographical, ecological and life history traits previously associated with extinction and extinction risk for bird species that have gone extinct as well as those that lack recent confirmed sightings and have therefore disappeared.

One in eight species is in peril

This timing coincides with the rise of scientific observation, resulting in a systematic documentation of plant and animal life. It is also the time when European exploration took off, leading to the disruption of ecosystems around the globe as a result of colonization and introduced species.

Today, 1,314 bird species are at risk of extinction, according to the IUCN Red List of Threatened Species, or about 12% of the total.

Many species, such as the ‘Akikiki (Oreomystis bairdi), endemic to the Hawaiian island of Kauai, are so rare that they are functionally extinct. Kittelberger photographed the pictured ‘Akikiki, also called Kauai’s creeper, in the Alaka‘i Wilderness Preserve in 2022, when it was believed around 70 or so remained in the wild; today, only one individual remains.

As with many other Hawaiian bird species, the main threat to the ’Akikiki comes in the form of introduced species, principally malaria-carrying mosquitoes and habitat-wrecking livestock, according to Hawaii’s Division of Forestry and Wildlife.

Read the full article by Brian Maffly in @TheU.