Research

Bacteriophages: Nature’s bacterial killers

June 18, 2024

Bacteriophages : Nature's bacterial killers

June 14, 2024
Above: Talia Karasov

Bacteriophages, viruses that attack and destroy bacteria, are everywhere in the natural world where they play a vital role in regulating microbe populations in ways that are not yet well understood.

New research led by the University of Utah and University College London (UCL) has found that plant bacterial pathogens are able to repurpose elements of their own bacteriophages, or phages, to wipe out competing microbes. These surprise findings suggest such phage-derived elements could someday be harnessed as an alternative to antibiotics, according to Talia Karasov, an assistant professor in the U’s School of Biological Sciences.

This result was hardly what she expected to find when she embarked on this research with an international team of scientists. Microbial pathogens are all around, but only a fraction of the time do they sicken humans, other animals or plants, according to Karasov, whose primary research interest is in interactions between plants and microbial pathogens. The Karasov lab is seeking to understand the factors that lead to sickness and epidemics versus keeping the pathogens in check.

“We see that no single lineage of bacteria can dominate. We wondered whether the phages, the pathogens of our bacterial pathogens, could prevent single lineages from spreading – maybe phages were killing some strains and not others. That’s where our study started, but that’s not where it ended up,” Karasov said. “We looked in the genomes of plant bacterial pathogens to see which phages were infecting them. But it wasn’t the phage we found that was interesting. The bacteria had taken a phage and repurposed it for warfare with other bacteria, now using it to kill competing bacteria.”

A thale cress specimen collected in 1866 in Germany and preserved in a herbarium in Tubingen. Credit: Burbano lab, University College London.

Mining herbarium specimens for their microbial DNA

Burbano has pioneered the use of herbarium specimens to explore the evolution of plants and their microbial pathogens. His lab sequences the genomes of both host plants and those of the microbes associated with the plant at the time of collection more than a century ago.

For the phage research, Burbano analyzed historical specimens of Arabidopsis thaliana, a plant from the mustard family commonly called thale cress, collected in southwestern Germany, comparing them and the microbes they harbored to plants growing today in the same part of Germany. Lead author Talia Backman wonders if tailocins could help solve the impending crisis in antibiotic resistance seen in harmful bacteria that infect humans.

“We as a society are in dire need of new antibiotics, and tailocins have potential as new antimicrobial treatments,” said Backman, a graduate student in the Karasov lab. “While tailocins have been found previously in other bacterial genomes, and have been studied in lab settings, their impact and evolution in wild bacterial populations was not known. The fact that we found that these wild plant pathogens all have tailocins and these tailocins are evolving to kill neighboring bacteria shows how significant they may be in nature.”

Discover the full story behind bacteriophages and their antibiotic potential by Brian Maffly at @The U. More on this story at earth.com.

Championing Representation & Advocacy in Healthcare

June 12, 2024

Championing Representation & Advocacy in Healthcare

June 12, 2024
Above: Kimberly Gamarra

Kimberly Gamarra, a graduate of the University of Utah’s School of Biological Sciences, was recently accepted to the U’s Spencer Fox Eccles School of Medicine. While Gamarra has been successful in her pursuit of her goals to work in the medical field,  her journey has been fraught with challenges.

 

Participating in the English as a Second Language (ESL) Express Registration event at SLCC as a peer mentor leader.

Gamarra’s exciting educational milestone boils down to personal triumph, mentorship, and resilience. Navigating her family’s adopted home of the U.S., she began her undergraduate studies early during high school, completing concurrent enrollment classes through Salt Lake Community College before finishing her degree at the U.

In the university setting Gamarra found guidance and community through the Refugees Exploring the Foundations of Undergraduate Education In Science (REFUGES) Bridge Program (REFUGES), designed to support students with tools for college and career readiness. Founded by physics faculty member Tino Nyawelo, the program proved to be a pivotal support system for Gamarra. “From the start, I've always wanted to do medicine," she reflects. “That was my goal. And so having Tino’s program, there was a huge help in acclimating to the new campus and getting to know faculty, staff, and other students. And it really helped me network really well from the start, and feel more comfortable.” Through the program, she not only found her footing in the academic landscape but also discovered her capacity for leadership and mentorship, being able to give back as a science and mathematics tutor.

Gamarra is quick to open up about her upbringing and how her family’s challenges during her childhood impacted her present journey: “My parents are immigrants from Peru and their transition to the U.S, especially navigating healthcare, was a challenge. I suffered from a brain tumor as a child, so a big motivation for them moving to the U.S. was to make sure I received the best treatment possible. This whole process opened my eyes to the strengths and struggles of our current healthcare system, and ways I can help make it better.” 

Drawing from her family's experiences, Gamarra is prepared to think beyond traditional healthcare expectations by providing care for her future patients on more than just a physical level, emphasizing the importance of equity, inclusion, and community on health and well-being. She has been involved in several projects that provide guidance to Latinx families about free health-related resources and volunteers her time as a Spanish and English translator. Her interactions with patients, families and mentors are what fueled her determination to continue pursuing medicine. She is particularly interested in helping foster a greater sense of trust between physicians and their patients, which she sees as key to success. 

At the Mitaka Picture Book initiative in Japan, reading Spanish to Japanese children and their families.

Transcending cultural and linguistic barriers

With an interest in global health and social justice, Gamarra envisions a career that transcends borders and barriers. In her final year at the U, she attended the Oxford Consortium for Human Rights based in the UK, where she drew a strong parallel between health and human rights. With her group she presented on climate refugees and the barriers to accessing healthcare, as well as discussing health from a cultural point of view considering the existence of traditional medicine. Upon returning to Utah, she helped create the podcast RadioNatura, opening up these discussions to a global audience. This commitment to removing cultural and linguistic barriers defines Gamarra's vision for her future in medicine. 

With a degree in biology and a minor in pediatric clinical research, Gamarra will begin medical school this August with an interest in pediatrics. She hopes to expand on her expertise and knowledge: “Presenting different studies that doctors in the University of Utah health community are doing really opened my eyes to the vulnerability of children,” she states. “I see the field of pediatrics as a promising one because I can have a long-term impact and build strong relationships with families, providing comprehensive care that considers the well-being of both the child and the family unit.” 

‘Doing More’ is a subjective term

Though Gamarra has experienced many ups and downs on her path, she has always remained focused on her goals. “I would be lying if I said this whole journey was smooth,” she admits. “It was actually extremely rocky. There were times I doubted myself because there was always a thought in my mind that I could be doing more. But I realized that ‘more’ is subjective. It is less about accumulating experiences and more about the reflections and growth that comes out of those experiences.” While Gamarra admits that she once admired people with busy calendars, she no longer glamorizes it: “Being ‘busy’ without time to self-reflect is not the path I want to take in my life.”

As she prepares to embark on the next chapter of her life — medical school — Gamarra carries with her the support of those who helped her along the way. “I just focus on the people that were there for me, and I think that because of the REFUGES Program, Tino is a wonderful person that was there for me. He was someone that saw me through this journey, and that is still with me through this next journey, which I value a lot.” 

In Kimberly Gamarra, the U’s School of Medicine has found more than just a future doctor, but an individual who will undoubtedly create change and strengthen communities wherever she goes.

By Julia St. Andre

Finding new ant species in a SLC backyard

June 5, 2024

Utah’s ant man found a new species in his backyard

June 5, 2024
Above: John "Jack" Longino, in the tropics

University of Utah professor Jack Longino’s research mainly takes him to Central America, but on the weekend he collects and examines the diverse ant species around him.

Jack Longino likes to spend his weekends close to the ground. He often wears a vest that holds fifteen tiny vials filled with alcohol and a backpack with about 100 more.

“People look at me and they think I’ve got a bullet belt,” he said.

Longino uses the vials to carefully collect and preserve ants. “I end up with thousands of tiny little bottles of alcohol with dead ants in them,” he said.

He has traveled and documented ants extensively in Central America, but Longino is “interested in ant diversity anywhere I am.”

Luckily, ants are just about everywhere and each zone — from the marshes of the Great Salt Lake to high elevation Alta to the West Desert — has its own set of species.

In 2018 Longino was hanging out in the backyard of his Salt Lake City home when he noticed an unusual group of ants normally found in tropical habitats. Very few of that particular species were recorded in the Western U.S. At first he assumed they had come from Southern Arizona, perhaps hitched a ride on potting soil.

Read the full article by reporter Sofia Jeremias in the Salt Lake Tribune. (Pay wall)

A Tale of Two Worms: Advancing Epigenetics

June 4, 2024

A Tale of Two Worms : Advancing Epigenetics

June 4, 2024
Above: Immunofluorescence in round worm. Credit: Audrey Brown

Why an important epigenetic gene is missing in some species of roundworm.


by Audrey Brown
Graduate Student, School of Biological Sciences

Have you ever wondered how a cell knows whether it’s supposed to be skin or muscle? Or philosophized about “nature vs. nurture,” that is, how contributions from both genetics and the environment influence physical phenotypes? Epigenetics, a relatively new field in biology, helps explain the mechanistic basis for this phenomenon—and is the field I have chosen to dedicate my doctoral studies at the University of Utah.

Audrey Brown

I sometimes find the easiest way to describe epigenetics is using a metaphor. Imagine that the DNA within a cell is an instruction manual. It contains all the instructions necessary for cellular functions — but this manual can also be modified. Epigenetic modifications (“epi” meaning “on top of”) are like “sticky-notes,” a set of additional instructions on top of the manual. These notes contain directions like “make more of this gene here” or “turn this gene off completely.” In reality, these notes take the form of chemical tags added to the DNA itself or to proteins associated with the DNA. Scientists like myself and my colleagues in Michael Werner’s lab at the School of Biological Sciences are trying to understand what type of information each of these modifications encodes, and how the set of modifications is changed by external environmental factors.

I recently co-authored a paper in Genetics addressing this last point. For this study, we created and compared lists of all the epigenetic genes present in these two worms. For the most part they contained a similar repertoire of epigenetic genes, yet we found one striking difference: P. pacificus is missing an epigenetic protein complex called PRC2. This was a surprising result since PRC2 is one of the most conserved epigenetic protein complexes, and is essential for various cellular functions, including cell differentiation and gene repression. So how is P. pacificus able to survive without it? We found one clue with the help of Ofer Rog’s lab at the U. We were able to detect the enzymatic output of the PRC2 complex (i.e. the specific “sticky-note” it writes), which led us to conclude that a different, yet unknown enzyme has taken over the function of PRC2 in P. pacificus.

Read more of Audrey Brown's article about these advancements in epigenetics in @The U.

Breakthrough in Geothermal Energy at Utah FORGE

June 3, 2024

Breakthrough in Geothermal Energy
at Utah FORGE

June 3, 2024
Above: The Utah FORGE site near Milford, Utah. PHOTO CREDIT: ERIC LARSON, FLASH POINT SLC.

In $218 million DOE-funded research project, University of Utah scientists aim to make enhanced geothermal a key part of world's energy portfolio.

A major University of Utah-led geothermal research project, funded by the U.S. Department of Energy (DOE), achieved a critical breakthrough in April after hydraulically stimulating and circulating water through heated rock formations a mile and a half beneath its drill site in the Utah desert and bringing hot water to the surface. The test results are seen as an important step forward in the search for new ways to use Earth’s subsurface heat to produce hot water for generating emissions-free electricity. The successful well stimulations and a nine-hour circulation test were the fruits of years of planning and data analysis at the Utah FORGE facility near Milford, 175 miles southwest of Salt Lake City.

More than two-thirds of the water that was injected underground and pushed through the fractured formation—acquiring heat on the way—was extracted from a second well, offering proof that enhanced geothermal systems (EGS) technology could be viable, according to John McLennan, a co-principal investigator on the project formally known as the Utah Frontier Observatory for Research in Geothermal Energy, or Utah FORGE.

“Nine hours is enough to prove that you have a connection and that you’re producing heat,” said McLennan, a U professor of chemical engineering. “It really is a Eureka moment. It’s been 60 years coming, and so this actually is significant.”

Kris Pankow, associate director of the U of U Seismograph Stations

Utah FORGE is a $218 million research project, involving numerous institutions and industry partners, funded by a DOE grant to the U’s Energy & Geoscience Institute. The project aims to develop and de-risk new geothermal technologies that could potentially be deployed all over the world, not just where conventional geothermal plants are sited.

For this recent test, FORGE personnel and industry specialists directionally drilled two boreholes—one for injecting water underground and the other for extracting it. The injection well is 10,897 feet long and drops to a depth of 8,559 feet below the surface. “We speculate, and we’ll see this in the 30-day test, that as we fill the fracture system back up, this number is going to get to where I’m suspecting it’s 85 to 90% efficiency,” McLennan said.

Equally promising was the absence of any noticeable ground shaking associated with the stimulations and circulation test. U seismologists led by geology professor Kris Pankow, associate director of the U of U Seismograph Stations, are overseeing an extensive network of seismometers to document ground movement associated with the project.

Discover more about this Breakthrough by visiting the full article by Brian Maffly at @The U.

Tapping coal mines for rare-earth materials

May 23, 2024

Tapping coal mines for rare-earth materials

May 23, 2024
Above: Michael Vanden Berg, a geologist with the Utah Geological Survey, examines a coal outcrop near Utah's old Star Point mine. Credit: Lauren Birgenheier

 

In a groundbreaking study led by the University of Utah, researchers have discovered elevated concentrations of rare earth elements (REEs) in active coal mines rimming the Uinta coal belt of Colorado and Utah.

This finding suggests that these mines, traditionally known for their coal production, could potentially serve as secondary sources for critical minerals essential for renewable energy and high-tech applications. "The model is if you're already moving rock, could you move a little more rock for resources towards energy transition? " Lauren Birgenheier, an associate professor of geology and geophysics, explains, In those areas, we're finding that the rare earth elements are concentrated in fine-grain shale units, the muddy shales that are above and below the coal seams."

Lauren Birgenheier

This research was conducted in partnership with the Utah Geological Survey and Colorado Geological Survey as part of the Department of Energy-funded Carbon Ore, Rare Earth and Critical Minerals project, or CORE-CM. The new findings will form the basis for a grant request of an additional $9.4 million in federal funding to continue the research.

"When we talk about them as 'critical minerals,' a lot of the criticality is related to the supply chain and the processing," said Michael Free, a professor metallurgical engineering and the principal investigator on the DOE grant. "This project is designed around looking at some alternative unconventional domestic sources for these materials."

The U-led study was published last month in the journal Frontiers in Earth Science. Team members included graduate students Haley Coe, the lead author, and Diego Fernandez, a research professor who runs the lab that tested samples.

“The goal of this phase-one project was to collect additional data to try and understand whether this was something worth pursuing in the West,” said study co-author Michael Vanden Berg, Energy and Minerals Program Manager at the Utah Geological Survey. “Is there rare earth element enrichment in these rocks that could provide some kind of byproduct or value added to the coal mining industry?”

Haley Coe, U geology graduate student, inspects drilling cores. Photo Credit: Lauren Birgenheier.

“The coal itself is not enriched in rare earth elements,” Vanden Berg said. “There's not going to be a byproduct from mining the coal, but for a company mining the coal seam, could they take a couple feet of the floor at the same time? Could they take a couple feet of the ceiling? Could there be potential there? That's the direction that the data led us.”

To gather samples, the team worked directly with mine operators and examined coal seam outcrops and processing waste piles. In some cases, they analyzed drilling cores, both archived cores and recently drilled ones at the mines. The team entered Utah mines to collect rock samples from the underground ramps that connect coal seams.

The study targeted the coal-producing region stretching from Utah’s Wasatch Plateau east across the Book Cliffs deep into Colorado. Researchers analyzed 3,500 samples from 10 mines, four mine waste piles, seven stratigraphically complete cores, and even some coal ash piles near power plants.

The study included Utah’s active Skyline, Gentry, Emery and Sufco mines, recently-idled Dugout and Lila Canyon mines in the Book Cliffs, and the historic Star Point and Beaver Creek No. 8 mines. The Colorado mines studied were the Deserado and West Elk.

Discover more about this groundbreaking research by visiting the full article by Brian Maffly at @The U.

Read more about this story at KUER.

U of U Part of $6.6M National Weather Forecasting Initiative

May 21, 2024

U of U Included in $6.6M National Weather Forecasting Initiative

The partnership with NOAA, other universities aims to improve predictive weather models

The University of Utah is one of a six-institution consortium recommended to receive up to $6.6 million from the National Oceanic and Atmospheric Administration (NOAA) to improve weather forecasting through enhanced data assimilation methods. 

The new Consortium for Advanced Data Assimilation Research will support six institutions that have been recommended to receive funding and will work together collaboratively under the new Consortium for Advanced Data Assimilation Research and Education (CADRE).  CADRE is led by the University of Oklahoma and includes Colorado State University, Howard University, University of Maryland, Pennsylvania State University and the University of Utah.

Dr. Zhaoxia Pu

"This NOAA funding allows our researchers to collaborate with leading experts across the country to tackle a key challenge in data assimilation methodology," said Atmospheric Sciences Professor Zhaoxia Pu, the Principal Investigator of the University of Utah for CADRE. "By improving data assimilation techniques, we can help make more accurate weather forecasting."

Data assimilation combines observational data sources like satellite, surface, air and ocean measurements with numerical weather prediction models to generate comprehensive analyses of evolving weather systems. This blending of information better estimates the atmospheric states and corrects forecast models in real-time, thus enhancing projections of weather extremes such as storm paths, intensities and precipitation.

Despite major forecasting accuracy improvements in recent decades, upgraded data assimilation methods are needed to leverage new technological capabilities like artificial intelligence. The CADRE consortium will focus its efforts on advancing the data assimilation components of NOAA's Unified Forecast System (UFS), a community-based, coupled, comprehensive Earth-modeling system.

Pu’s team will be focusing their research on the coupled data assimilation efforts to improve weather forecasting from short-range to sub-seasonal to seasonal time scales. Atmospheric processes are significantly influenced by interactions with the land and ocean. Pu’s team will develop effective coupled data assimilation methods to better represent the land-atmosphere-ocean interactions within NOAA's UFS. Pu will also dedicate time to training graduate students through research projects, outreach activities with NOAA Laboratories and the University of Reading, UK, and through on-campus lectures on data assimilation methods. Students from the City College of New York will also participate in training activities.

"Data assimilation is a comprehensive scientific topic involving various types of data, data science and numerical modeling strategies. I welcome interactions and collaborations in atmospheric sciences, mathematics, physics and AI data science disciplines both on campus and beyond," Pu stated.

The $6.6 million will be funded by the Inflation Reduction Act and is part of the Biden Administration's Investing in America initiative. To learn more about this announcement, read the official NOAA release here. 

By Bianca Lyon

Toxic Thalium: Humans changing the chemistry of the Baltic Sea

May 6, 2024

changing chemistry of the Baltic Sea

May 6, 2024

Above: Assistant Professor of Geology & Geophysics Chad Ostrander stands in front of the Elisabeth Mann Borgese research vessel.

Human activities account for a substantial amount — anywhere from 20% to more than 60% — of toxic thallium that has entered the Baltic Sea over the past 80 years, according to new research by scientists affiliated with the Woods Hole Oceanographic Institution (WHOI) and other institutions.

Chad Ostrander, lead author of the study, preparing a short sediment core collected from the East Gotland Basin during the investigation. - Credit: Colleen Hansel, ©Woods Hole Oceanographic Institution

Currently, the amount of thallium (element symbol TI), which is considered the most toxic metal for mammals, remains low in Baltic seawater. However, the research, using stable isotope analysis, suggests that the amount of thallium could increase due to further anthropogenic, or human induced, activities, or due to natural or human re-oxygenation of the Baltic that could make the sea less sulfide rich. Much of the thallium in the Baltic Sea, the largest human-induced hypoxic area on Earth, accumulates in the sediment thanks to abundant sulfide minerals.

“Anthropogenic activities release considerable amounts of toxic thallium annually. This study evidences an increase in the amount of thallium delivered by anthropogenic sources to the Baltic Sea since approximately 1947,” according to the journal article, “Anthropogenic forcing of the Baltic Sea thallium cycle,” published in Environmental Science & Technology.

“Humans are releasing a lot of thallium into the Baltic Sea, and people should be made aware of that. If this continues — or if we further change the chemistry of the Baltic Sea in the future or if it naturally changes — then more thallium could accumulate. That would be of concern because of its toxicity,” said Chadlin Ostrander lead author of the article which he conducted as a postdoctoral investigator in WHOI’s Department of Marine Chemistry and Geochemistry. Currently, he is an assistant professor in the Department of Geology & Geophysics at the University of Utah.

For the study, the researchers set out to better understand how thallium and its two stable isotopes 203Tl and 205Tl are cycled in the Baltic Sea. To discern modern thallium cycling, concentration and isotope ratio data were collected from seawater and shallow sediment core samples. To reconstruct thallium cycling further back in time, the researchers supplemented their short core samples with a longer sediment core that had been collected earlier near one of the deepest parts of the sea. They found Baltic seawater to be considerably more enriched in Tl than predicted. This enrichment started around 1940 to 1947 according to the longer sediment core.

Read the full press release from Woods Hole Oceanographic Institution here.

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U Atmospheric Scientists Team Up for $4.8M Snowfall Research Project

May 6, 2024

U atmospheric scientists team up for $4.8M snowfall research project

May 6, 2024
Above: Atmospheric Sciences Professor and Storm Peak Laboratory Director Gannet Hallar and students on the roof of Storm Peak Lab. Photo credit: Melissa Dobbins.

The S2noCliME Field Campaign aims to better predict snowfall processes that are critical to water supply in the Intermountain West

 

 

Gannet Hallar stands with a cloud imaging probe, which will measure the size and shape of ice particles in clouds during the field campaign. Photo credit: Melissa Dobbins.

In a new $4.8 million research project funded by the National Science Foundation, faculty from the University of Utah are partnering with lead investigators from the University of Michigan and other universities to better understand how snowfall processes are impacted by complex mountainous terrain. The multi-institutional team will conduct the Snow Sensitivity to Clouds in a Mountain Environment (S2noCliME) Field Campaign during the 2024-2025 winter season in northwest Colorado's Park Range, centered on the U's unique research station, Storm Peak Laboratory.

The Intermountain West is experiencing warmer, drier conditions and declines in snowpack due to climate change, putting communities, water resources, industries like skiing, and sensitive ecosystems at heightened risk. Accurate prediction of future snowfall accumulation in mountains is critical but challenged by the variable effects terrain has on precipitation patterns.

"Mountain snowpack is a vital source of water for communities across the western states," said Jay Mace, U professor of atmospheric sciences and a lead on the remote sensing components of the field campaign. "By deploying an integrated network of ground-based, airborne and satellite instruments, we can gain valuable insights into the chain of processes shaping snowfall, from large weather systems down to the microscale."

The U’s Storm Peak Laboratory, a premier high-elevation atmospheric monitoring station in Steamboat Springs, Colorado, will play a central role. During the upcoming winter season, the field site will host multiple radar systems, precipitation sensors, cloud particle imagers and other specialized instrumentation provided by the U and partner institutions. 

Claire Pettersen, an assistant professor of climate and space sciences and engineering at the University of Michigan, is the principal investigator of the project, leading the deployment of snow sensing equipment and multi-wavelength remote sensors at the midmountain site. We hope that our catalog will ultimately improve winter storm forecasts and tell western cities when to expect a drought because of insufficient snowpack,” said Pettersen.

The coordinated deployment brings together more than 30 cutting-edge instruments from five research universities. It aims to collect an unparalleled dataset documenting the impacts of orographic effects on snowfall from the broadest atmospheric scales down through the cloud microphysics. By pairing measurements of snowflake size and shape with radar measurements of clouds, the researchers will build a large catalog of data showing how storm systems change as they move over mountains, which will improve forecasts of snowfall and snowpack in these areas.

"This campaign gives us a rare opportunity to integrate specialized radars, balloon measurements, surface instrumentation and more into one cohesive study of snowfall formation processes over mountains," said Atmospheric Sciences Professor Gannet Hallar, director of Storm Peak Laboratory and co-investigator of the S2noCliME project. "The impacts of declining snowpack are far-reaching for the economy and way of life in the West. This combined data will help advance our models and predictive capabilities."

The S2noCliME project also includes scientists from the University of Washington, the University of Wisconsin-Madison, Colorado State University and Stony Brook University. 

Read the announcement from the University of Michigan here.

By Bianca Lyon