The Next Antibiotic Revolution: Viruses to the Rescue

The Next Antibiotic Revolution: Viruses to the Rescue


Dec 09, 2024
Above: Talia Backman – Ph.D. student, School of Biological Sciences, shares a micrograph of tailocins.

From multicellular organisms, like us humans, to single-cell bacteria, living things are subject to attack by viruses. Plants, animals and even bacteria have evolved strategies to combat pathogens, including viruses that can threaten health and life.

Talia Backman, a University of Utah doctoral candidate wrapping up her final year in the School of Biological Sciences, found her project and niche in studying bacteria and the viruses that infect them.

She studies how bacteria create and use weapons, called “tailocins,” by repurposing genes from viruses.

“I’m especially interested in how bacteria have taken this a step further,” Backman said, “using remnants of past viral infections as a novel defense mechanism.”

“Phage” is the word that refers to the viruses that infect bacterial cells. While phages do not attack human cells, a lot can be learned from the strategies used by bacteria to survive a viral infection. Working with Talia Karasov, the principal investigator and assistant professor of biology (yes, they share the same first name), Backman recently helped make an unexpected discovery.

Repurposing viruses

“The bacterial strains (Pseudomonas) that I am studying are essentially repurposing the viruses that infect them,” Backman said, “retaining features from the infectious particles that ultimately help them to kill or co-exist with other strains of bacteria. These repurposed phage parts are called ‘tailocins.’ Understanding the role tailocins may be playing in shaping the prevalence, survival, and evolutionary success of certain bacterial strains is not well understood and is a major focus of the research in the Karasov lab.

Research on bacteria, and their unique viral pathogens, might just offer a novel solution to the antibiotic crisis. Beyond revealing how microbial communities combat infection, compete and evolve is the adjacent opportunity and potential to discover a new class of antibiotics.

Read the full article in @School of Biological Sciences.

2024 Clarivate’s Most Cited

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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New tools for peering into cell function.

New tools for peering into cell function


Sep 9, 2024
Above: Ming Hammond, professor of chemistry. PHOTO CREDIT: Dave Titensor, University of Utah

U chemists discover how key contrast agent works, paving the way to create markers needed for correlative microscopy.

Two labs at the University of Utah’s Department of Chemistry joined forces to improve imaging tools that may soon enable scientists to better observe signaling in functioning cells and other molecular-scale processes central to life.

Rodrigo Noriega, assistant professor of chemistry and co-author of the study.

The Noriega and Hammond labs, with complementary expertise in materials chemistry and chemical biology, made critical discoveries announced this month in the Journal of the American Chemical Society that could advance this goal. Their joint project was kickstarted through a team development grant from the U College of Science and the 3i Initiative to encourage faculty with different research interests to work together on big-picture problems.

“We’re trying to develop a new kind of imaging method, a way to look into cells and be able to see both their structural features, which are really intricate, while also capturing information about their activity,” said co-author Ming Hammond, a professor of chemistry. "Current methods provide high-resolution details on cellular structure but have a challenging ‘blind spot’ when it comes to function. In this paper, we study a tool that might be applied in electron microscopy to report on structure and function at the same time.”

Biological samples often need “markers,” or molecules that are the source of detectable signals, explained co-author Rodrigo Noriega, an assistant professor of chemistry. A widely used type of markers are flavoproteins which, when photoexcited, trigger a chemical reaction that yields metal-absorbing polymer particles whose high contrast in electron microscopy is easily seen.

Scientists had long assumed that a mechanism involving singlet oxygen generation, a special kind of reactive oxygen species, was at play. However, the U team found that electron transfer between the photoexcited marker and the polymer building blocks is the main contributor to the process.

You can read the full story by Brian Maffly in @TheU.

 

Scientists Find Hope in Cone Snail Venom

Scientists Find Hope in Cone Snail Venom


Aug 23, 2024
Above : Ho Yan Yeung, PhD (left) and Thomas Koch, PhD (right, also an author on the study) examine a freshly-collected batch of cone snails. Image credit: Safavi Lab.

Based on work by Toto Olivera, the father of research on cone snail venom, scientists are now finding clues for how to treat diabetes and hormone disorders in a toxin from one of the most venomous animals on the planet.

An international research team led by University of Utah scientists has identified a component within the venom of a predatory marine cone snail, the geography cone, that mimics a human hormone called somatostatin, which regulates the levels of blood sugar and various hormones in the body. The hormone-like toxin’s specific, long-lasting effects, which help the snail hunt its prey, could also help scientists design better drugs for people with diabetes or hormone disorders, conditions that can be serious and sometimes fatal.

The results were published Aug. 20 in the journal Nature Communications.

A blueprint for better drugs

Somatostatin acts like a brake pedal for many processes in the human body, preventing the levels of blood sugar, various hormones, and many other important molecules from rising dangerously high. The cone snail toxin, called consomatin, works similarly, the researchers found—but consomatin is more stable and specific than the human hormone, which makes it a promising blueprint for drug design.

By measuring how consomatin interacts with somatostatin’s targets in human cells in a dish, the researchers found that consomatin interacts with one of the same proteins that somatostatin does. But while somatostatin directly interacts with several proteins, consomatin only interacts with one. This fine-tuned targeting means that the cone snail toxin affects hormone levels and blood sugar levels but not the levels of many other molecules.

In fact, the cone snail toxin is more precisely targeted than the most specific synthetic drugs designed to regulate hormone levels, such as drugs that regulate growth hormone. Such drugs are an important therapy for people whose bodies overproduce growth hormones. Consomatin’s effects on blood sugar could make it dangerous to use as a therapeutic, but by studying its structure, researchers could start to design drugs for endocrine disorders that have fewer side effects.

Consomatin is more specific than top-of-the-line synthetic drugs—and it also lasts far longer in the body than the human hormone, thanks to the inclusion of an unusual amino acid that makes it difficult to break down. This is a useful feature for pharmaceutical researchers looking for ways to make drugs that will have long-lasting benefits.

Learning from cone snails

Finding better drugs by studying deadly venoms may seem unintuitive, but Helena Safavi, associate professor of biochemistry in the U’s Spencer Fox Eccles School of Medicine and the senior author on the study, explained that the toxins’ lethality is often aided by pinpoint targeting of specific molecules in the victim’s body. That same precision can be extraordinarily useful when treating disease.

“Venomous animals have, through evolution, fine-tuned venom components to hit a particular target in the prey and disrupt it,” Safavi said. “If you take one individual component out of the venom mixture and look at how it disrupts normal physiology, that pathway is often really relevant in disease.” For medicinal chemists, “it’s a bit of a shortcut.”

Among Safavi’s coauthors are faculty from the U’s School of Biological Sciences, including Baldomero Olivera and Samuel Espino. The U has been a hotspot for research into the venom’s pharmacological properties since Olivera arrived in Utah in 1970 from his native Philippines, bringing his interest in cone snails with him.

Read the full, original story by Sophia Friesen in UofU Health.
Read about Toto Olivera’s 2022 Golden Goose Award for early research in cone snails here.

A Framework for Cancer Ecology and Evolution

A Framework for Cancer Ecology and Evolution


July 17, 2024

Why do the vast majority of cancers arise late in subjects’ lives?

Fred Alder. Credit: Mathew Crawley

A traditional explanation in the development of cancers, known as the somatic theory, is a paradigm focused on mutations in individual cells. In this theory a cascade of approximately six mutational changes in a single cell is the source that triggers cancer.  This theory explains the rapidly increasing “power function” that describes how cancer incidence increases with age.

But this power function which lines up with cancer’s six classic hallmarks is now being challenged by a different paradigm that casts doubt on the primacy of individual cells in cancer development. It also challenges the notion that cancer marks a strict change between “normal” and aberrant tissues, particularly as the body ages.

In a paper published today in The Royal Society Interface out of the United Kingdom, “A modeling framework for cancer ecology and evolution” is explored by University of Utah mathematics professor Frederick Adler with a joint appointment in biology.

Cancer's complexity

 

Adler says he has struggled for a long time to come up with an alternative modeling approach for cancer that has the flexibility to capture the complexity of cancer, while standing by the dictum that cancer cells are still cells. “It involved a plane trip where I worked out an extremely complicated approximate version of the method before figuring out, on solid ground, that the exact version was thoroughly simple.” 

Simple didn’t just mean elegant, but also getting results in a reasonable amount of time by optimizing code, something he can appreciate as the current Director of the busy School of Biological Sciences, one of the largest academic units at the University of Utah. 

The dynamics of escape in a person with imperfect initial control.  We see replacement by increasingly dark shades of gray that indicate cells that are growing faster and faster, leading to an increase in the total cell population (black line at top) above the healthy level (horizontal orange line).

Adler’s findings build on those of others that countermand the primacy of individual cells. These include observations of mutations common in non-cancerous tissues, and sometimes more common than in nearby cancers. “This implies,” the paper states, “that cancers depend on interactions with the surrounding tissue.” A second emphasis on cancer ecology and evolution is now highlighting “the ecology of nutrients, acids and physical factors and the role of cell interactions.”

“Detailed study of adults shows that few if any of their cells are ‘normal,’” says Adler. “Tissues are instead made up of lineages with ever-increasing numbers of aberrant traits, many of which promote excess growth. The vast majority of these incipient growths are contained by controls within those cells and by other cells.”

In Adler’s parsing of the ecological paradigm, senescence theory plays a critical role, focusing on the breakdown of the system of controls within and around individual cells. “[M]any cancers,” for example, “develop much later than their originating oncogenic mutations.” Furthermore, mutant cells in his models are restrained “by systems that remove their growth advantage, but which can weaken with age due to changes such as impaired intercellular communication. Remarkable data on genetic diversity in healthy tissues show that cancer-related mutations are ubiquitous, and often under positive selection despite not being associated with progression to cancer.”

Overview of CAGRM framework. Cells include an arbitrary number of potential lineages, beginning with all cells in the unmutated lineage C0 and evolving first into C1 and eventually a branching evolutionary tree of lineages here indicated collectively by Ci. There are four forms of regulation (indicated by flat-headed arrows): contact inhibition by other cells (C ), inhibition by antigrowth factor (A), depletion of growth factor (G) and depletion of resources (R). Mutualist cells can aid cell replication by suppressing antigrowth factor or by supplementing growth factor or resources.

Tracking the dual nature of cells

 

In the paper, Adler first presents a modeling framework which incorporates evolution, stochasticity (a measure of how random a process is, or the quality of lacking a predictable order or plan) and control and breakdown of control. Using a differential equation, the model then tracks the dual nature of individual cells as ecological competitors for resources and space. 

Using this framework Adler then tested whether the ecological model of cancer initiation generates realistic age-incidence patterns similar to the somatic mutation theory. Another test was made to determine how initial defects in the control systems accelerate the process. 

In this comprehensive systems view, cancer, and an incipient cancer in particular, is not an invader. “It is a set of cells,” the paper reads, “that escape the many layers of internal and tissue level regulation, and then grow to damage the host. The success of a cancer, or equivalently the failure of the regulatory system, requires that the cancer co-opts or evades the systems of control and repair.”

This model/framework, according to the author, assumes a particular structure of the control system but has capacity for “several other extensions” to make it more “realistic.” Those extensions would address, for example, cell differentiation and a clearer class of driver mutations for the genetic model of quantitative trait. Another might address why the mutualist cells in the tests maintain a constant phenotype in spite of what we know about how cells alter behavior in cancer’s presence.

Statistically, we understand that cancer emerges more frequently in older individuals. But how and why is what Adler is attempting to determine. His model, says Adler, “reproduces the rapid increase of cancer incidence with age, identifies the key aspects of control, and provides a complement to the focus on mutations that could lead to new treatment strategies.”

Fred Adler points out that the control system in the model differs greatly across species in concert with their body size and lifespan, thus revealing a paradox known as Peto’s:  cancer rates are similar across organisms with a wide range of sizes and lifespan. “This robustness,” concludes the paper, “is a special case of the principle that all biological systems must be overbuilt to deal with uncertainty.” Referencing Shakespeare’s Hamlet, Adler states that this development in excess of demand exists “to survive ‘the thousand natural shocks that flesh is heir to’… This model seeks to place those shocks in the ecological and evolutionary context that makes long life possible.” 

 

by David Pace

Read about Fred Adler's related work in modeling cancer development, specifically with breast cancer.

 

Journey to the Center of Biotech

Journey to the Center of Biotech 


July 8, 2024
Above: Heng Xie

“I guess I just can’t help being a visionary,” Heng Xie jests, reflecting on her career since leaving academia. 

Xie earned her PhD in biology from the University of Utah in 2004 and where she remained as a postdoc for several years. At the time, she never imagined herself working industry. Yet to her surprise, she amassed extensive experience in biotechnology. In her first foray from academia, she taught eighth-grade science and helped build the charter school’s AP biology program.

While she loved teaching, Xie always felt the urge to venture out and gain experience in molecular biology which she also enjoyed. As such, new technological developments in a local biotechnology startup, IDbyDNA, presented her call to action. She recalls “the startup company was pushing for a new technology that was obviously going to be the future. Now the question was, who was going to make it a reality? Why not us?”

To finally embrace the uncertainty of industry was scary, but Xie knew this was her time to act. “I can always go back to teach, but this leap of faith, if I didn’t take it, I may not have another opportunity,” she says. In fact, while learning new skills herself, she never stopped teaching and mentoring others. 

Hypothesis-free Diagnostics

IDbyDNA is a local metagenomics company with an innovative algorithm that simultaneously profiles tens of thousands of microorganisms (or pathogens) in any sample by massive parallel sequencing, known as Next Generation Sequencing (NGS). Xie says this technology is fundamentally different from other available tests because it is hypothesis-free. “We’re not making any guesses, educated or not; we just treat everybody the same, and we sequence everything in there. And by analyzing the sequence in the sample, bioinformatics can tell you what it is. You don’t have to say ‘Tell me if it’s the flu.' It will tell you, ‘No, it’s not the flu, it’s something else.’” 

By taking this approach to diagnosis, IDbyDNA circumvents two major problems. “The first issue is [the] diversity of the potential cause of the disease. The second issue is [one of timing as] some of the really dangerous pathogens that cause diseases such as tuberculosis, can take a long time to grow. By the time you can actually grow it and identify it, the patient's disease has progressed, and, [by then,] they might have been in the ICU for weeks.” 

Hybrid Capture

Though these major concerns were sidestepped, other problems became apparent. “One problem we saw at IDbyDNA was when you get a patient sample and you start to sequence the DNA, the majority of the DNA is the host DNA because the human genome is orders of magnitude larger than the pathogen genome,” explains Xie. “Even a single human cell is going to give you much more sequencing information than the pathogen. So, you actually are not going to have the level of sensitivity you want for it to be clinically applicable.”

To bypass this problem, one can enrich the pathogen signal by selectively pulling the pathogen sequences (with complementary DNA) from the sample before analyzing. The challenge here is that the diversity of the pathogens would require extremely high complexity capturing, which means high-complexity DNA synthesis.

At IDbyDNA, Xie started as a research scientist, co-developing the Explify® clinical diagnostic platform and left as an associate director after six years. The company was eventually acquired by Illumina, a giant sequencing company. 

Her next adventure in industry after IDbyDNA was as principal scientist at GenScript, a company that develops and manufactures gene synthesis products and services used by researchers in academia, pharmaceutics and biotech. Xie joined the Seattle campus because of the CustomArray technology that synthesizes millions of different DNA molecules on a semiconductor chip. This high-complexity, low-cost production of DNA became the natural extension of Xie’s earlier interest.  

“When I went there [Genscript], this was pre-production, and I helped them evaluate and quantify how good they are and help them improve the product,” says Xie. Her work over nine months resulted in reduced costs and streamlined application of NGS technology in product development. 

Precision Oncology

From GenScript, Xie took the position of senior director of pharma services at NeoGenomics Laboratory, a company dedicated to precision oncology. This newest endeavor is the perfect combination of her other experiences: a hypothesis-free approach applied with hybrid sequencing technology that can provide targeted therapies for cancer patients. At NeoGenomics, biopsies of tumors are sequenced and matched back to the mutation that caused them.

“Then, if the clinician needs to target the specific cancer, they can select suitable drugs that have been approved or are in clinical trials to [make a] recommendation to the patient based on the sequencing results.” This highly targeted therapy means that the patient doesn't have to suffer general chemo, Xie says. She and her team have launched several impactful tests since she joined NeoGenomics. More exciting tests are getting ready for the market. 

Accelerating the pace

It took a while for Xie to leave academia, but she hasn’t looked back since. She has been dedicated to accelerating the pace in the biotech industry, making innovations at the top of the supply chain that impact research in industry and academia further down, or serving patients with state-of-the-art diagnostic technologies. While earning her PhD at the U, Xie never imagined the exciting career she would create for herself. 

“[W]hat I absorbed in school was that there is no value outside academia because everything else is not as scientifically rigorous and not as innovative, not as cutting edge, not at the very boundary of human knowledge.” 

But Heng Xie’s success at all levels of the biotech industry is living proof of the abundant exciting opportunities students have and a testament to the growth of science beyond academia. Her experiences showcase how rigorous research in academia impacts society through the commercialization of innovative technologies. 

by Lauren Wigod 

Delve into the puzzle of ice crystallization and uncover its secrets.

Delve into the puzzle of ice crystallization and uncover its secrets


July 5, 2024
Above: A screen capture from a slow-motion movie covers mere nanoseconds — when water is tuned to a critical point called the liquid-liquid transition.

Making ice requires more than subzero temperatures. The unpredictable process takes microscopic scaffolding, random jiggling and often a little bit of bacteria.

We learn in grade school that water freezes at zero degrees Celsius, but that’s seldom true. In clouds, scientists have found supercooled water droplets as chilly as minus 40 C, and in a lab in 2014, they cooled water to a staggering minus 46 C before it froze. You can supercool water at home: Throw a bottle of distilled water in your freezer, and it’s unlikely to crystallize until you shake it.

Freezing usually doesn’t happen right at zero degrees for much the same reason that backyard wood piles don’t spontaneously combust. To get started, fire needs a spark. And ice needs a nucleus — a seed of ice around which more and more water molecules arrange themselves into a crystal structure.

Valeria Molinero, a physical chemist at the University of Utah, builds computer simulations of water to study ice nucleation.

The formation of these seeds is called ice nucleation. Nucleation is so slow for pure water at zero degrees that it might as well not happen at all. But in nature, impurities provide surfaces for nucleation, and these impurities can drastically change how quickly and at what temperature ice forms.

For a process that’s anything but exotic, ice nucleation remains surprisingly mysterious. Chemists can’t reliably predict the effect of a given impurity or surface, let alone design one to hinder or promote ice formation. But they’re chipping away at the problem. They’re building computer models that can accurately simulate water’s behavior, and they’re looking to nature for clues — proteins made by bacteria and fungi are the best ice makers scientists know of.

Understanding how ice forms is more than an academic exercise. Motes of material create ice seeds in clouds, which lead to most of the precipitation that falls to Earth as snow and rain. Several dry Western states use ice-nucleating materials to promote precipitation, and U.S. government agencies including the National Oceanic and Atmospheric Administration and the Air Force have experimented with ice nucleation for drought relief or as a war tactic. (Perhaps snowstorms could waylay the enemy.) And in some countries, hail-fighting planes dust clouds with silver iodide, a substance that helps small droplets to freeze, hindering the growth of large hailstones.

But there’s still much to learn. “Everyone agrees that ice forms,” said Valeria Molinero, a physical chemist at the University of Utah who builds computer simulations of water. “After that, there are questions.”

You can read the full story in Quanta magazine. Read the published research @PNAS.

Life On Other Planets … and in a student’s mind

Life On Other Planets … and in a student’s mind


June 13, 2024
Above: Mary Fairbanks BS'23, biology

A DNA repair system known as the GO DNA repair system removes oxidized guanine. This helps protect the system from mutating, and while scientists understand how it works, the origin of this mechanism isn’t well understood.

That’s where the Martin Horvath Lab comes in and, in particular, Mary Fairbanks BS’23. She and her team in the School of Biological Sciences at the University of Utah explore structural biology and biochemistry by researching microbes from the Lost City Hydrothermal Field, an area of marine alkaline hydrothermal vents located in the Atlantic Ocean. 

As with Fairbanks, who gained hands-on experience creating experiments and directly participating in research, other lab members worked on the project as undergraduates before graduating. They include Payton Utzman BS’22 and Briggs Miller BS’22 who along with Fairbanks and graduate student Vincent Mays researched microbes that live at the bottom of the ocean where there is little oxygen and even less sunlight. Because of the lack of oxygen in the environment where these microbes thrive, the fact that researchers found GO DNA repair genes is important: it shows a need for genes that repair DNA that has been put under stress from oxygen. Their research was recently published in PLOS

Acting like a scientist

"Working in Dr. Horvath’s lab has taught me how to be curious and be dedicated to a project,” says Fairbanks. “Being able to design my own experiments has given me the opportunity to act as a scientist. I have grown through research and it continues to expand my view of the possibilities of innovation.” 

Horvath first learned that one of the GO repair genes called MutY might be present at the Lost City Hydrothermal Field from a student in his Molecular Biology of DNA Lab course, Emily Dart HBS’16. Horvath knew that Dart was working with William Brazelton, a fellow biologist who had recently collected DNA from Lost City. Searching that Lost City DNA, Dart and her teammates found genes encoding at least portions of MutY.

“Since that first analysis,” says Horvath, “the sequence technology improved, more samples from another expedition generated metagenomes with better coverage, and we now have functional tests that show these MutYs from the bottom of the ocean actually work to prevent mutations in lab strains of bacteria.” That these discoveries stemmed from basic science research by undergraduates, he says, is “something that I am very proud to celebrate!”

How life might evolve on other planets

GO DNA repair genes are advantageous even in environments without much oxygen. Since hydrothermal fields like the Lost City Hydrothermal Field are similar to the environment of early Earth, this indicates that these repair systems evolved before the Great Oxidation Event.

Fig 5. LCHF MutY chemical motifs. (A) Conservation and diversity of MutY-defining chemical motifs are depicted with a sequence logo for the 160 LCHF MutYs. These motifs are associated with biochemical functions including DNA binding, enzyme catalysis, attachment of the iron-sulfur cofactor, and recognition of the damaged OG base.

Insights like this can help develop models of how life might evolve on other planets. Planets that lack the abundance of oxygen that modern Earth has may have life evolving in a similar way to microbes that live near hydrothermal vents. Since these microbes have repair systems that deal with oxidative stress, it’s reasonable to consider that life on other planets may as well.

The group also discovered the role that these repair genes, including MutY, play in hydrothermal microbes, by associating GO DNA repair with metabolic pathways. These pathways produce oxygen as a byproduct, so MutY may play a part in fixing DNA damage caused by metabolic processes.      

Life on other planets may take many different forms, and similarly, learning science also takes many forms beyond the classroom. “I’ve been encouraged to ask questions and explain findings to form a cohesive pattern that tells a story,” says Fairbanks. She credits the lab experience as helping her “see a project from start to finish. I have been able to improve my critical thinking skills and laboratory technique, as well as adapt to change.” 

That adaptation to change is a good lesson to learn as empirically observed far below the surface of the ocean but also on a personal level for Fairbanks and her young researcher cohorts. Findings such as these may show how DNA-based life forms rely on fixing damage caused by oxidation, even in environments without oxygen. And they give scientists a clue as to how life may look on other planets by forming models of life in environments unlike Earth’s. But the “findings” are clearly internal as well for young, developing scientists who will never forget their time examining and interpreting data in the Horvath Lab. 

As Martin Horvath intones of this research, “Life finds a way.” 

As do young minds like that found embodied in Mary Fairbanks who, now headed for a career in the medical field, concludes, “I believe my experience in research will make me a more open-minded thinker.”

by CJ Siebeneck

Meet Lokiceratops: Giant Blade-Wielding Dinosaur


Meet Lokiceratops:
A Giant Blade Wielding Dinosaur


June 21, 2024
Above: Reconstruction of Lokiceratops surprised by a crocodilian in the 78-million-year-old swamps of northern Montana, USA.
Image ©Andrey Atuchin for the Museum of Evolution in Maribo, Denmark.

A remarkable, new species of horned, plant-eating dinosaur is being unveiled at the Natural History Museum of Utah. The dinosaur, excavated from the badlands of northern Montana just a few miles from the USA-Canada border, is among the largest and most ornate ever found, with two huge blade-like horns on the back of its frill. The distinctive horn pattern inspired its name, Lokiceratops rangiformis, meaning “Loki’s horned face that looks like a caribou.” The study included the most complete analysis of horned dinosaur evolution ever conducted, and the new species was announced today in the scientific journal PeerJ.

More than 78 million years ago, Lokiceratops inhabited the swamps and floodplains along the eastern shore of Laramidia. This island continent represents what is now the western part of North America created when a great seaway divided the continent around 100 million years ago. Mountain building and dramatic changes in climate and sea level have since altered the hothouse world of Laramidia where Lokiceratops and other dinosaurs thrived. The behemoth is a member of the horned dinosaurs called ceratopsids, a group that evolved around 92 million years ago during the Late Cretaceous, diversified into a myriad of fantastically ornamented species, and survived until the end of the time of dinosaurs. Lokiceratops (lo-Kee-sare-a-tops) rangiformis (ran-ɡi-FOHR-mees) possesses several unique features, among them: the absence of a nose horn, huge, curving blade-like horns on the back of the frill—the largest ever found on a horned dinosaur—and a distinct, asymmetric spike in the middle of the frill. Lokiceratops rangiformis appeared at least 12 million years earlier than its famous cousin Triceratops and was the largest horned dinosaur of its time. The name Lokiceratops translates as “Loki’s horned face” honoring the blade-wielding Norse god Loki. The second name, rangiformis, refers to the differing horn lengths on each side of the frill, similar to the asymmetric antlers of caribou and reindeer.

PHOTO CREDIT: MARK LOEWEN.
Completed reconstruction of Lokiceratops mounted for display. Study authors Brock Sisson (left) and Mark Loewen (right) peer through the frill fenestrae (windows) of Lokiceratops.

Lokiceratops rangiformis is the fourth centrosaurine, and fifth horned dinosaur overall, identified from this single assemblage. While ceratopsian ancestors were widespread across the northern hemisphere throughout the Cretaceous period, their isolation on Laramidia led to the evolution of huge body sizes, and most characteristically, distinctive patterns of horns above their eyes and noses, on their cheeks and along the edges of their elongated head frills. Fossils recovered from this region suggest horned dinosaurs were living and evolving in a small geographic area—a high level of endemism that implies dinosaur diversity is underestimated.

“Previously, paleontologists thought a maximum of two species of horned dinosaurs could coexist at the same place and time. Incredibly, we have identified five living together at the same time,” said co-lead author Mark Loewen, a paleontologist at the Natural History Museum of Utah and professor in the Department of Geology & Geophysics at the University of Utah. “The skull of Lokiceratops rangiformis is dramatically different from the other four animals it lived alongside.”

The fossil remains of Lokiceratops was discovered in 2019 and cleaned, restored and mounted by Brock Sisson, paleontologist and founder of Fossilogic, LLC in Pleasant Grove, Utah. “Reconstructing the skull of Lokiceratops from dozens of pieces was one of the most challenging projects my team and I have ever faced,” said Brock, “but the thrill of bringing a 78-million-year-old dinosaur to life for the first time was well worth the effort.”

Discover more about Lokiceratops by visiting the full article by Mark Loewen at @The U.
Read more about the story in Discover Magazine, ABC 4 News, KSL News, Science Daily, Science News.

Utah’s fir trees at risk from balsam woolly adelgid

Utah's fir trees at risk from
balsam woolly adelgid


June 20, 2024
Above: A drone photograph in Farmington Canyon shows the several level of infestation of balsam woolly adelgid infesting subalpine fir.
PHOTO CREDIT: MICKEY CAMPBEL

A nonnative tree-killing insect is invading northern Utah, attacking subalpine fir and potentially triggering yet another die-off of the region’s long-stressed conifer forests.

Introduced from Europe into the Pacific Northwest about a century ago, the balsam woolly adelgid (BWA), or Adelges piceae, was first detected in Utah in 2017 and has been spreading around the Wasatch Mountains, visibly affecting many of the popular recreation canyons outside Salt Lake City.

New research from the University of Utah, conducted in partnership with the U.S. Forest Service, has documented the current extent of the adelgid infestation and created a model for predicting its severity around the Uinta-Wasatch-Cache National Forest.

The study documented a clear relationship between the infestation’s severity and temperature, according to lead author Mickey Campbell, a research assistant professor in the Department of Geography (soon to be merged with the Environmental Studies program and renamed the School of Environment, Society, and Sustainability.)

PHOTO CREDIT: MICKEY CAMPBELL The crowns of infested fir trees exhibit crown deformities.

“We took that climate-to-severity relationship along with a series of climate projections and we were able to map current and future exposure to BWA damage at a high spatial resolution,” Campbell said. “The idea [is], in 2040, 2060, 2080 and 2100, based on these different climate projections, determining how exposed these areas are to the potentially damaging effects of BWA. And indeed, we find that for an insect that prefers warmer areas, a warming climate is going to provide it with more opportunity to cause damage.”

The role of climate change

The study appears this month in the journal Forest Ecology and Management. Co-authors include U Biology Professor William Anderegg, director of the Wilkes Center for Climate Science and Policy. [The center hosts its annual Climate Summit on May 14-15, where Anderegg will give opening remarks.]

According to Anderegg, the new study suggests climate change is playing a role in Utah’s adelgid infestation.

“The main pieces of evidence are how strongly temperature is related to the spread and severity of BWA,” said Anderegg, a specialist in forest ecology. “That tells us at the very least as temperatures go up, we should be concerned about more spread and higher severity infestation.” Covering the Wasatch, Uinta, Bear River and a few lesser mountain ranges in northern Utah, this national forest is among the nation’s busiest for recreation. It features five major ski areas that border several others and sees more visits than all of Utah’s national parks combined.

Read the full article by Brian Maffly at @TheU.

Hear the Interview of Dr. Mickey Campbell ( Lead Author and research assistant professor in the Department of Geography) with Ross Chambless on the spread of balsam woolly adelgid in Utah on The Wilkes Center for Climate Science & Policy page.