homenews | College of Science

Ants and Trees: A Tale of Evolutionary Déjà Vu in the Rainforest

July 19, 2024

Ants are famous for their regimented and complex social behaviors. In the tropics, they are also famous for forming mutualisms with plants. Certain species of trees have conspicuous hollow swellings that house ants, often feeding the ants with specialized ant food. In return, the ants are pugnacious bodyguards, swarming out to aggressively defend the plant against enemies. Scientists have observed these mutualisms for centuries, but an enduring question is how these intriguing interactions evolved in the first place.

That remains a mystery, but new research led by University of Utah field biologist Rodolfo Probst offers insights that could broaden our understanding of ant-plant symbioses.

Published last week in the Proceedings of the Royal Society B, his research focused on an ant genus called Myrmelachista. Most Myrmelachista species nest in dead or live stems of plants, without any specialized mutualistic association. But one group of species in Central America was known to nest only in the live stems of certain species of small understory trees, in a specialized symbiosis similar to other ant-plant mutualisms. These tiny yellow ants hollow out the stems without harming the host plants, and can be found throughout Central America.

Jack Longino. Credit: Rodolfo Probst

Probst made a remarkable discovery. Using DNA sequence data to unravel their evolutionary history, he found that these nine species occurred as two clusters in different parts of the evolutionary tree. That means that this complex relationship, with all its distinctive characteristics, evolved twice from non-specialist ancestors.

His two coauthors are renowned entomologist Jack Longino, better known among U students as The Astonishing Ant Man for his expertise and vast personal collection of ant specimens kept on campus, and former U School of Biological Sciences’ postdoctoral researcher Michael Branstetter, now with U.S. Department of Agriculture’s Pollinating Insect Research Unit at Utah State University.

Probst is a postdoctoral researcher in the School of Biological Sciences and the university’s Science Research Initiative, or SRI, and was recently recognized with the Outstanding Postdoctoral Researcher Award by the College of Science. Through the SRI, Probst has involved U undergraduates in his research. For example, students accompanied Probst and Longino to Costa Rica with funding support from the U’s Wilkes Center for Climate Science & Policy.

With continuing help from SRI undergraduates, Probst is looking to conduct whole genomic sequencing to tease out the genes involved in ant-plant associations, looking “under the hood” of a phenomenon that has intrigued naturalists for centuries.

Read more about the story on ants and trees by Brian Maffly @TheU.

Rethinking Carbon Offsets

July 18, 2024

Libby Blanchard

It was the dawn of carbon-off-setting, emitting one place and then reducing or removing emissions elsewhere and calling that climate neutral.

Following the Kyoto Protocol negotiations in 1996/97, industrialized countries, including the U.S., picked up on the idea of carbon crediting and carbon off-setting and explored flexible market mechanisms that, according to Libby Blanchard, would potentially make it more economically feasible for industrialized countries to meet the goals and carbon-reduction metrics of the 2015 United Nations-brokered Paris Agreement.

Three and half decades after that first experiment in Guatemala with carbon off-sets the idea seems to have hit an inflection point. “A carbon credit becomes an offset when it’s used to trade against emissions somewhere else,” reiterates Blanchard, a postdoctoral research associate at the Wilkes Center for Climate Science & Policy and the School of Biological Sciences here at the University of Utah. “And a carbon credit is supposed to be one ton of carbon dioxide equivalent reduced or removed from the atmosphere over a predetermined period of time. The big problem with carbon credits is a large majority are not real or are what we call over-credited, or both, meaning that they’re not representing or are over-representing the amount of carbon dioxide equivalent actually reduced or removed for the atmosphere."

In this episode of the Talking Climate podcast, produced by the Wilkes Center for Climate Sciences & Policy, Ross Chambless, Wilkes Center community engagement manager, interviews Blanchard on a new “Contribution Approach” replacement of the struggling carbon offsets market.

Read more about the Nature-based climate solutions in an article published in One Earth.

Listen to the full podcast and view the transcript.

Watch a video with Libby Blanchard below.

A Framework for Cancer Ecology and Evolution

July 17, 2024

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.

What do cycling and rocks have in common?

July 15, 2024

I’m not talking about the Olympics, but the Tour de France, which kicked off on June 29 in Florence, Italy and will finish July 21 in Nice, France. This is the first time the iconic bicycle race won’t finish in Paris, due to the city hosting the Summer Olympics.

The star they’re highlighting rises above the competition, literally. It’s also below and all around.

Peter Lippert and Sean Hutchings

The Geo Tour de France project (Geo TdF) is a blog exploring the geology of the various stages of the bike race. Lippert and Hutchings are two of the five North American contributors to the blog this year. They covered Stage 14, a 152-kilometer ride through the Pyrenees held Saturday and won Saturday by overall race leader Tadej Pogacar of Slovenia in just over four hours.

“The centerpiece of the stage is the Col du Tourmalet, a very famous fabled climb in the Tour de France that has lots of amazing history,” said Lippert, an associate professor in the Department of Geology & Geophysics and director of the Utah Paleomagnetic Center. “This is going to be one of the really decisive stages of the Tour this year.”

The entire race covers 3,500 kilometers (2,175 miles) in 21 stages.

“I’ve always loved this project, because it’s just such a fun way to share our science and share how we see the world with the public and particularly a public that’s probably not often thinking about the geology,” Lippert said.

For Lippert and Hutchings, as well as many of their peers across the world, geology and cycling go hand in hand.

“Riding a bike up and down a mountain gives you a lot of time to see how the mountains put together the rocks you’re riding over in the landscapes that you’re on,” Lippert said. “We’re both trained geologists for most of our lives so it’s hard not to always be thinking about [geology].”

Utah in particular boasts captivating and diverse geological features.

“It’s mountain biking Candyland around here,” said Hutchings, a graduate research assistant in the U of U Seismograph Stations. “It’s fun to be able to climb up to the top of the hill and it’s hard to not interact with rocks on the way as well.”

“You have this new identity with the landscape you’re on if you’re able to understand what’s going on beneath your feet and what made the landscape,” Lippert said. “I think cycling is a really great high impact sense of place type of experience. You’re going a little bit slower. You get to look around.”

Geo Tour de France project

This same sentiment was the original inspiration for Geo TdF project creator Douwe van Hinsbergen, professor of geology at the Netherlands’ Utrecht University.

“He wanted to explore a different way of sharing geology with the public,” Lippert said. “This is a total goldmine.’

Fans who watch the livestream of the race are inadvertently watching hours of spectacular geological features. The Geo TdF project enhances the viewing experience by telling geological stories that ground the competition in the larger history of the landscape.

Lippert first contributed to the blog two years ago, and this time around included Hutchings. The pair worked together during Hutchings’ bachelor’s degree at the U and often bike together.

“I know nothing about Pyrenean geology, so this was a great learning opportunity for me,” Hutchings said. “For graduate school, I’ve dipped more into the seismology realm, so getting back to my geology roots was a fun exercise.”

Col du Tourmalet. Photo credit: Gilles Guillamot, Wikimedia Commons

Tectonic training camp

Stage 14 passed through Pyrenees, the mountains on France’s border with Spain, with an average grade of 7.9%. That’s just under 95 miles at an average grade more than twice as steep as the incline from President’s Circle to the Natural History Museum of Utah.

“Let’s think big” is what Lippert and Hutchings thought when they were presented with the opportunity to cover this pivotal stage of the race.

“I mean the Tour de France is big, the Pyrenees are big, tectonics are big. Sean is more of a geophysicist working with earthquakes and things like that,” Lippert said. “My expertise is in collisional mountain builds, like what happens when oceans close and mountains form. So we thought let’s just go back to basics and keep it big.”

What could be bigger than beginning with the ancient supercontinent Pangea? For their portion of the project, Lippert and Hutchings focused on the creation of the Pyrenees mountain range which began with the separation of Pangea and subsequent plate collisions, a process they describe as a “tectonic training camp.”

A Wealth of information

Some readers might be wondering if these passionate geologists will eventually run out of topics to discuss, even though the Tour course changes each year. Lippert and Hutchings aren’t concerned about that at all.

“One nice thing about geology is that rocks usually stay put and you can go back to check them out year after year. So the rocks don’t change, but the way that we can talk about them does. The limit is our creativity now, what the rocks can provide, because they’re full of really good stories,” Lippert said. “There’s a wealth of information that a single rock can tell you. Where it came from, and the time it took to get there, and what it looked like at the time.”

Berton Earnshaw Named College of Science Senior Fellow

July 15, 2024

Berton Earnshaw

The University of Utah College of Science has announced that Berton Earnshaw has accepted the role of Senior Fellow. As a Founding Fellow at Recursion, a leading clinical-stage “techbio” company (defined as one focused on leveraging data and technology to improve, enhance, and accelerate life science processes), and as Scientific Director of Recursion’s AI research lab Valence Labs, Earnshaw has led the development and deployment of many of the machine learning capabilities employed in the company’s drug discovery workflows. He also directs multiple research programs across Recursion and Valence Labs.

“I first met Berton in the math department during his PhD studies,” said Dean Peter Trapa. “It’s great to see him come full circle with the U as a Senior Fellow in the College of Science. Currently, he’s at the top of his game in machine learning as it relates to drug development and will add appreciably as an executive advisor to the College and its research priorities.”

Earnshaw earned his bachelor’s and master’s degrees in mathematics from Brigham Young University and, in 2007, earned a PhD in mathematics from the U while working with its mathematical biology group. There he designed biophysical models of protein trafficking at synapses during episodes of learning and memory formation. He was a postdoctoral researcher at both the U and Michigan State University and has taught as an adjunct professor in the U’s Department of Mathematics since 2018.

Earnshaw has worked in many scientific and leadership roles in industry before arriving at Recursion as Director of Data Science Research in 2017, including as CTO of Perfect Pitch (now Boomsourcing), Director of Data Science and Operations at Red Brain Labs (acquired by Savvysherpa) and Principal and Senior Scientist at Savvysherpa (acquired by UnitedHealth Group). Earnshaw has also served as a member of the Utah State Auditor’s Commission on Protecting Privacy and Preventing Discrimination.

Outside of work, Earnshaw enjoys traveling together with his wife and five children and loves being outdoors, eating well, investing, and reading everything from fiction to philosophy to theoretical physics.

“The opportunities offered by today’s innovations in AI and the life sciences to radically impact our lives for good are extraordinary,” said Earnshaw. “I am honored and thrilled to be working with Dean Trapa to ensure that the College of Science is a leader in preparing its students to take advantage of these opportunities.”

Earnshaw joins Tim Hawkes, attorney and former Utah legislator, who was announced as the inaugural senior fellow in 2023. The College of Science senior fellows represent a variety of industries and provide key insights and guidance to leadership and faculty.

A once-in-a-career discovery: the black hole at Omega Centauri’s core

July 11, 2024

Through a small telescope, it looks no different from other so-called globular clusters; a spherical stellar collection so dense towards the center that it becomes impossible to distinguish individual stars. But a new study, led by researchers from the University of Utah and the Max Planck Institute for Astronomy, confirms what astronomers had argued about for over a decade: Omega Centauri contains a central black hole.The black hole appears to be the missing link between its stellar and supermassive kin—stuck in an intermediate stage of evolution, it is considerably less massive than typical black holes in the centers of galaxies. Omega Centauri seems to be the core of a small, separate galaxy whose evolution was cut short when it was swallowed by the Milky Way.

“This is a once-in-a-career kind of finding. I’ve been excited about it for nine straight months. Every time I think about it, I have a hard time sleeping,” said Anil Seth, associate professor of astronomy at the U and co-principal investigator (PI) of the study. “I think that extraordinary claims require extraordinary evidence. This is really, truly extraordinary evidence.” A clear detection of this black hole had eluded astronomers until now. The overall motions of the stars in the cluster showed that there was likely some unseen mass near its center, but it was unclear if this was an intermediate-mass black hole or just a collection of the stellar black holes. Maybe there was no central black hole at all.

A medium Level panel zoom of the Omega Centauri star cluster’s intermediate black hole likely position. PHOTO CREDIT: ESA/HUBBLE & NASA, M. HÄBERLE (MPIA)

“Previous studies had prompted critical questions of ‘So where are the high-speed stars?’ We now have an answer to that, and the confirmation that Omega Centauri contains an intermediate-mass black hole. At about 18,000 light-years, this is the closest known example for a massive black hole,” said Nadine Neumayer, a group leader at the Max Planck Institute and PI of the study. For comparison, the supermassive black hole in the center of the Milky Way is about 27,000 light-years away.

A range of black hole masses

In astronomy, black holes come in different mass ranges. Stellar black holes, between one and a few dozen solar masses, are well known, as are the supermassive black holes with masses of millions or even billions of suns. Our current picture of galaxy evolution suggests that the earliest galaxies should have had intermediate-sized central black holes that would have grown over time, gobbling up smaller galaxies done or merging with larger galaxies.

Such medium-sized black holes are notoriously hard to find. Although there are promising candidates, there has been no definite detection of such an intermediate-mass black hole—until now.

“There are black holes a little heavier than our sun that are like ants or spiders—they’re hard to spot, but kind of everywhere throughout the universe. Then you’ve got supermassive black holes that are like Godzilla in the centers of galaxies tearing things up, and we can see them easily,” said Matthew Whittaker, an undergraduate student at the U and co-author of the study. “Then these intermediate-mass black holes are kind of on the level of Bigfoot. Spotting them is like finding the first evidence for Bigfoot—people are going to freak out.”

Neutrino Oscillation Research Advances

July 9, 2024

Neutrinos are also incredibly small and light. They have some mass, but not much and they rarely interact with other matter. They come in three types or "flavors": electron, muon, and tau.

Cosmic rays travel through space then crash into the earth's atmosphere and produce air showers that Include neutrinos and many other types of particles. When neutrinos are produced and start traveling, they can change from one flavor to another. The atmospheric neutrinos are then detected by DeepCore, a denser array of sensors in the center of the IceCube detector at the South Pole.This process is called neutrino oscillation and the IceCube Detector, a massive neutrino detector buried deep in the ice at the South Pole, has a special area called DeepCore that can detect lower-energy neutrinos.

Scientists at the IceCube Neutrino Observatory in Antarctica have made a breakthrough in measuring neutrinos. Using advanced computer techniques, they've achieved the most precise measurements to date of how these particles change as they travel through space, helping us understand fundamental properties of the universe that could lead to new discoveries in physics.

Shiqi Yu

Shiqi Yu, a research assistant professor in the Department of Physics & Astronomy at the University of Utah and others who published their findings recently in Physical Review Letters analyzed data from over 150,000 neutrino events collected over nine years (2012-2021). They used advanced computer programs called convolutional neural networks (CNNs) to process this data. The team made the most precise measurements ever of two important properties related to neutrino oscillation: Delta m²₃₂ and sin²(θ₂₃). These numbers help describe how neutrinos change as they travel.

“We also carefully studied the systematic uncertainties that arise from our imperfect knowledge of our models and chose some to use as free nuisance parameters that fit together with the physics parameters for our data,” says Yu.

Using CNNs, which use three-dimensional data for image classification, Yu and co-lead of the study Jessie Micallef first developed use cases for the CNNs to focus on the DeepCore region and trained them to reconstruct different properties of particle interactions in the detector. They then used the CNN reconstructions to select qualified neutrino interactions that happened in or near the DeepCore region to produce a neutrino-dominated dataset with well-reconstructed energies and zenith angles.

Jessie Micallef

Yu notes that the CNN-reconstructed analysis-level dataset is already being used for other neutrino oscillation analyses, such as determining the neutrino mass ordering and non-standard neutrino interactions and for atmospheric tau neutrino appearance analyses.

“The atmospheric neutrino dataset from DeepCore exhibits relatively high energies in the oscillation analyses, which is unique compared to existing accelerator-based experiments,” says Yu. “Given our dataset and independent analysis, it is interesting to see agreement and consistency in physics parameter measurements.”

This research helps confirm and refine our understanding of how neutrinos — fundamental particles that can tell us a lot about the universe — behave. The techniques developed here, animated by machine learning, can be used in future studies to learn even more about neutrinos and the universe. Those future studies will be informed by IceCube which is planning an upgrade in 2025-2026 that will allow for even more detailed measurements of neutrinos.

By studying neutrino detection and the phenomenon of neutrino oscillation, scientists like Shiqi Yu hope to answer big questions about the nature of matter, energy and the cosmos.

From Curious Volunteer to Dinosaur Discoverer

July 9, 2024

As a young adult, Carpenter wasn’t sure if college was for her, but she did want to reconnect with her childhood love of paleontology. She started doing volunteer fieldwork with the Natural History Museum of Utah and her passion led Carrie Levitt-Bussian, the paleontology collections manager, to suggest she intern at the museum. There was just one catch. Carpenter would need to be a student at the University of Utah.

“I took the shot and applied for the U and luckily I got in,” said Carpenter.

Recent U graduate Savhannah Carpenter is the a co-author on a paper about the world’s newest horned dinosaur.

Once at the U, Carpenter immediately started taking dinosaur classes and met paleontologist and faculty member, Mark Loewen. Impressed by her communication skills, Loewen asked her to be a teaching assistant for his course. “Sometimes I would just turn the class over to her and let her answer questions,” Lowen said. “It is amazing to watch her think on her feet.”

According to Loewen, having people who can communicate science like Carpenter is essential.“I have lots of colleagues in the field who are amazing researchers and I respect their work,” he said. “But they can’t get people excited about it. The future of scientific research, and the funding of scientific research, really hinges on whether we can get other people excited about what we are doing.”

As part of her undergraduate studies, Carpenter also worked on ceratopsian research with Loewen. Through the Department of Geology and Geophysics, she was even able to get course credit for this work. Recently the 2024 U grad joined him and other researchers as a co-author on a paper identifying a new type of dinosaur, Lokiceratops rangiformis. “I was really excited to share Lokiceratops with the world because no one has seen him in 78 million years and it’s nice to welcome him back,” she said.

“Sometimes being a science person looks like playing in the dirt or rock climbing and making observations,” Carpenter said. “It’s not always doing chemistry in a lab. Fieldwork really helped bring me back to my roots and realize we are all science people. It just looks different for everybody.”

Undergraduate research played a key role in helping Carpenter connect with her coursework.

Read more about Savhannah Carpenter's journey @The U.

Journey to the Center of Biotech

July 8, 2024

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.

July 8, 2024

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.

Ants and Trees: A Tale of Evolutionary Déjà Vu in the Rainforest

U biologist Rodolfo Probst finds multiple ant species that have independently evolved the same specialized relationship with understory trees

Rethinking the Carbon Offsets Market

Around 1989 an energy company was trying to see if they could plant trees in Guatemala and then use the absorption of carbon from those trees to offset their emissions of a new coal-fired power plant in the United States.

A Framework for Cancer Ecology and Evolution

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

Cancer's complexity

Tracking the dual nature of cells

What do cycling and rocks have to do with each other?

University of Utah geologists Peter Lippert and Sean Hutchings are helping bring attention to the hidden star of a major sporting event this summer.

Geo Tour de France project

Tectonic training camp

A Wealth of information

BERTON EARNSHAW NAMEd COLLEGE OF SCIENCE SENIOR FELLOW

A deep learning and AI expert, Earnshaw joins the College’s Leadership Team.

A once-in-a-career discovery: the black hole at Omega Centauri’s core

Omega Centauri is a spectacular collection of 10 million stars, visible as a smudge in the night sky from Southern latitudes.

A range of black hole masses

Neutrino Oscillation Research Advances

In the world of particle physics, electrical charges define the terms. While electrons have a negative charge, the appropriately named “positron" has a positive charge. But then there are neutrinos which have no charge at all.

From Curious Volunteer to Dinosaur Discoverer

Savhannah Carpenter’s route to being the only student listed on the research team credited with finding the world’s newest horned dinosaur didn’t follow a straight line.

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Journey to the Center of Biotech

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

Hypothesis-free Diagnostics

Hybrid Capture

Precision Oncology

Accelerating the pace

Delve into the puzzle of ice crystallization and uncover its secrets

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

From Curious Volunteer to
Dinosaur Discoverer