Research

Crab Nebula

June 2, 2020

Utah scientists detect Crab Nebula using innovative gamma-ray telescope.

Scientists in the Cherenkov Telescope Array (CTA) consortium today announced at the 236^th meeting of the American Astronomical Society (AAS) that they have detected gamma rays from the Crab Nebula using a prototype Schwarzschild-Couder Telescope (pSCT), proving the viability of the novel telescope design for use in gamma-ray astrophysics. University of Utah faculty and staff in the Department of Physics & Astronomy are key members of the international research team announcing this technological breakthrough.

Animation showing 18 gamma-ray events from the Crab Nebula.

“The Crab Nebula is the brightest steady source of TeV, or very-high-energy, gamma rays in the sky, so detecting it is an excellent way of proving the pSCT technology,” said Justin Vandenbroucke, associate professor, University of Wisconsin. “Very-high-energy gamma rays are the highest energy photons in the universe and can unveil the physics of extreme objects including black holes and possibly dark matter.”v

Detecting the Crab Nebula with the pSCT is more than just proof-positive for the telescope itself. It lays the groundwork for the future of gamma-ray astrophysics. “We’ve established this new technology, which will measure gamma rays with extraordinary precision, enabling future discoveries,” said Vandenbroucke. “Gamma-ray astronomy is already at the heart of the new multi-messenger astrophysics, and the SCT technology will make it an even more important player.”

The use of secondary mirrors in gamma-ray telescopes is a leap forward in innovation for the relatively young field of very-high-energy gamma-ray astronomy, which has moved rapidly to the forefront of astrophysics. “Just over three decades ago, TeV gamma rays were first detected in the universe, from the Crab Nebula, on the same mountain where the pSCT sits today,” said Vandenbroucke. “That was a real breakthrough, opening a cosmic window with light that is a trillion times more energetic than we can see with our eyes. Today, we’re using two mirror surfaces instead of one, and state-of-the-art sensors and electronics to study these gamma rays with exquisite resolution.”

The initial pSCT Crab Nebula detection was made possible by leveraging key simultaneous observations with the co-located VERITAS (Very Energetic Radiation Imaging Telescope Array System) observatory. “We have successfully evolved the way gamma-ray astronomy has been done during the past 50 years, enabling studies to be performed in much less time,” said Wystan Benbow, director, VERITAS. “Several future programs will particularly benefit, including surveys of the gamma-ray sky, studies of large objects like supernova remnants, and searches for multi-messenger counterparts to astrophysical neutrinos and gravitational wave events.”

The pSCT - photo: Amy C. Oliver

Located at the Fred Lawrence Whipple Observatory in Amado, Arizona, the pSCT was inaugurated in January 2019 and saw first light the same week. After a year of commissioning work, scientists began observing the Crab Nebula in January 2020, but the project has been underway for more than a decade.

“We first proposed the idea of applying this optical system to TeV gamma-ray astronomy nearly 15 years ago, and my colleagues and I built a team in the U.S. and internationally to prove that this technology could work,” said Vladimir Vassiliev, principal investigator, pSCT. “What was once a theoretical limit to this technology is now well within our grasp, and continued improvements to the technology and the electronics will further increase our capability to detect gamma rays at resolutions and rates we once only ever dreamed of.”

David Kieda, professor at the U and dean of the Graduate School, was principal investigator of the U pSCT team and system engineer of the telescope. Along with Harold Simpson, facilities director of the U’s Department of Physics & Astronomy, and graduate research assistant Ahron Barber, Kieda led the design and fabrication of multiple auxiliary systems for the telescope: sun protection, signal cable, power and communication systems and the specification and selection of the telescope’s drive system. The Utah team also solves a big problem—how to keep the telescope’s sophisticated high speed camera cool.

“The camera is like a racecar engine the size of the toaster—it generates a lot of heat,” Kieda said. “We can’t vent the heat near the camera because that would distort the local air and affect the telescope performance. So we came up with a sophisticated cooling system using high capacity heat exchangers and fans in the camera, cooled by a remotely located chilled water supply.”

Kieda was also tasked with integrating all the telescope subsystems originating from teams around the country into a workable system.

“I call this ‘putting the ship in the bottle’. It’s the same thing building cameras—how do I actually get the pieces together correctly?” Kieda said. “The telescope camera weighs nearly a thousand pounds. You have to stage the lifts, position it, and install it in tight quarters without damaging the secondary mirrors , while keep everybody safe. It was a challenge—this is the first time anyone has built this type of telescope.”

The pSCT was made possible by the contributions of thirty institutions and five critical industry partners across the United States, Italy, Germany, Japan, and Mexico, and by funding through the U.S National Science Foundation Major Research Instrumentation Program.

“That a prototype of a future facility can yield such a tantalizing result promises great things from the full capability, and exemplifies NSF’s interest in creating new possibilities that can enable a project to attract wide-spread support,” said Nigel Sharp, program manager, National Science Foundation.

Now demonstrated, the pSCT’s current and upcoming innovations will lay the groundwork for use in the future Cherenkov Telescope Array observatory, which will host more than 100 gamma-ray telescopes. “The pSCT, and its innovations, are pathfinding for the future CTA, which will detect gamma-ray sources at around 100 times faster than VERITAS, which is the current state of the art,” said Benbow. “We have demonstrated that this new technology for gamma-ray astronomy unequivocally works. The promise is there for this groundbreaking new observatory, and it opens a tremendous amount of discovery potential.”

About the pSCT

The SCT optical design was first conceptualized by U.S. members of CTA in 2006, and the construction of the pSCT was funded in 2012. Preparation of the pSCT site at the base of Mt. Hopkins in Amado, AZ, began in late 2014, and the steel structure was assembled on site in 2016. The installation of the pSCT’s 9.7-m primary mirror surface —consisting of 48 aspheric mirror panels—occurred in early 2018, and was followed by the camera installation in May 2018 and the 5.4-m secondary mirror surface installation—consisting of 24 aspheric mirror panels—in August 2018. Scientists opened the telescope’s optical surfaces and observed first light in January 2019. It began scientific operations in January 2020. The SCT is based on a 114 year-old two-mirror optical system first proposed by Karl Schwarzschild in 1905, but only recently became possible to construct due to the essential research and development progress made at the Brera Astronomical Observatory, the Media Lario Technologies Incorporated and the Istituto Nazionale di Fisica Nucleare, all located in Italy. pSCT operations are funded by the National Science Foundation and the Smithsonian Institution.

For more information visit https://www.cta-observatory.org/project/technology/sct/

About CTA

CTA is a global initiative to build the world’s largest and most sensitive very-high-energy gamma-ray observatory consisting of about 120 telescopes split into a southern array at Paranal, Chile and a northern array at La Palma, Spain. More than 1,500 scientists and engineers from 31 countries are engaged in the scientific and technical development of CTA. Plans for the construction of the observatory are managed by the CTAO gGmbH, which is governed by Shareholders and Associate Members from a growing number of countries. CTA will be the first ground-based gamma-ray astronomy observatory open to the worldwide astronomical and particle physics communities. *Adapted from a release written by Amy Oliver, Fred Lawrence Whipple Observatory.

For more information visit http://cta-observatory.org/

Media Contacts

Dave Kieda, Dean of the Graduate School; professor, Department of Physics & Astronomy
dave.kieda@utah.edu

Lisa Potter, research/science communications, University of Utah Communications
lisa.potter@utah.edu

Hedgehogs and Undergrads

April 26, 2020

The students’ fresh, undaunted determination to scientific inquiry, combined with a lack of preconceived notions and a willingness to learn, were key factors that enabled their groundbreaking discoveries.

Corvin Arveseth, BS’21, can’t remember when he wasn’t fascinated by science and biology. So, when he came to the University of Utah and declared his majors in biology and biochemistry, he knew he wanted hands-on experience in research. “I didn’t know anything [about the] Hedgehog (Hh) signaling [pathway] until I read an advertisement put out by Ben Myers in a biology department newsletter looking for undergraduate researchers,” he says. “After reading some background information and meeting with Ben about the Hh pathway, I became intrigued with the work being done in his lab.”

The Hh pathway he’s referring to is akin to a master set of instructions for animal development and regeneration. It controls the formation of nearly every organ in the human body. Signaling pathway like Hh serve as a molecular “telephone wire” from the cell surface to the nucleus. When cells in our bodies communicate with one another, signals are relayed along these molecular telephone wires, turning on expression of genes involved in growth, differentiation, or in some cases skin and brain cancers.

The Hh pathway got its unusual name from decades-old genetic studies in fruit flies, where mutations in critical developmental genes led the flies to take on a bristly hedgehog-like appearance. However, versions of the Hh pathway operate throughout the animal kingdom, controlling development, stem cell biology, and cancer in many different contexts.

But even after many years of effort by labs all over the world, surprisingly little was known about how the Hh pathway actually works at a molecular level. Scientists knew that the signals conveyed by these molecular telephone wires were fundamental to human development and disease, but they didn’t know what the signals were, or how they were transmitted intracellularly. Consequently, health researchers’ ability to control Hh signaling in many diseases including cancer had been limited.

So, this is a story not just about a seemingly intractable research question, which is de rigeur in scientific circles, but how a team of largely undergraduate students in a four-year-old lab worked together under enormous odds to shake loose that answer. Myers says that that it was because of inexperience, not in spite of it, that the undergraduates in his lab were able to make these discoveries. These students’ fresh, undaunted determination to scientific inquiry, combined with a lack of preconceived notions and a willingness to learn, were key factors that enabled their groundbreaking discoveries.

Two papers, both with U undergraduates as first or co-first authors, were the gratifying result.

Mysterious pathways

When Myers first set up his lab at the U in 2018, the key molecule in the Hh pathway that grabbed his attention was SMOOTHENED (SMO), a so-called “transmembrane protein” that spans across the cell membrane from the outside to the interior. SMO was known to be critical for transmitting signals from the cell surface to the nucleus. But what were the five or six steps between receiving the message and turning on gene expression? There was a “major disconnection about how this worked,” says Myers.

The twenty-five-year-old mystery was indeed tantalizing. It was “this interesting mystery coupled with the importance of Hh function,” says Aveseth, “in developmental and cancer biology [which] hooked me right away,”

Spearheading the project

Arveseth was the point of the spear for this project begun at the beginning of his sophomore year. But there were many others on the team, all of whom are “both incredibly smart, and also very kind and a lot of fun to work with,” according to Myers. This includes Nate Iverson, a third year chemistry major with an interest in cellular signaling. “Having HCI in close connection with the University gave me greater access to research possibilities, and I was able to find an opening in the Myers lab studying Hedgehog signal transduction.”

And then there was biology major Isaac Nelson, who worked tirelessly to produce a freezer full of carefully prepared, purified fragments of SMO for biochemical studies, only to hit a brick wall when he and Myers were unable to formulate a good hypothesis to drive an experiment. “It was only after starting up an international collaboration,” says Myers, “that the critical experiments snapped into view for us.” This led Nelson to send his samples to one of the lab’s new collaborators in Germany, and they used his samples to try an experiment that worked right away. In the midst of a raging pandemic, Nelson’s purified proteins helped to launch a new and entirely unexpected phase of the project, expanding the collaboration to include other scientists around the world.

“It was another scenario,” says Myers, “where everyone worked well together.”

Recent graduate Madison “Madi” Walker, BS’21, with a cell and molecular emphasis, was also part of the team. She is still working in the Myers lab studying another critical aspect of SMO signaling, namely the interaction between SMO and the enzyme G protein-coupled receptor kinase 2. Earlier, former undergraduate Jacob Capener, BS’20, assisted in the work.

Another critical member of the Myers lab team is Will Steiner, BS’21, who is currently collaborating with Arveseth and Nelson to purify SMO in complex with its binding partners in order to work out their atomic structures. He became interested in this area of research after taking the cell biology and biochemistry course at the U. “Biochemistry was particularly compelling and got me excited about the chemical reactions behind human physiology,” he says.

It starts in the classroom

Rigorous courses were critical in preparing Myers’ undergraduate team for the hands-on research that led to their remarkable findings in the lab. He has nothing but kudos for the U’s curriculum. “Coursework before the lab experience [for undergraduate researchers] was very, very good here. In general, I’ve been lucky to attract motivated and curious students to my lab. They are inspired to push the research forward. They are all up to the challenge. And they have a great esprit de corps. They all work incredibly well together as a team to drive the science forward.”

That kind of correlated teamwork was not necessarily easy to enact under the circumstances. “Fortunately, we were able to finish the last key experiment of the first paper,” says Myers, in March 2020, just before the pandemic started to take hold and shut lab work down. He’s always believed that having undergraduates get a taste of cutting-edge research is important. They “shouldn’t have to work on something trivial… . What’s exciting about science is to push the boundaries.”

And yes, for Myers and the other senior members of his lab, including graduate students Danielle Hedeen and Aram Centeno, lab manager Ju-Fen Zhu, and former lab technician John Happ, “you have to be committed to helping everybody in your lab, even if they’re neophytes.” Clearly it’s been worth it. “And being a little bit of a neophyte is good,” he says, “because you don’t talk yourself out of doing experiments that are simple, unorthodox.”

Asking the right questions

What Myers is trying to say, and seems to have proven over the course of the past three years and now the publication of two discovery-laden papers, is that their remarkable findings stemmed from the initial naïve view that the SMO protein didn’t fit the mold of other proteins as was previously assumed. He and Arveseth took a guess that SMO might be directly coupled to a critical intracellular signaling molecule called PKA. This was a rather wild idea, since there were few if any examples of transmembrane proteins that directly interacted with PKA. “It was a guess, how it might work, and a couple of months later: big discovery. Our initial guess was on the right track. There was a whole new unexpected thing going on but that made sense.”

Though early on the team suspected what they had discovered was important, “we didn’t know if we had a full explanation of how the system worked. We weren’t sure if it was the main event or an auxiliary event.” In the first paper, published in the journal PLOS Biology last year, they explained that: what they thought they knew, and what they weren’t sure about . . . yet.

But it was only after the pandemic was in full force that the team pivoted to the second exciting phase of the project, expanding to include Susan Taylor’s lab at the University of California, San Diego, one of the world’s foremost authorities on the PKA molecule the Myers team had implicated in their research.

Taylor and her colleagues had a critical insight regarding the SMO-PKA interaction which eventually formed the basis of a second manuscript, currently in press in the journal Nature Structural and Molecular Biology. “It is a truly remarkable and inspiring collaboration that continues to this day, and I am so proud of how everybody was able to join forces and overcome so many obstacles created by the COVID-19 pandemic,” says Myers. And his team is anticipating that even more exciting discoveries are on the horizon. Eventually, this work may lead to better drugs to treat some of the diseases that result from aberrant Hh signaling, including various skin and brain cancers.

In all, with the resulting two papers, the project turned out to be a “best case scenario that wasn’t planned,” and a lesson of how important it is to keep an open mind, which often leads to big discoveries. Concludes Myers, “To be honest, it comes down to the willingness to try new things and to have the ability to work together as a team. In reality, this would have been way too much for any individual scientist, even a highly trained one, to do alone.”

Success is never final, however. And Arveseth, recipient of no less than ten scholarships and awards during his sojourn at the U, is now on his way to Washington University in St. Louis. There he will begin an MD/PhD program as a physician-scientist this fall. There he will focus on hematology and oncology. His colleagues are also pursuing their academic and research careers full-steam ahead. They, along with their mentor, Ben Myers are a testament to the notion that persistence in knowledge gathering pays off but that it must be paired and even driven by a relentlessly open mind.

Courtship Condos

April 8, 2020

Dean Castillo

Playing to the ethic of pursuing pure science, new faculty member Dean Castillo is driven by research questions not necessarily the research organism. While working on his bachelor’s and even before that while growing up in rural northern California, he worked with “tons of different organisms,” he says, including fungi. So it wasn’t difficult for him as a geneticist to move from his earlier subjects such as tomatoes and nematodes at Indiana University, where he earned his PhD, to fruit flies (Drosophilia) during his postdoc at Cornell and now at the University of Utah.

The question for Castillo was the same: how do natural and sexual selection shape mating interactions and behaviors, species interactions, and ultimately speciation?

The focus of Castillo, a recent faculty arrival at the School of Biological Sciences, remains evolutionary interactions between organisms, whether in “fruit” or the flies that feed on the yeast of that fruit. Genes determine behavior, and in the case of the fruit fly the female can mate with more than one male and store different sperm in different organ “storage areas” before determining which sperm will be used. How does that anatomically happen and what genes are motivating the female to determine which sperm is used?

Drosophilia - Fruit Flies

“Why does one female mate but another doesn’t?” he further asks. Once his lab determines how and where sperm from two different males is being stored in one female they will pursue other areas of inquiry: finding the genes that control female choice in the brain and, instead of pollen competition from his tomato days, it’s now sperm competition.

The equipment Castillo uses for his research includes one centimeter-high glass “condos” for the tiny flies with removable “gates.” From cotton-topped vials where the flies live on a bed of molasses and yeast, the researcher inserts a female in one side of a bifurcated chamber and a male in the other. Once the researcher lifts the gate between the sides, they can observe the eternal mating behavior of the two sexes on the micro level.

Behavior is only part of the Castillo lab’s integrative approach which combines these condo experiments with population and molecular genetics to understand the genetic basis of sexual behaviors. The approach is also designed to explore the reduction or cessation of reproduction between members of different species. (Think of crossing a horse and a donkey to produce a mule, which is sterile). Comparative genomics can help track this “reproductive isolation,” as it is termed, across the tree of life.

Drosophilia - Fruit Flies

“By studying the mechanistic and genetic links between sexual selection and reproductive isolation we can determine the influence of these forces on generating biodiversity,” says Castillo, sitting in the adjacent office to his lab on the fourth floor of the Aline W. Skaggs biology building. The almost feral view out his windows eastward to the Wasatch is a reminder of one of the big attractions to taking a position at the University of Utah: its stunning setting and, perhaps more importantly, its accessibility to wild nature. In fact, the flies that Castillo studies are easily found in the area, including in American Fork Canyon and Zions National Park. His wife Deidra, who with Dean also earned her PhD from Indiana University at Bloomington, begins her research soon in the Vickers lab one floor down. It turns out that there is overlap between her research in plant-insect interactions and Vickers’ research in moth olfaction and neuroethology.

Managing courtship condos to get at basic biology questions like how genes control behavior can seem random, even mercurial. This is especially true when compared to the careful planning required to procure one’s own family when both parents are academics. (The Castillos have three children, including a one-year-old.) It turns out that their first child was born during qualifying exams. Later, number two entered the scene while they were both defending their theses, the third during their postdocs prior to their move to Utah.

Dean Castillo with a few thousand research subjects.

For the time being, the five Castillos will be staying put except, perhaps, for combining science with mountain and high-desert camping trips looking for fruit flies.

Discover 2019

February 4, 2020

Running with Scissors

January 4, 2020

Jamie Gagnon

One could argue that the age of genomes is divided between before CRISPR-Cas9 and after CRISPR-Cas9 (commonly referred to as just “CRISPR”). As a Harvard post-doc studying the genes involved in embryo development, James (Jamie) Gagnon remembers in 2012 that “pivotal moment” when these “really nice pair of scissors now easy to make” came on the scene.

“Before CRISPR,” says Gagnon whose interest early on had been more in engineering than biology, “we were all using the earlier generation of genome editing tools. Even so, we were able to determine that after making a mutation in a cell, when it divided, the change that had been made was inherited.”

The new “scissors” rapidly scaled up genome editing, allowing researchers to more easily alter DNA sequences and modify gene function. At the time CRISPR was inspiring others to move from the research model of smaller organisms like the c. elegans, a transparent worm made up of approximately 1,000 cells, to much larger ones like zebrafish. “The power of genetics,” Gagnon says, “is that zebrafish are now genetically accessible model of all vertebrates, including humans which share 70 percent of genes with fish.”

Zebrafish Research subjects

The impulse for Gagnon’s current work in vertebrate lineage and cell fate choice happened in Northern Maine, during a winter-mountaineering trip with his friend and fellow researcher Aaron McKenna whom he met while they were undergraduates at Worcester Polytechnic Institute in Massachusetts. There in the wilds, not far from Vermont where Gagnon grew up, ensued an extended conversation between the two which started to form a deeply complex but exciting research question.

“If we want to study how embryos grow, we have to do it in a living animal,” Gagnon remembers acknowledging to McKenna. “We knew we needed to do it [research] in live animals, complete and whole. I couldn’t shut up about it for several days,” he says, smiling. “Everyone was mutating genes.” It seems that at the time, and perhaps still to this day, ‘Let’s break a gene and see if you’re right about what it does’, was pro forma.

Zebrafish Scale

Instead, the developmental biologist (Gagnon) and the computational researcher (McKenna) decided to pick up where others had ended (and published), using technology in a creative way to mark cells with a genetic barcode that could later be used to trace the lineage of cells. The two were suddenly using data sets of CRISPR-scissor mutations to figure out how cells actually developed in zebrafish.

Still, the prevailing question for Gagnon the researcher is how does biology build an animal with millions of cells, all sharing information and all shape-shifting at the same time? And how does science then best go about studying that?

How does science turn chaos and cacophony into a symphony that is the marvel of a living organism?

A symphony orchestra isn’t a bad metaphor for the edge of science that Gagnon and his lab and colleagues find themselves standing at. (It helps, perhaps, that his wife Nikki, a trained studio artist, works at the Utah Symphony | Utah Opera.) “For thirty years,” says Gagnon, people have been deciphering the genome code … one of the worst computer codes ever written.” Just how bad is bad? Imagine three billion letters in one long line with no punctuation or formatting.

The Gagnon Lab

Perhaps it’s the engineer in him, but to get at that unwieldy code, he sees his task as finding additional tools to regulate CRISPR activity. These tools include doing base-editing and using self-targeting guide RNAs to facilitate cells themselves making a record of what they’re doing, what they’re listening to, as it were, as they play their own “score” of development. “We want to turn the single, really good sharp knife of CRISPR,” he explains “into a Swiss Army knife” to figure out the score of an organism’s symphonic work.

The micro-scissors of CRISPR that appear to have issued a sea change in genomic studies, he hopes, can be used to “force cells to make notes along the way” of their own developmental journey. “Every time the oboe plays,” he says, returning to the metaphor, “we want the player [the cell] to make a record and journal entry on it.”

Illustration by The Gagnon Lab

“In early embryos, there are multiple languages or instruments being used by a finite number of cells to communicate with other cells and to build an animal,” he continues. To which language/instrument does a cell “listen” to, and what choices (expression) does it make as a result?

In a sense Jamie Gagnon is no longer just trying to “decode” the genome, but to use CRISPR to make a version, readable to humans, of what cells are doing in real time and how. In short he’s looking for the creation of a cell-generated Ninth Symphony, a complex but coordinated record of how development occurred that a Beethoven would be proud to conduct.

It may be dangerous to run with scissors, something parents routinely warn their children of, but it turns out that a really good pair of them can do more than the obvious: they can inspire other technologies that promise to bend the arc of science towards even greater aspirations.

by David Pace

Electrochemistry

January 3, 2020

Henry S. White

From energy storage and generation to nanoscale 3D battery architectures to the transport of drugs through human skin, Henry White’s research is pioneering and highly imaginative within the field of electrochemistry. His work on nanoscale electrochemistry was groundbreaking and has developed into a significant field of research with various applications. Professor of Chemistry Shelley Minteer commented that White “greatly enjoys complex problems and is the electrochemist to go to when you have complex mass transport phenomena to understand.”

There’s an obvious reason why Henry White is considered one of the most influential and innovative electrochemists of his generation: he wears his passion and thoroughness for research on his sleeve. White maintained a strong research group funded by the National Institutes of Health, National Science Foundation, the Department of Energy, and the Department of Defense while serving for six years as Chair of the Department of Chemistry, then five years as Dean of the College of Science. His administrative service was a commitment back to an institution that allows him to do what he loves most: teaching and research.

Henry S. White

Now that he can once again devote all of his time to research and teaching, White is thrilled to be immersed in the frontiers of electrochemistry—asking relevant and innovative questions for our generation’s complex problems. As the Widtsoe Presidential Chair, he continues to train postdoctoral fellows, undergraduates, and graduate students in electrochemistry. The Widtsoe Chair specifically is valuable in providing funding for students to do high risk and truly innovative research that they wouldn’t otherwise be able to do.

“There are a lot of great questions” in the field of electrochemistry says White. Research isn’t just about solving a problem, it’s about learning how to ask interesting and original questions—something White finds a lot of joy in doing.

“Electrochemistry is a fascinating area of science, and a very diverse area, comprising many fundamental research topics in chemistry, materials science, physics, and engineering. It is also extremely relevant in providing potential solutions to many problems that society faces, especially in providing means for developing sustainable energy sources. I’ve been very fortunate during my career to have had the necessary funding and resources to work on very basic science questions in this area. And I’ve been even more fortunate to be able to work with incredibly talented students and postdocs at the University of Utah, many who have continued to work on electrochemical problems in both industry and academics.”

Dr. Hang Ren, a former postdoc of White’s who is now an Assistant Professor at Miami University in Ohio, focused on electrical measurements on individual DNA molecules trapped inside a protein nanopore while training with White. They were able to trap a single DNA molecule for hours, and watch its motional dynamics, and monitor chemical reactions via the change in electrical current through the protein.

In a second research project, they used platinum electrodes with radii as small as 5 nanometers to measure the nucleation rates of bubbles. They were able to generate a single nanobubble at the electrode surface, measure the nucleation rate, and infer the geometry of the smallest stable bubble that contained as few as 25 molecules. “This is a fundamentally important problem in the field of electrocatalysis, where bubbles are often formed and disrupt the catalytic processes on the electrode,” says Professor Ren.

Dr. Rui Gao, Dr Henry S. White, & Dr Koushik Barman.

White trains his students and postdocs on how to be a researcher, to ask innovative questions, and to be relentlessly rigorous in their approach. As he works with undergraduate and graduate students as well as postdocs, his methods are significantly influencing the next generation of scientists to continue a legacy of research excellence. After training with White for years, Professor Ren affirms that “Henry’s research approach is very unique. In addition to solving scientific problems elegantly, he is especially great at asking fundamental scientific questions. He is also highly innovative and very good at exploring new directions in electrochemistry. I was greatly influenced by my postdoc training with him.”

Henry White’s research is often cited by other researchers and is foundational in the fields of electrochemistry and analytical chemistry. “Henry has an uncommon disposition for innovation in undertaking both experimental and theoretical challenges in his research,” says Joel Harris, Distinguished Professor of Chemistry. White’s research has been recognized in major awards from the Society of Electroanalytical Chemistry, the Royal Society of Chemistry, the ACS Division of Analytical Chemistry, and the Electrochemical Society. He is also a Fellow of the American Academy of Arts and Sciences, the American Chemical Society, and the American Association for the Advancement of Science.

Commutative Algebra

January 3, 2020

Srikanth Iyengar

“When we first study advanced math, we learn to solve linear and quadratic equations, generally a single equation and in one variable,” said Srikanth Iyengar, Professor of Mathematics at the U. “But most real-world problems aren’t quite so easy—they often involve multiple equations in multiple variables.”

Finding explicit solutions to such equations is generally not feasible nor useful—it’s much more helpful to look for overall structure in the collection of all possible solutions. These solution sets are called algebraic varieties. The word algebraic indicates their origin is from polynomial equations, as opposed to equations involving things like trigonometric and exponential functions. Over the centuries, mathematicians have developed various tools to study these objects. One of them is to study functions on the space of solutions, and algebra is a good way to begin. These functions form a mathematical structure called a commutative ring. Commutative algebra is the study of commutative rings and modules, or algebraic structures over such rings.

Iyengar’s research focuses on understanding these structures, which have links to different areas of mathematics, particularly topology and representation theory.

Iyengar joined the Mathematics Department in 2014. He grew up in Hyderabad, India, and received a master’s degree and Ph.D. from Purdue University. Before joining the U, he taught at the University of Nebraska-Lincoln.

The foundation of commutative algebra lies in the work of 20th century German mathematician David Hilbert, whose work on invariant theory was motivated by questions in physics.

Srikanth Iyengar, Professor of Mathematics at the University of Utah

As a subject on its own, commutative algebra began under the name “ideal theory” with the work of mathematician Richard Dedekind, a giant of the late 19th and early 20th centuries. In turn, Dedekind’s work relied on the earlier work of Ernst Kummer and Leopold Kronecker. The mathematician responsible for the modern study of commutative algebra was Wolfgang Krull, who introduced concepts that are now central to the study of the subject, as well as Oscar Zariski, who made commutative algebra a foundation for the study of algebraic varieties.

“One of the things I enjoy about my research is how commutative algebra has so many connections to other things,” said Iyengar. “It makes for rich and lively research. Commutative algebra is continually reinvigorated by problems and perspectives from other fields.” Funding for Iyengar’s research is from the National Science Foundation. The Humboldt Foundation and the Simons Foundation have also provided support.

Commutative rings arise in diverse contexts in mathematics, physics, and computer science, among other fields. Within mathematics, besides functions on algebraic varieties, examples of commutative rings include rings of algebraic integers—the stuff of number theory. Commutative rings also arise, in myriad ways, in the study of symmetries of objects—algebraic topology, graph theory, and combinatorics, among others. One of the areas of physics where commutative algebra is useful is with string theory.

In recent years, ideas and techniques from commutative algebra have begun to play an increasingly prominent role in coding theory, in reconstructions, and biology with neural networks. While not everything Iyengar does day-to-day (or perhaps even in the span of a few years) has a direct impact in the field, mathematicians have a way of impacting other areas far from their original source, often decades later. There are many striking examples of this phenomenon. The “unreasonable effectiveness of mathematics” is well known. The phrase is part of a title of an article published in 1960 by Eugene Wigner, a Hungarian-American mathematician and theoretical physicist.

“I work by thinking about a piece of mathematics—perhaps it’s a research paper or a problem I run into somewhere in a textbook or a talk,” said Iyengar. “This sometimes leads to interesting research projects; at other times, it ends in a dead end. My perspective on research is that it’s more like a garden (or many interconnected gardens) waiting to be explored, rather than peaks to be climbed. Sure, there are landmarks but there’s rarely a point when I can say, Well, this is it—there’s nothing more to be achieved.’’

TreeTop Barbie

December 11, 2019

When Nalini Nadkarni was a young scientist in the 1980s, she wanted to study the canopy – the part of the trees just above the forest floor to the very top branches.

But back then, people hadn't figured out a good way to easily reach the canopy so it was difficult to conduct research in the tree tops. And Nadkarni's graduate school advisors didn't really think studying the canopy was worthwhile. "That's just Tarzan and Jane stuff. You know that's just glamour stuff," Nadkarni remembers advisors telling her. "There's no science up there that you need to do."

They couldn't have been more wrong. Over the course of her career, Nadkarni's work has illuminated the unique and complex world of the forest canopy.

She helped shape our understanding of canopy soils — a type of soil that forms on the tree trunks and branches. The soil is made up of dead canopy plants and animals that decompose in place. The rich soil supports canopy-dwelling plants, insects and microorganisms that live their entire life cycles in the treetops. If the canopy soil falls to the forest floor, the soil joins the nutrient cycles of the whole forest.

She also discovered that some trees are able to grow above-ground roots from their branches and trunks. Much like below ground roots, the aerial roots can transport water and nutrients into the tree.

During Nadkarni's early work as an ecologist she began to realize something else: There weren't many women conducting canopy research.

Nadkarni was determined to change this. In the early 2000s, she and her lab colleagues came up with the idea of TreeTop Barbie, a canopy researcher version of the popular Barbie doll that could be marketed to young girls.

She pitched the idea to Mattel, the company that makes Barbie. "When I proposed this idea they said, 'We're not interested. That has no meaning to us," says Nadkarni. "We make our own Barbies."

Nadkarni decided to make them herself anyway. She thrifted old Barbies; commissioned a tailor to make the clothes for TreeTop Barbie; and she created a TreeTop Barbie field guide to canopy plants. Nadkarni sold the dolls at cost and brought TreeTop Barbie to conferences and lectures.

Her efforts landed her in the pages of The New York Times, and word eventually got back to Mattel. The owners of Barbie wanted her to shut down TreeTop Barbie due to brand infringement.

Nadkarni pushed back.

"Well you know, I know a number of journalists who would be really interested in knowing that Mattel is trying to shut down a small, brown woman who's trying to inspire young girls to go into science," she recalls telling Mattel.

Mattel relented. The company allowed her to continue her small-scale operation. By Nadkarni's count, she sold about 400 dolls over the years.

Then in 2018, more than a decade after Nadkarni started TreeTop Barbie, she got an unbelievable phone call. National Geographic had partnered with Mattel to make a series of Barbies focused on exploration and science. And they wanted Nadkarni to be an advisor.

"I thought, this is incredible. This is like full circle coming around. This is a dream come true," says Nadkarni.

For its part, Mattel is "thrilled to partner with National Geographic and Nalini," a spokesperson told NPR.

Nadkarni knows that everyone might not approve of her working with Barbie. Barbie's role in creating an unrealistic standard of beauty for young women has been debated. Nadkarni has also wrestled with how she feels about it.

"My sense is yes she's a plastic doll. Yes she's configured in all the ways that we should not be thinking of how women should be shaped," says Nadkarni. "But the fact that now there are these explorer Barbies that are being role models for little girls so that they can literally see themselves as a nature photographer, or an astrophysicist, or an entomologist or you know a tree climber... It's never perfect. But I think it's a step forward."

Nadkarni is an Emeritus Professor at The Evergreen State College, and currently is a professor in the School of Biological Sciences at the University of Utah.

Nalini Nadkarni's story has appeared in The Washington Post, Time Magazine, Taiwan News, News India Times, Philadelphia Inquirer, National Geographic, The Guardian, Science Friday, San Francisco Chronicle, India Today, India Times, KSL News, Salt Lake Tribune, USA Today, BBC, The Morning Journal, CNN, UNEWS, Star Tribune, National Science Foundation, Continuum, TreeHugger, and many others.

Research Funding

December 5, 2019

Total Research Funding

Through the accumulated efforts of University faculty, students and staff, the U achieved its most successful research funding year ever in 2019, passing a $540 million milestone. The final total is $547 million, composed of grants large and small, from donors in all 50 states.

Recognized as a Top-Tier 1 research university—The University’s research vision is to cultivate national and international research community through excellence, innovation, and interdisciplinary research at the University of Utah.

In addition to the U’s diverse research portfolio, the institution is also a catalyst for economic growth and innovation, creating over 302 spin-out companies—and 16,000 jobs—from the university’s inventions and technologies.

With the determination and support of our research community, the University of Utah will continue to develop cutting-edge research to enhance the lives of current and future generations to come.

Going with the Flow

October 10, 2019

John Sperry

Retiring botanist studied how plant's xylem tissue carries phenomenal amounts of water to tree leaves where it evaporates and influences regional weather patterns.

John Sperry grew up in Normal, Illinois, but his interest in plants–eventually their vascular function–would propel him into work that was far from standard in botany via Duke University and, eventually Harvard where he earned his PhD. At Harvard his Swiss-born mentor Martin Zimmermann was considered among the top plant physiologists in the world and a scholar whom Sperry credits with, more than anyone else, “showing him how” to do research. Even so Zimmermann strongly questioned the ability of Sperry’s proposed, novel technique to measure the blockage of vascular flow by cavitation.

It was the ultimate success of that technique and new discoveries of how vascular tissues, or xylem in particular, function in conducting water and dissolved nutrients upward from roots, that would become the subject of Sperry’s PhD thesis. And it was that thesis and the questions it spawned that laid the foundation of all of the research he would do for the next 30+ years, including a stint as a post-doc at the University of Vermont prior to his arrival at the University of Utah in 1989.

“As humans, we are acutely aware of the importance of maintaining vascular function,” Sperry’s Research Statement reads. “To plants it is no less critical. My laboratory investigates hydro-vascular structure and function in plants in relation to their ecology, physiology, and evolution.” The scale of this function in plants is, he explains, a “phenomenal process. The sheer quantity of water moved through plants often exceeds river flow on a watershed scale,” he explains. “The plant's xylem tissue carries all of this water to the leaves where it evaporates and influences regional weather patterns.”

It takes “watershed scale” flow for plants to obtain CO2 from the atmosphere through their open stomata. It’s counter-intuitive, but the transport is driven by negative liquid water pressure, “a remarkable fact,” says Sperry “that will always irritate physicists” who often aren't as familiar with metastable fluids as is a plant physiologist.

Sperry and his lab study how plant form and function have evolved. To do this they have developed more efficient technologies for the larger data sets required. Sperry custom designed centrifuge rotors to quickly expose the vascular system of plants to a known negative pressure. This in turn has allowed him to create the kinds of vulnerability curves which improve prediction of plant water use and to help move his research toward macro applications in forests to predict plant responses to climate change.

What does the coordination look like between regulation of photosynthesis and environmental conditions? The answer lies in predicting what the stomata will do. Stomata are typically found in the epidermis of plant leaves. Specialized “guard cells” surround stomata and function to open and close stomatal pores, balancing the trade-off of water evaporation for required carbon dioxide.

“We … concentrate on the fundamental carbon-for-water trade-off that confronts all terrestrial plants,” continues Sperry. “Photosynthesis requires the plant surface to be porous to CO2 diffusion, but at the cost of also being porous to evaporative water loss.” Indeed, the xylem has been called "the vulnerable pipeline,” part of an elaborate system that includes “a transport system that teeters on the edge of physical possibility.” Failed water transport, or “cavitation,” is caused by water stress or freezing. Over the years, Sperry has learned that some plants are more vulnerable to this kind of “spectacular failure” than others. “This turns out to be part of the answer to the question of why some plants grow where they do when others cannot,” says Sperry. Vulnerability to cavitation provides the key to predicting how stomata respond to environmental cues, a missing element that Sperry and colleagues have integrated into predictive models for how plants respond to their environment.

Sperry with his centrifuge.

It’s not surprising then that Sperry’s work in plant hydraulics–the water stresses and trade-offs they face–has had a profound impact on predicting how rapid environmental change will affect the future of plants and forests. This according to U ecologist and Sperry colleague William “Bill” Anderegg. Before his own appointment in Biology, Anderegg, who was studying Colorado forests, spent time in Sperry’s lab. There he learned first-hand what was confirmed later for him about Sperry’s mentoring of young researchers.

“I attended a major conference in the field recently,” says Anderegg, “where there was a ‘mentor tree’–an artistic set of wooden branches where young scientists anonymously wrote the name of someone who had changed their career…. John's name was all over the tree and was the most frequent name by far.”

Sperry will retire from the University of Utah in December, so it’s a time to look back on a career that started, in retrospect, as early as kindergarten in his hometown of Normal. “Of course I was also obsessed with being a truck driver,” he adds. “But I did draw lots of trees and enjoyed watching our teacher demonstrate the ascent of food coloring in the transpiration stream of a celery stalk.”

But like a true scientist he is always looking forward as well, not just finding a home for that centrifuge with the custom-made rotors, but enlisting the programming skills of undergraduate lab associate Henry Todd. Todd, together with lab mates Martin Venturas and Yujie Wang, is facilitating climate change simulations of 520 combinations of 8 species in 20 sites across the country based on six climate projections and two emissions scenarios … over 30 years.

John Sperry will not be parsing through this kind of macro data for much longer, limiting himself to just a few more papers and farewell meetings. Retirement will allow him more time to adventure with his wife Holly in their truck camper and to be in his favorite laboratory: the outdoors. He and his canoeing buddies also look forward to expanding their summer-long explorations of northern wilderness, a place where you can travel over 600 miles under your own steam and not see another soul for a month and a half. Sperry is harking to the dictum: "no one on their death bed wishes that they had spent more time at work."

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Running with Scissors

Electrochemistry

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Commutative Algebra

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TreeTop Barbie

Research Funding

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Going with the Flow

Going with the Flow

Retiring botanist studied how plant's xylem tissue carries phenomenal amounts of water to tree leaves where it evaporates and influences regional weather patterns.