Sahar Kanishka

Undergraduate Research Award


Sahar Kanishka

Biology major receives 2021 Outstanding Undergraduate Researcher Award.

Sahar Kanishka remembers daily where her family came from, where they are now, and what opportunity there is for her at the School of Biological Sciences (SBS).

“I’ve always wanted to be a doctor ever since I was younger,” she recently explained in a video interview. “Because my family’s from Afghanistan and they actually fled from the Soviet invasion, they were telling me how the medical resources over there were very scarce when they were escaping. Like things we take for granted here [in the United States]. I want to be able to give back in some way. And that’s my way of giving back, becoming a doctor and contributing what I’ve learned here.”

What Kanishka, now in her junior year as an honors student, is learning happens largely in the Gagnon lab at the SBS where she and her colleagues are studying vertebrate lineage and cell fate choice along with cell signaling and genome engineering. Their subject model is the living zebrafish with which they are attempting to answer the question of how biology builds an animal with millions of cells. The question is complicated by the fact that those millions of cells are continually sharing information while shape-shifting at the same time.

Zebrafish

A living organism is the culmination of science turning chaos and cacophony into a kind of marvelous symphony. Using CRISPR-Cas9 gene-editing technology, the Gagnon lab is busy marking cells with a genetic barcode that could later be used to trace the lineage of cells that in the zebrafish are similar to other vertebrates, including humans.

The micro “scissors” of CRISPR is no longer just being used to decode the genome, but to make a version, readable to humans, of what cells are doing in real time and how. It’s research that’s contributing to a sea change in genomic studies, and Kanishka is there at the bench experiencing it firsthand. The way Jamie Gagnon, Principal Investigator who holds the Mario Cappechi Endowed Chair at SBS, puts it, the research Kanishka is doing “may lead to a holy grail method for developmental biology—the ability to record developmental history, in living animals, with molecular and spatial resolution.”

Little wonder then that the Undergraduate Research Program at the University of Utah chose Kanishka for this year’s award. In his nomination letter Gagnon, who referred to Kanishka as having “transitioned quickly into an independent scientist," also wrote that he has been “impressed with Sahar’s poise, focus and commitment to research over the last year, which has been particularly challenging for our undergraduate researchers… . Sahar is already the face of STEM research in the College.”

Kanishka’s journey at the U threaded through ACCESS, a signature program of the College of Science. It was a scholarship and mentorship experience that led to re-figuring what research could be. Instead of working primarily on a computer in isolation and doing anatomy lessons from a book, ACCESS and SBS provided her with a hands-on approach in its full cadaver lab. As a pre-med student hoping to earn a joint medical degree and doctorate, Kanishka’s turn as a teaching assistant to professor Mark Nielsen gave her added invaluable experience. ACCESS also gave her a practical skill set, like creating her first research poster and then presenting it publicly.

The ACCESS program

The same has been true in the Gagnon lab where she says you are free to mold your research experience to your own expectations. Research at the U “fosters an environment of curiosity of real research. It’s really beautiful,” she says, “to have someone [like Gagnon] believe in you like that.” This, she concedes, in spite of feeling at times like an imposter as the child of an immigrant family and as a woman. She’s had to “learn through lots of struggles.”

Some lessons from those struggles have been hard won. “You can’t just put science in a box and tell it what to do,” she explains. “I have to allow it the freedom to seek to understand the world rather than to just understand me.” Her joint undergraduate degree in business administration speaks to Kanishka’s sense of the intersectionality of all learning. She was especially impressed with a recent visit by Reshma Shetty, the inaugural SBS Distinguished Lab Alumni who worked with Baldomera “Toto” Olivera in his lab and is a co-founder of Boston-based Gingko Bioworks, a bio-engineering start-up.

But the ballast in Kanishka’s life--both that of her academic career’s and that of her personal story’s--continues to be family. That includes not only her younger sister and parents here in Utah, but also her extended family in Afghanistan and beyond. “I hate that we’re separated by distance,” she says, referring to her overseas cousins, aunts and uncles as “my other parents and siblings. I owe everything to them. They mean everything to me.”

Until she and her extended family are all at least on the same side of the globe, Kanishka has both advice and a caution for her undergraduate colleagues. “Figure out if you want to do something by actually doing it,” she advises, recommending internships for high schoolers not bound for college, including through a program she helps facilitate as a volunteer called Talent Ready Utah. “College can be a business,” she warns, “pumping out students” for a job market they may not resonate with or even prosper in.

But Sahar Kanishka is optimistic about things as well. When asked about the pandemic and the social and economic upheaval, she proffers a winning smile, while adding, “I’m excited to see how college will change and adapt.”

 
by David Pace
 

Beckman Abstract

  • Lineage tracing in zebrafish with CRISPR prime editing (S. Kanishka)
    All embryos develop from a single cell. We use lineage tracing to map the relationships between individual cells and back to the initial founding cell. These lineage trees can help us understand how cells acquire their fates during normal development, and how that can go wrong in human disease. An emerging method for lineage tracing in embryos uses cellular barcodes. Cellular barcodes individually tag cells with a unique set of mutations specific to that cell. As cell divisions occur, the barcode is passed on to the progeny cells and a lineage tree can constructed based on cells that share similar barcodes. The CRISPR-Cas9 system for gene editing is an ideal tool for creating a huge diversity of cellular barcodes in embryos. However there are limitations with CRISPR-Cas9, including unpredictable indel formation and difficulties in recovering barcodes from cells. In this project, a modified CRISPR system known as prime editing will be applied in zebrafish, and utilized for lineage tracing. Prime editing allows for precise genome editing by inserting user-specified genetic sequences at a target site in the genome. I hypothesize that we can use prime editing to insert a huge library of user-specified barcodes into the genome of developing zebrafish. Because these barcodes are defined by the experimenter, they can be recovered at the end of the experiment using RNA in situ hybridization. In principle, lineage tracing with prime editing will allow us to discover the spatial arrangement of related cells in intact embryos and tissues. We hope to use lineage tracing with prime editing to understand the mechanisms of heart regeneration in zebrafish.

T. Mitchell Aide

T. Mitchell Aide

Distinguished Alumnus, Biology

Following his graduation with a bachelor’s from University of Texas - San Antonio, California native T. Mitchell (Mitch) Aide ended up in Utah … but via Panama. It was in Central America where he first met School of Biological Sciences (SBS) professors Lissy Coley and Tom Kursar doing tropical forest research. Aide would eventually become Coley’s first graduate student at the University of Utah. Lissy and Tom were “different than some other advisors,” says Aide. “They showed how high-quality research did not have to exclude enjoying life.”

The relationship proved to be a productive one. Aide graduated from U with a PhD in 1989 and continued in his career as a researcher and professor. Recently he was presented the School of Biological Sciences 2021 Distinguished Alumni Award.

During his sojourn at the U (1982-1990) Aide says that the cohort of professors there “created an environment of high-quality research and education

Stand-up guy on Stand up paddleboard (SUP)

without being aggressively competitive.” He remembers the personal and financial support of the department staff when a house he lived in with other graduate students burned down. His graduate work included a single-authored publication in Nature in 1988, demonstrating that the synchrony of production of young leaves for a community of tropical trees may have evolved as an adaptation to reduce herbivory by insects.

Since then he has published more than 140 peer-reviewed articles. And, after Smithsonian and Fulbright postdoctoral fellowships in Panama and Colombia, respectively, he took a position at the University of Puerto Rico - Río Piedras in 1992, where he is now a full professor.

His research interests cover a diversity of topics related to tropical forest ecology, including plant/animal interactions, forest dynamics, population dynamics, restoration ecology, land change, community ecology, conservation, ecological informatics, and ecoacoustics. Presently, his research focuses on land-use change and its implication for biodiversity conservation.

“In addition to Mitch’s own scientific contributions,” wrote Coley in the nomination letter for the alumni award, Aide “has mentored an enormous number of students, most from Latin America. These include 18 Master’s students, 11 PhD students, over 50 undergraduates and eight postdoctoral fellows. His mentorship of the next generation of scientists has had profound impacts on education and conservation in Latin America.”

Aide has also started a company to monitor biodiversity. “This was motivated by his concern for the alarming loss of species in nature,” says Coley, before explaining that her former student’s innovation was to deploy many low-cost acoustic recorders in nature and then analyze the sounds to quantify changes in the community or to track individual species of interest.

“His company developed the sophisticated but user-friendly Automated Remote Biodiversity Monitoring Network (ARBIMON) platform so researchers can analyze these recordings for their own research,” continues Coley. “His goal is to have permanent acoustic biodiversity monitoring stations in thousands of sites throughout the world, including eco-tourism sites, research stations, protected areas, and threatened areas.”

A consummate researcher, academic and now founder of a company, Aide enjoys water sports, including surfing and snorkeling. After more than 40 years publishing on tropical ecology and conservation, and “seeing our poor progress in conserving tropical biodiversity,” he says with some rue, “I will try a different approach—write a novel.”

During this time of pandemic, personal and societal reflection is the order of the day. Aide expects that there will be substantial changes to higher education. Even so, he advises today’s students to “identify what you are good at and what you enjoy and dedicate 110%” to it.

As a 2021 SBS distinguished alumnus, Mitch Aide is an excellent model for dedication and hard work—even when pivoting late in an esteemed career towards fiction writing to further the cause of and raising consciousness about the critical need for conservation.

 
by David Pace
 

NAS Membership

mary beckerle elected to the national academy of science


The National Academy of Sciences has elected Mary Beckerle, PhD, Huntsman Cancer Institute (HCI) CEO and distinguished professor of biology and oncological sciences at the University of Utah (U of U), as a member. Beckerle is among 120 newly elected members announced in a press release during the annual meeting of the National Academy of Sciences.

Election as a member in this organization is widely accepted as a mark of excellence in scientific achievement and is considered one of the highest honors a scientist can receive. Of its more than 2,400 current members, approximately 190 have received a Nobel Prize, according to the National Academy of Sciences.

Beckerle shared she was “very surprised” to learn of her election to the prestigious group. She received a phone call this morning from a member of the National Academy of Sciences informing her of her election. Within minutes, she then received a flood of phone calls, emails, and text messages from colleagues congratulating her. “It was the most connected I have felt to my scientific community since the pandemic began, and it was lovely to be in touch with so many colleagues from around the world,” added Beckerle.

Beckerle’s research discovered a new pathway that is crucial in enabling cells to respond to mechanical signals in their environment. Such signals are now known to regulate cell growth and movement, two behaviors that yield critical insights into cancer biology. The Beckerle Lab is currently focused on understanding the molecular mechanisms underlying this pathway and its impact on tumor progression, particularly in Ewing sarcoma, a rare but deadly bone cancer that typically affects children and young adults.

“Dr. Beckerle’s election to the National Academy of Sciences affirms what her colleagues see every day. She is a driving force as an individual scientist, yet Dr. Beckerle’s hallmark is collaborative leadership that allows teams of scientists to achieve more together than they ever could alone,” said Michael L. Good, MD, University of Utah interim president and CEO of University of Utah Health. In addition to leading HCI, Beckerle holds the Jon M. Huntsman Presidential Endowed Chair and also serves as associate vice president for cancer affairs at the U of U. Beckerle is only the 27th faculty member in the history of the U of U to be elected to the National Academy of Sciences.

Beckerle joined the U of U faculty in 1986, when she set up her first independent laboratory as a young scientist. Prior to coming to Utah, she earned her PhD in molecular, cellular, and developmental biology from the University of Colorado at Boulder, where she received a Danforth Fellowship. She completed postdoctoral research at the University of North Carolina at Chapel Hill and received a Guggenheim Fellowship for her studies at the Curie Institute in Paris.

She has received numerous accolades for her research, including the National Cancer Institute Knudsen Prize in recognition of her contributions to research on the genetic basis of cancer. She is also an elected fellow of other distinguished scientific organizations, including the American Philosophical Society, the American Academy of Arts and Sciences, and the Academy of the American Association for Cancer Research.  She served as President of the American Society for Cell Biology and is a member of the Medical Advisory Board of the Howard Hughes Medical Institute.

As CEO of HCI, she led the organization to achieve its first-ever designation as a National Cancer Institute-Designated Comprehensive Cancer Center, the highest possible status of a cancer research institute. She also has led HCI’s clinical programs to recognition as among the nation’s Best Cancer Hospitals, according to U.S. News and World Report. Beckerle was appointed as a member of then-Vice President Biden’s Cancer Moonshot Blue Ribbon Panel, where she co-chaired the working group on Precision Prevention and Early Detection.

“It is an incredible honor to be named alongside exceptionally talented colleagues who are part of the National Academy of Sciences,” said Beckerle. “Scientific research is fascinating and motivating work, yet as a scientist, I often feel impatient. Each day, I work with the understanding that people are counting on the scientific community to make discoveries that will improve health, develop better treatments for diseases, enhance quality of life, and, wherever possible, prevent development of diseases like cancer. It is deeply humbling to see my contributions, and those of the many people who have worked in my lab over several decades, recognized in this way. My sincere hope is that the work of my research team will contribute to Huntsman Cancer Institute’s vision of delivering a cancer-free frontier.”

Beckerle adds that the National Academy of Sciences has a major impact in shaping science policy. She looks forward to the opportunity to contribute to the national dialogue on how to advance scientific innovation and impact via her role as a member of this organization.

first published by Ashlee Harrison of Huntsman Cancer Institute in @theU

AAAS Membership

Valeria Molinero elected to the american academy of arts and sciences


Valeria Molinero, Distinguished Professor and Jack and Peg Simons Endowed Professor of Theoretical Chemistry, is among the 252 newly elected members of the American Academy of Arts and Sciences. The Academy honors excellence and convenes leaders from every field of human endeavor to examine new ideas, address issues of importance to the nation and the world and work together.

Among those joining Molinero in the Class of 2021 are neuroscientist and CNN medical correspondent Sanjay K. Gupta, Pulitzer Prize-winning investigative journalist Nikole Hannah-Jones of the New York Times and media entrepreneur Oprah Winfrey.

Molinero joins 16 other members affiliated with the U, including Nobel laureate Mario Capecchi, Huntsman Cancer Institute CEO Mary Beckerle and Distinguished Professor of Anthropology Kristen Hawkes. The U’s first member was chemist and National Medal of Science recipient Henry Eyring, elected in 1958. Molinero currently directs a center for theoretical chemistry named for Eyring.

“I am surprised and elated by this recognition,” Molinero said. “My most pervasive feeling is gratitude:  to my trainees and collaborators for sharing with me the joy of science and discovery, to my colleagues and scientific community for their encouragement and recognition, and to the University of Utah for the support that has provided me throughout all my independent career.”

Molinero and her lab use computational simulations to understand the molecule-by-molecule process of how ice forms and how polymers, proteins and other compounds can either aid or inhibit the formation of ice. In 2019, the U awarded her its Distinguished Scholarly and Creative Research Award. In 2020, she and her colleagues received the Cozzarelli Prize from the journal Proceedings of the National Academy of Sciences for finding that the smallest nanodroplet of water that can form ice is around 90 molecules. Their research has application ranging from climate modeling to achieving the perfect texture of ice cream.

“This is not surprising, as Vale is just an outstanding scientist and colleague,” said Matt Sigman, chemistry department chair.

“Vale Molinero is among the most influential theoretical and computational chemists of her generation,” said Peter Trapa, dean of the College of Science. “ Today’s announcement is a fitting recognition of her exceptional career.”

The College of Science now features eight Academy members, including five from the Department of Chemistry.

The Academy was founded in 1780 by John Adams, John Hancock and others who believed the new republic should honor exceptionally accomplished individuals and engage them in advancing the public good. Studies compiled by the Academy have helped set the direction of research and analysis in science and technology policy, global security and international affairs, social policy, education and the humanities.

Current Academy members represent today’s innovative thinkers in every field and profession, including more than 250 Nobel and Pulitzer Prize winners.

first published by Paul Gabrielson in @theU

Patterns in Sound

Fernando Guevara Vasquez


U mathematicians create quasiperiodic patterns using sound waves.

Mathematicians and engineers at the University of Utah have teamed up to show how ultrasound waves can organize carbon particles in water into a sort of pattern that never repeats. The results, they say, could result in materials called “quasicrystals” with custom magnetic or electrical properties.

The research is published in Physical Review Letters.

“Quasicrystals are interesting to study because they have properties that crystals do not have,” says Fernando Guevara Vasquez, associate professor of mathematics. “They have been shown to be stiffer than similar periodic or disordered materials. They can also conduct electricity, or scatter waves in ways that are different from crystals.”

Quasiperiodic two-dimensional pattern by Fernando Guevara Vasquez

Non-pattern patterns

Picture a checkerboard. You can take a two-by-two square of two black tiles and two white (or red) tiles and copy and paste to obtain the whole checkerboard. Such “periodic” structures, with patterns that do repeat, naturally occur in crystals. Take, for example, a grain of salt. At the atomic level, it is a grid-like lattice of sodium and chloride atoms. You could copy and paste the lattice from one part of the crystal and find a match in any other part.

But a quasiperiodic structure is deceiving. One example is the pattern called Penrose tiling. At first glance, the geometric diamond-shaped tiles appear to be in a regular pattern. But you can’t copy and paste this pattern. It won’t repeat.

The discovery of quasiperiodic structures in some metal alloys by materials scientist Dan Schechtman earned a 2011 Nobel Prize in Chemistry and opened up the study of quasicrystals.

Since 2012, Guevara and Bart Raeymaekers, associate professor of mechanical engineering, have been collaborating on designing materials with custom-designed structures at the microscale. They weren’t initially looking to create quasiperiodic materials—in fact, their first theoretical experiments, led by mathematics doctoral student China Mauck, were focused on periodic materials and what patterns of particles might be possible to achieve by using ultrasound waves. In each dimensional plane, they found that two pairs of parallel ultrasound transducers suffice to arrange particles in a periodic structure.

But what would happen if they had one more pair of transducers? To find out, Raeymaekers and graduate student Milo Prisbrey (now at Los Alamos National Laboratory) provided the experimental instruments, and mathematics professor Elena Cherkaev provided experience with the mathematical theory of quasicrystals. Guevara and Mauck conducted theoretical calculations to predict the patterns that the ultrasound transducers would create.

Creating the quasiperiodic patterns

Cherkaev says that quasiperiodic patterns can be thought of as using, instead of a cut-and-paste approach, a “cut-and-project” technique.

If you use cut-and-project to design quasiperiodic patterns on a line, you start with a square grid on a plane.  Then you draw or cut a line so that it passes through only one grid node. This can be done by drawing the line at an irrational angle, using an irrational number like pi, an infinite series of numbers that never repeats. Then you can project the nearest grid nodes on the line and can be sure that the patterns of the distances between the points on the line never repeats. They are quasiperiodic.

The approach is similar in a two-dimensional plane. “We start with a grid or a periodic function in higher-dimensional space,” Cherkaev says. “We cut a plane through this space and follow a similar procedure of restricting the periodic function to an irrational 2-D slice.” When using ultrasound transducers, as in this study, the transducers generate periodic signals in that higher-dimensional space.

The researchers set up four pairs of ultrasound transducers in an octagonal stop sign arrangement. “We knew that this would be the simplest setup where we could demonstrate quasiperiodic particle arrangements,” Guevara says. “We also had limited control on what signals to use to drive the ultrasound transducers; we could essentially use only the signal or its negative.”

Into this octagonal setup, the team placed small carbon nanoparticles, suspended in water. Once the transducers turned on, the ultrasound waves guided the carbon particles into place, creating a quasiperiodic pattern similar to a Penrose tiling.

“Once the experiments were performed, we compared the results to the theoretical predictions and we got a very good agreement,” Guevara says.

Custom materials

The next step would be to actually fabricate a material with a quasiperiodic pattern arrangement. This wouldn’t be difficult, Guevara says, if the particles were suspended in a polymer instead of water that could be cured or hardened once the particles were in position.

“Crucially, with this method, we can create quasiperiodic materials that are either 2-D or 3-D and that can have essentially any of the common quasiperiodic symmetries by choosing how we arrange the ultrasound transducers and how we drive them,” Guevara says.

It’s yet to be seen what those materials might be able to do, but one eventual application might be to create materials that can manipulate electromagnetic waves like those that 5G cellular technology uses today. Other already-known applications of quasiperiodic materials include nonstick coatings, due to their low friction coefficient, and coatings insulating against heat transfer, Cherkaev says.

Yet another example is the hardening of stainless steel by embedding small quasicrystalline particles. The press release for the 2011 Nobel Prize in Chemistry mentions that quasicrystals can “reinforce the material like armor.”

So, the researchers say, we can hope for many new exciting applications of these novel quasiperiodic structures created by ultrasound particle assembly.

Find the full study here.

 

by Paul Gabrielsen, first published in @theU

Amanda Cangelosi

Amanda Cangelosi receives U's Early Career Teaching Award


Amanda Cangelosi, instructor (lecturer) in the Mathematics Department, has received the 2021 Early Career Teaching Award from the University of Utah. The award is given to outstanding young faculty members who have made significant contributions to teaching at the university. Specifically, the University Teaching Committee looks for a faculty member who has distinguished her or himself through the development of new and innovative teaching methods, effectiveness in the curriculum and classroom, as well as commitment to enhancing student learning.

“I’m honored to receive this award and recognition from the university,” said Cangelosi. “Since my work focuses on the preparation of future Utah K-12 teachers, which intersects with social justice goals in a foundational way, this award means that the U cares about dismantling systemic oppression. There is nothing more systemic than K-12 education, and thus no more impactful space to invest one’s energy.”

In her approach to teaching, Cangelosi believes it's important for children to have math teachers who are skillfully trained to break the unhealthy and dangerous cycle of students who make value judgments about their self-worth based upon their achievement (or lack of) in math. “Issues of mathematical status and power between students in a math classroom need to be recognized and attended to by teachers so children don’t label themselves as “stupid” or, equally-dangerously, as “smart” relative to each other,” she said.

To overcome social divisions and stratifications within the classroom, Cangelosi believes teachers need to focus on creating productive, collaborative, and student-centered learning activities, implementing culturally relevant lessons, using multiple approaches to teaching math, and embracing unconventional approaches. Implementing these strategies require teachers to engage in challenging identity work, understanding the history of education in the U.S., embracing heterogeneous classrooms, and engaging in anti-bias and anti-racist training within mathematical contexts.

In her own teaching, Cangelosi draws heavily from the mainstream math education literature. For example, several of her students were personally affected from watching and reflecting upon Danny Martin's Taking a Knee in Mathematics Education talk from the 2018 annual conference of the National Council of Teachers of Mathematics.

Cangelosi’s teaching contributions include the following:

  • She taught a math lab class at Bryant Middle School for the 2019-2020 academic year to deepen productive collaborations between the U and local schools, thereby creating a seamless practicum space for undergraduate Math Teaching majors, while providing long-term outreach to the local community.
  • Inspired by Utah State University’s teaching practicum, in 2011 she established the current innovative structure of the Math 4095 course—including funding (often out of her own pocket) for mentor teachers, which resulted in onsite, fully-contained classrooms at local schools for University of Utah teaching majors.
  • During the pandemic, she created a sustainable and equitable virtual after-school tutoring program that allowed local high school students to meet with math undergraduates for homework support.
  • She created sanitized manipulatives kits to be distributed to her students for use in online synchronous lectures and labs, to help maintain the integrity of her hands-on collaborative Math 2000/4010/4020 classes during the COVID-19 pandemic.
  • She helped develop course curricula for Math 2000, Math 1010, and Math 4090/4095, introducing and modifying resources from her previous work as a secondary math teacher at The Urban School of San Francisco, bringing what are now mainstream practices to the University of Utah.
  • She has made numerous community, school-district-level, and Utah State Board of Education (USBE) contributions, such as diverse teacher recruitment, committees, and professional development.

“I love approaching old concepts in new, nontraditional ways, because we so often confound our understanding of concepts with the arbitrary conventions that we use to communicate them,” she said. “This often challenges student perceptions of classroom status and power in productive ways, often flipping the previously conditioned dynamic on its head and inviting students to rewrite their mathematical identities in a positive light.”

Cangelosi received her Bachelor of Science degree in Mathematics Education, as well as a Master’s of Statistics degree from Utah State University. She also has a post-baccalaureate degree in mathematics from Smith College. She joined the U’s Math Department in 2011.

 

by Michele Swaner - first published @ math.utah.edu