Unraveling Bacterial Genomes

At the University of Utah's Department of Chemistry, faculty member Aaron Puri and graduate student Delaney Beals are pioneering research to decode bacterial genomes by understanding their natural environments. Their project, which began with Puri's pilot experiments during his postdoctoral fellowship, focuses on linking methanotroph phenotypes to genotypes using a spatially resolved model ecosystem.

Graduate student Delaney Beals and faculty member Aaron Puri

Puri, who started his research group in 2019, brings a diverse and impressive background to the project. With triple bachelor's degrees from the University of Chicago, a PhD in chemical and systems biology from Stanford University, and postdoctoral research at the University of Washington, Puri's expertise spans chemical tools for host-pathogen interactions and genetic tools for methane-oxidizing bacteria. Now a faculty member in the Henry Eyring Center for Cell & Genome Science, his work centers on the biological chemistry of bacteria that grow on one-carbon compounds like methane and methanol.

Beals, a fifth-year PhD candidate, contributes vital expertise in the chemical ecology of methane-oxidizing bacterial communities. Originally from North Carolina with a bachelor's from UNC Asheville, Beals was drawn to Puri's lab due to its focus on bacterially derived natural products. "By studying how a particular microbe behaves in the natural environment versus in the lab,” she explains, “we can better understand the ecological context in which various compounds are produced, and thus improve efforts to capitalize on a naturally occurring process."

Their research aims to uncover how bacteria use natural products to interact with each other and the environment. Puri elucidates the challenge: "We live in a time where we have virtually unlimited access to bacterial DNA (genome) sequences. But we have a hard time making sense of the vast majority of this information in the lab." To address this, the team grows bacteria in conditions closer to their natural environment, which has revealed exciting insights. Puri notes, "We can use relatively simple materials to uncover new bacterial behaviors in the lab in a reproducible manner."

The Puri-Beals collaboration has yielded significant findings, showing that bacterial behavior varies depending on their location within the model ecosystem. This research has potential applications in alternative energy, agriculture, and health by optimizing the use of microbes for various purposes. Their work not only advances our understanding of bacterial genetics but also paves the way for practical applications with far-reaching societal impacts.

As Puri emphasizes, "This work underscores that it is critical to think about the environment the bacterium of interest came from to understand what the genes in bacterial DNA are doing, since that is where they evolved." This approach promises to enhance our ability to harness microbes as sources for new natural products and to optimize their use in diverse applications.

Decoding Human Milk Oligosaccharides

In the aftermath of the 2022-2023 infant formula shortage, the research of Professor Gabe Nagy and graduate student Sanaz Habibi (they/their) has taken on newfound significance. Their project, focused on characterizing human milk oligosaccharides (HMOs), addresses crucial sugars in human milk that play a vital role in infant development.

Gabe Nagy and graduate student Sanaz Habibi

The complexity of HMOs presents a significant challenge, with potentially over 200 different compounds, yet authentic references are currently available for only about 30 of them. Nagy and Habibi are at the forefront of developing new analytical techniques to enhance HMO characterization, which could have profound implications for improving infant formula and understanding infant nutrition.

Habibi, who joined Nagy's lab in 2021, brings expertise in analytical chemistry and instrumentation from their undergraduate studies at Virginia Commonwealth University. Their research utilizes high-resolution cyclic ion mobility spectrometry-mass spectrometry (cIMS-MS) to analyze HMOs. Habibi explains their journey: "I became very interested in the cIMS-MS instrument that was being used in his lab, despite having little to no background in IMS or MS. I realized that Gabe's lab was the best fit for me to learn a different type of separation technique and increase my knowledge of mass spectrometry for studying an important class of carbohydrates."

Further elaborating on their innovative approach Nagy says, "We aim to develop advanced methods using ion mobility separations and mass spectrometry. These methods aim to decipher the structures of all possible HMOs, addressing the gap in understanding caused by the lack of comprehensive reference materials." This work involves constructing collision cross section databases, which provide numerical descriptions of the size, shape, and charge of ions—crucial for accurately identifying both known and unknown HMOs in real human milk samples.

The team's work is particularly timely, as Nagy points out: "The world of sugar analysis has lagged behind other fields by 10-20 years, and we believe that our lab could develop new tools in order to bridge this gap." The duo’s research not only contributes to solving immediate challenges in infant nutrition but also has broader implications for analytical chemistry.

Nagy and Habibi are optimistic about the wider applicability of their tools and methods. They envision their advancements being adopted by laboratories worldwide across various molecule classes. Habibi emphasizes the potential of their work "to enhance the comprehensive profiling of human milk using our developed methods."

This pioneering research has the potential to empower other disciplines such as biology and medicine by providing access to advanced analytical tools. As infant nutrition continues to be a critical area of study, the work of Nagy and Habibi stands at the forefront of efforts to improve our understanding and application of human milk components in infant formula and beyond.

At the University of Utah, six chemistry professors are the face of their discipline to thousands of students. 

At the Department of Chemistry, excellence and innovation converge in an extraordinary educational endeavor: moving over 2,000 students each semester through foundational chemistry classes.

This remarkable feat is achieved through a cutting-edge curriculum delivered by six passionate educators known as the "teachers of thousands": Jeff Statler, Elizabeth Greenhalgh, Ryan DeLuca, Kaci Kuntz, Holly Sebahar, and Greg Owens. These instructors, all six of whom are featured here, possess a rare skill set that allows them to present fundamental chemistry with competence, patience, and an uncanny ability to inspire. In their classrooms and labs, aspiring chemists and future medical professionals alike find themselves immersed in an unparalleled learning environment. These six are supported by other faculty dedicated to curriculum development and fostering a robust space for scientific curiosity.

Greg Owens

Greg Owens

When Greg Owens walks into the classroom, he’s in paying-it-forward mode. He attended college in rural Georgia where two of his chemistry professors had just arrived from the U and inspired him to transfer there. They facilitated a spot for Owens in the REU program where he spent his summer after his junior year working in Tom Richmod’s lab, learning valuable skills and techniques. “That experience solidified my interest in academics and in going to graduate school,” he says.

Owens attended UCLA for graduate school where he focused on teaching and used his Utah connection to sneak a toe back in the door after finishing his dissertation. Since 2002, he has instructed classes ranging from 115 to 230 students, totaling over 19,000 students taught throughout his career so far. Owens' graduate work in inorganic chemistry provided him with comprehensive knowledge of the field, making general chemistry a natural choice for his teaching career. Even as a TA in graduate school, he enjoyed opening students’ eyes not only to the world of atoms and molecules but also to the satisfaction of problem-solving.

General chemistry represents for many students their first opportunity to apply mathematics and fundamental principles to understand how things work and how seemingly unrelated phenomena are connected. The course allows them to move beyond memorization and learn to navigate through a series of logical steps to solve complex problems.

In recent years, Owens’s teaching style has evolved from traditional lecturing of hundreds of students in a classroom setting to asynchronous instruction. In these “online courses,” students engage with course materials independently through Canvas, which includes textbooks, instructional videos, problem sets, practice quizzes, and discussion boards. There are no set class meetings, allowing students to study at their own pace and convenience. This approach offers flexibility and freedom while also placing significant responsibility on the student.

One of his favorite classes to teach is the first semester of chemistry for students aiming to enter nursing school. He often finds that many students in these classes initially believe they lack aptitude for math and science, leading to a lack of confidence at the start of the course. However, their strong motivation to succeed in nursing school drives them forward. “It’s rewarding to witness these students’ growing confidence as they recognize the subject’s relevance to their career path and discover their capability in science and math, far exceeding what they had previously believed possible.”

Reflecting on fond memories from these types of classes, he recalls a humorous incident involving Halloween and students’ cell-phones to which, in the early days, he had a particular aversion to especially when they rang ringing loudly during class, including during exams. One Halloween, a student surprised everyone by running down the lecture hall dressed in a homemade cell-phone costume, distributing candy to the audience amidst laughter.

Throughout Owens’s teaching career, he has managed to help his students see their world in very different ways and comprehend complex ideas they initially thought were beyond their abilities. “Every semester,” he says, “I’m in awe of the students who refuse to give up, overcoming enormous hardship and personal tragedy to excel in their studies. He believes in giving students space as wide as rural Georgia and opportunity to learn how to learn and make mistakes, advising incoming students interested in chemistry to get involved with a research lab as soon as possible. This is where students’ knowledge, skills, and interests can grow exponentially.

Jeff Statler

Jeff Statler

Originally from Iowa, Jeff Statler taught physics and chemistry in public high schools for about 22 years and worked with professors Ron Ragsdale, Jerry Driscoll, and Tom Bebee for many of those years. He has always had an innate drive to live around the mountains and the desert and moved to Utah about 35 years ago. In 2010, professors Ragsdale, along with Henry White and Greg Owens, recruited Statler to transition into the Department of Chemistry full-time where he’s been since 2011. Even with an early and abiding passion for the physical sciences and mathematics, chemistry was not his first choice, but he saw the need for chemistry teachers. It helps that he gets to do really cool demonstrations.

Statler has also taught analytical chemistry, physics, and mathematics, but general chemistry may be his favorite. On a Wednesday before Labor Day weekend, he opens a classroom jam-packed with about 350 students with careful, deliberative class procedurals. He is quick to reiterate what the learning objectives are of chapters, distinguishing between what students will be tested on and what content is strictly for their enrichment. He is aware of how big his subject is and how distracting some lines of inquiry can become. “Don’t worry about chapter two until this weekend,” he says. “There’s a lot physics and a lot of quantum mechanics, mostly enrichment stuff, not part of the learning objectives.” He talks strategy, as if he’s enrolled himself. “I won’t test you on that,” he says answering a question about prioritizing.”Pretty much all the rest of this it’s all chapter one and essentials.” The rest of it? “Be mesmerized, bewildered, by it, but, no you don’t have to memorize anything. I’ll give you all the equations you will need.  I’ll emphasize the equations you’ll need and we’ll practice them.” The way he scans the bank of students above him in class is intimate, improbably giving eye contact, it seems, to everyone.

Clearly, he’s skilled at reassuring students that there’s a sequence of things. “I’m big not on memorization but on patterns… We’re almost anti-memorization,” around here.

As he introduces the subject matter for the class—why white light is made of the colors of the rainbow and electromagnetic fields–prisms and spectrums—he projects five statements on the multiple screens throughout the lecture hall: some of the statements are true, others are false and others are just made up. “Mingle, chat, ask your neighbor what they think,” he says and suddenly, his TAs are trailing up the stairs, scanning the clusters of chatting students, listening in on the conversations, making themselves available for questions, making comments . . . being present.

This interactive, “inverted classroom” approach meets students where they are. In these large classes of between 250 to 350 students, getting students to interact with each other is crucial. His favorite aspect about teaching students who are not necessarily studying chemistry is simply sharing his fascination with science and nature with all STEM students. “Teaching and learning are always so individual in many ways,” he admits, and he can only hope that whatever impact he might have is overall positive and motivating. How he has been impacted is not so variable. “Students always inspire and motivate me and keep me ‘thinking young’ with their fresh questions, perspectives, and unique needs and backgrounds.”

Just the herculean endeavor of teaching 12,000 students over his 35-year career to thrive and flourish in chemistry brings Jeff Statler all the rewards he could ever hope for. And his embodied wonder as he conducts the light experiments his face down close and itself awash in light, the detail of it, in turn, projected above, is chemistry in action, pedagogy in the flesh.

HOLLY L SEBAHAR

Holly Sebahar

It all started with frogs. “I had a strong interest in frog ecology so I had declared a biology major which meant I was required to take organic chemistry,” says Holly Sebahar, a first-generation college student from Minnesota. “I fell in love with the subject and could not get enough of it.” In particular, she says, it was the mechanistic side of organic chemistry. “The fact that a small set of rules can be used to predict and explain a wide range of reactions was fascinating to me. I also love applying our knowledge of organic chemistry to understand biochemical pathways and how drugs work.”

After earning her PhD, she interviewed for both industrial and academic jobs. “Eventually it was my love of interacting with students that helped me to decide to become a professor.”

At the U, with class sizes that range from 200 to 340, Sebahar aspires to challenge her students and to provide a supportive and encouraging environment with lots of resources to help them find success. “I believe that having a large team of teaching and learning assistants and supplemental instructors is the key to supporting so many unique students,” she says. “We try offer a wide variety of office hours and review sessions, a diverse set of communication styles, lots of chances to talk about the chemistry and ask questions . . . and learn from their mistakes.”

Learning from mistakes is embedded in Sebahar’s course culture, “where mistakes are embraced and utilized instead of feared.” Tapping not only TAs but learning assistants through the College of Science’s Center for Science and Mathematics Education, she claims that because these leaders have recently taken the class “they remember how challenging it was and are able to provide excellent advice about how to study and how to approach each of the challenging topics.” Instructional staff also serve as mentors and provide important major/career advice.

The diversity in Sebahar’s large lectures is staggering: older students with different levels of family and job responsibilities; those with little or no preparation in chemistry and few if any established study skills and test-taking abilities; gender; preferences for working independently and those who prefer group work; race, gender . . . differing goals. It requires that the instructor be nimble, flexible and innovative.

As an HHMI UPSTEM Faculty Fellow, an instructor in Being Human in STEM, a member of the Chemistry Articulation Team and an inaugural member of the Department of Chemistry’s Diversity, Equity, and Inclusion Committee, all inform her attempt to create an inclusive classroom setting. “I try to constantly ask myself ‘who will be left out if I design my course this way?’ she writes in her teaching philosophy statement, an ambitious, comprehensive and detailed plan for reaching and succeeding with students across multiple spectra. “I strive to create a highly structured class with clear expectations, several lines of communication, and as much flexibility as possible to try to reach the many learning styles and accommodate the busy schedules inherent in a class of 300 students.”

An example of this penchant for innovation, Sehabar held Zoom lectures for students that thrive having a set schedule and who wish to interact with the instructor, other students, and the TAs during lecture. The recorded lectures are also posted for those students that work the night shift prior to the lecture or wish to watch the lecture at their own pace with the ability to pause and rewind as desired.

Sebahar maintains a 6:1 ratio between students and TAs who are aware when a student is going through a difficult time. “This has become increasingly important to me as I have witnessed more and more students struggling with mental health issues each year,” she says.  “Adding the pandemic, recession, and protests on top of the normal stressors has been extremely difficult this year. [2023-24]...  By identifying issues early, we have been able to refer several students to the counseling center, the student emergency fund and the Dean of Students.”

To countervail attrition in student enrollment and graduation, attention must be paid not only to securing resources but recognizing varied signals of student distress. It’s a high-touch approach to student success that over the past 22 years—700 students per year—has grandly totaled over 15,000 students. Her mantras? “Don’t focus on the negatives. Take time to get to know your students and enjoy their energy, enthusiasm and unique gifts and talents. Keep learning so your passion for the subject doesn’t fizzle.”

With that navigation set, it’s little wonder that Holly Sebahar found her bliss in teaching not in spite of a frog pond but because of it.

Kaci Kuntz

Kaci Kuntz

For Kaci Kuntz, the louder the groan, the happier she is. This may take some explaining.

Known for her expressive personality and love of glitter, this associate professor (lecturer) decorates her office and coordinates her wardrobe with sequins and bright colors. Students appreciate her exuberant teaching style, and her tradition of sharing daily jokes helps engage them in the learning process.

And so it goes that when her “joke of the day” elicits a massive groan from over 300 students Kuntz knows that though they disdain her jokes, they comprehend the chemistry behind them. Mission accomplished.

As with her Teaching Thousands colleagues, whose teaching style is interactive and inclusive, Kuntz is also keen on historical context. In General Chem 1, state -the-art science starts at 460 BCE when philosophers hypothesized that matter was made of fire, water, air, and earth. Over the course, she advances all the way to the current “state-of-the-art” science. It is truly unique to cover 680+ years of science and its advancement in a single course.

Then, in General Chemistry II, she dives more deeply and applies chemical concepts to experimental conditions with all of the complexities encountered. In Kuntz’s opinion, General Chemistry II is the most useful course in chemistry because it teaches how to design a proof-of-concept experiment for investigating a hypothesis. She loves teaching this course knowing that students can walk out of it with the skills needed to become scientists. Since starting at the U she has taught lectures with as few as 30 students and as many as 360 for a career total of around 4,000 students so far.

“The student mind is compassionate and has much to learn,” she states. “I cannot speak on behalf of the students, but I hope I’ve empowered them to be confident in their knowledge and their ability to succeed in chemistry, their education, and their career pursuits.”

In class, Kuntz follows brief lectures with interactive problem-solving sessions, allowing students to apply concepts and address common misconceptions. When students hesitate, she sits beside them to offer guidance—a practice she acknowledges with a glittering laugh that might seem 'annoyingly' interactive, though students appreciate her approach and authenticity. Her commitment to student advocacy includes revamping General Chemistry labs to reduce fees and enhancing laboratory safety procedures.

Ryan DeLuca

Ryan DeLuca

If the classroom is a molecule writ large, Ryan Deluca is the bonding agent of its constituent atoms, his students. Standing at the front of a class of 250-plus he is the glue that, in chemistry, defines the smallest identifiable unit into which a pure substance can be divided and still retain the composition and chemical properties of that substance.

A Utah native and U alumnus who returned to the U to teach after a postdoctoral fellowship at Stanford University, DeLuca is captivated by the intricacies of molecular mechanisms, the art of synthesizing compounds, and the analytical challenge of elucidating reaction pathways. But this hydrogen bond-of-a teacher of thousands is also captivating to his acolytes who the first week of class may find such subjects baffling.

DeLuca loves introducing students from various disciplines to the marvels of organic chemistry or “o-chem.” “It’s incredibly rewarding for me to see students, who may not have a primary interest in chemistry, develop an appreciation for the subject,” he says.

O-chem is relevant to many fields, and DeLuca enjoys helping students understand its applications and significance in their respective areas of study. He facilitates this by by employing a problem-based teaching approach, believing that students learn best through active engagement and practical application of concepts. While o-chem, a requirement for pre-med/pre-nursing students and other majors, can be daunting, DeLuca finds that tackling challenging problems helps students develop critical thinking and problem-solving skills. He emphasizes the importance of perseverance and provides ample resources to support students’ learning journeys.

To ensure effective learning in diverse class settings (from 25 students to 350), DeLuca utilizes peer-directed learning and provides strong support from teaching assistants. Overall, DeLuca has recorded 29 chemistry courses over the past seven years, reaching a total of approximately 3,600 students best served, he believes, by doing problem-solving in real time. In this way he believes students can better understand the thought process behind tackling difficult questions. “I emphasize the importance of engaging actively with the material and understanding that chemistry is a cumulative subject,” he says, “where each concept builds on the previous one.”

These active learning strategies for students take place not only in lectures but in those micro- even atomic-sized interactions with DeLuca out of class, with TAs, and, critically, with one another. Ever the chemical bonder, DeLuca engineers each semester, and in each course, a dynamic, intricate-as-a-clock (or a galaxy) molecular structure where student atoms move, interact, vibrate, rotate and translate with success within differing materials and environments.

Our modern society faces many challenges, two of which being alternative energy sources and low cost electronics for daily use.