How Microbes Combat Climate Change

How microbes can combat climate change

Chemist Jessica Swanson works with bacteria that eat methane, a powerful greenhouse gas, out of the atmosphere.

 

While carbon dioxide gets much of the focus in the climate debate, methane, the main flammable component of natural gas, also drives planetary warming. Molecule for molecule, CH4’s heat-trapping potential is 34 times greater than that of CO2 (on a 100-year time scale) and it’s pouring into the atmosphere from both human and natural sources, posing a significant threat to global climate systems.

Now scientists from around the world are exploring various strategies for removing methane from the atmosphere in the hopes of slowing climate change.

University of Utah chemist Jessica Swanson has retooled her lab to help develop a process that would harness methane-eating bacteria, known as methanotrophs, which naturally break down methane into carbon dioxide and organic compounds. She aims to discover ways to enable methanotrophs to effectively pull methane from the air at low concentrations in next-generation bioreactors.

“I’m hopeful that the more we understand methanotrophs, the more we can also facilitate open-system, nature-based solutions,” Swanson said.

Methane accounts for at least 25% of planetary warming, according to the Environmental Defense Fund. The gas is naturally oxidized in the atmosphere resulting in a shorter half-life than CO2, but methane sources are surpassing the oxidizing capacity of the atmosphere at a shocking rate—partially due to a positive feedback cycle between warming and natural emissions from wetlands and permafrost. The consequence is rapidly increasing atmospheric methane concentrations that pose a serious risk of near-term warming.

Read the full article by Brian Maffly in @TheU.

$7M to build better life sciences workforce

$7Mto build bigger, better life sciences workforce

 

Utah’s life sciences industry is booming—so much so that there’s a gap between the workers that bioscience companies need to grow and the college graduates to fill those jobs.

A new partnership between the state of Utah, higher education, and life sciences industry leaders aims to keep Utah competitive globally by training and supporting students entering the workforce with highly technical skills. The University of Utah and Utah State University will be leading the effort to close that gap.

On Monday, Nov. 20, Utah Gov. Spencer Cox announced a Life Science Workforce Initiative that will kick off his administration’s priority to bolster bioscience at a press conference hosted at bioMérieaux.

“We know that this sector is part of the bright future of Utah,” Cox said. “We’re so excited for what is already happening here, but we have to meet the needs of today and the needs of tomorrow. And we do that by giving more opportunities to incredible students and companies here in the state of Utah.”

The goal of the initiative is to close the anticipated workforce gap between the needs of bioscience companies and the number of potential employees available. From 2012 to 2021, the state’s job growth in life sciences was the highest in the country, but Utah companies still need more workers. From biological technicians to specialized Ph.D. researchers, the skilled workforce degrees Utah companies need include biochemists, chemical engineers, materials scientists and others.

BioUtah, an industry trade association, teamed up with the Utah System of High Education’s Talent Ready Utah agency (TRU) to connect legislators with industry and university leaders from every state college and university to help state elected and education leaders better understand the needs of the life sciences workforce.

The initiative is modeled after the state’s Engineering Initiative, which was launched in 2001 to boost the number of engineering graduates each year and has increased Utah’s new engineer numbers by 240%. Like the Engineering Initiative, the state will provide financial incentives to Utah colleges and universities for additional high-yield degree graduates. The state estimates life sciences degrees could grow by 1,250 graduates.

Read the full article in @theU.

SRI Story: Lauren Wigod

This is me out on the frozen bed of the Great Salt Lake, collecting soil and water samples. It might be sunny, but it was freezing, and I think I still have salt stuck in my boots.

 

 

My name is Lauren, I’m a senior majoring in biology and philosophy of science, and I was a member of the first cohort of the Science Research Initiative (SRI), first-year research program in the College of Science. For my project in the antibiotic discovery stream, led by Dr. Josh Steffen, I cultured a library of halophilic bacteria that thrive in the Great Salt Lake. In a time when most of my classes were online, the SRI offered the opportunity for hands-on learning, both in a lab and in the field. In just my second semester, I was gaining valuable research skills and synthesizing concepts from my other classes. 

We took a closer look at our benchwork (an example is pictured to the left) with weekly journal clubs. Dr. Steffen helped us tackle academic articles that were directly applicable to our research and in turn enforced our understanding of the fundamental ideas at play.

These exercises combined with my work in philosophy of science and a year-long novel writing workshop through the Honors College spurred the realization that my true passion lies in science communication. 

 

 

 

 

 

 

Oh … and during my spare time I took a job at the stock room in the Department of Chemistry where, among other things, for BeReal, I wielded bolt cutters that were almost my height. En garde!

 

When I told Dr. Steffen that I loved science but didn’t think research was for me, he helped me find a role where I could play to my strengths and apply my scientific expertise.

Now, as a science writer intern for the College of Science (I’m posing here with my fellow interns), I talk to students and faculty about their research and turn their experiences into stories that everyone can engage with regardless of their background.

zebrafish (Danio rerio)

So, it turned out that laboratory research didn’t end up being the path for me. Even so, my participation in the SRI has been one of my most radical experiences at the U. During my time in the program, I developed confidence in the lab, professional connections and a lasting community within the College of Science. One of my favorite projects I covered was a paper from the Gagnon Lab about a chemical sunscreen called gadusol found in zebrafish. The research paper reading skills I learned from the SRI came in handy on that one!

There may be a point in your academic career at the U where, like me, you aren’t sure you even belong at the university – or in science at all. But the SRI and Dr. Steffen helped me see that a career in science can take many forms, not just being “at the bench” but wordprocessing away on a laptop telling stories about science. Sky’s the limit for you as a science major as well. 

I am honored to have been among the first cohort of SRI students and gratified to see how the program has already developed in the few years since its conception. Already, SRI scholars are producing great work, and I’m excited to hear (and write about) their imminent discoveries across all disciplines of science. 

 

by Lauren Wigod
Science Writer Intern

SRI Stories is a series by the College of Science, intended to share transformative experiences from students, alums, postdocs and faculty of the Science Research Initiative. To read more stories, visit the SRI Stories page.

Read more College of Science stories by Lauren Wigod here.

Forming Ice: Molinero

Forming ice: there’s a fungal protein for that

The way ice forms is a lot more interesting than you think. This basic physical process, among the most common in nature, also remains somewhat mysterious despite decades of scientific scrutiny.

A cryomicroscopic image of a hexagonal ice crystal grown in a Fusarium acuminatum ice nucleator (IN) extract. Credit: PNAS

Now new research from the University of Utah, with Germany’s Max Plank Institute for Polymer Research and Idaho’s Boise State University, is shedding fresh light on the role of biological agents—produced by fungi of all things—in ice formation.

Contrary to what we have been taught in school, water won’t necessarily freeze at 0 degrees Celsius (32 degrees F) because of the energy barrier inherent in phase transitions.

Completely pure water won’t freeze until it cools to as low as -46 C. This is because water molecules require particles on which to build the crystals that lead to ice, a process called nucleation. Organisms have evolved various ways to control ice formation as an adaption to survive in cold environments.

So the most efficient ice-nucleating particles are biological in origin, produced in bacteria and fungi, and even insects, but the molecular basis and precise mechanisms of “biological ice nuclei” has not been well understood.

Valeria Molinero, a theoretical chemist with the University of Utah’s College of Science, is at the forefront of sorting out this mystery, which holds potential implications for improving our understanding of how life affects precipitation and climate.

Read the full article by Brian Maffly in @TheU

SRI Story: Little Things Matter

little things matter

 

Ali Bouck (they/them) has always found enjoyment in the little things in life. Really little things. A scientist from a young age, Ali has been fascinated by what made seemingly simple processes work on a molecular level. 

Ali naturally gravitated towards chemistry classes in high school. Upon the recommendation of an influential teacher, Ali became more inspired by a future in chemistry and completed a pharmacy technician certification program to gain real-world experience in the field. Working as a pharmacy tech proved valuable for Ali; however, they craved work that was more “behind the scenes” of pharmacological development. This epiphany led Ali to recognize that research was their long-term career goal.

But what does a research-based academic and career trajectory look like? For Ali, and many other students like them, those opportunities are mysterious or unknown. This is where the Science Research Initiative (SRI) comes in.

During their second year at the U, Ali came across the new SRI program in the College of Science. Its mission: to place first and second-year science students in discovery-based research, thereby providing the skills and experience to prepare them for academic and professional success.

Ali immediately applied, though didn’t expect to be admitted. “I worried it was an exclusive program that was difficult to get into,” Ali says. So when Director Josh Steffen contacted Ali several weeks later to personally welcome them to the Science Research Initiative, they were “shocked.” That small but personal connection made a big difference to Ali, and demonstrated to them the accessibility of the SRI. 

After taking a one-credit course on research methods, Ali joined an SRI research stream, a specific area of study with a cohort of students, led by a faculty member. More specifically for Ali, it was Ryan Stolley’s Underexplored Molecular Architectures stream, which explores the behavior of atoms, the principles of organic chemistry and chemical experimentation. This was a natural fit for Ali’s interests in the infinitesimal. The stream also exposed them to methods of analysis, project management and practical lab experience. But for Ali, it was much more than that.

“I learned how to read scientific papers and [developed] my leadership and science communications skills,” says Ali. These skills helped them ascend to other research opportunities, scholarships and recognitions, which culminated in graduation with a bachelor’s degree in chemistry, along with several emphases.

Now in their first year as a bioscience PhD student, Ali reflects on their SRI experience with gratitude. “I received individualized support that helped me with my goals and authentically supported my wellbeing,” says Ali. Additionally, the tangible skills and knowledge they gained, is allowing them to study the development of novel organic and biosynthetic products as a graduate student. “As I learned different techniques in the lab. I found a love for organic synthesis, but having worked as a pharmacy technician throughout my undergraduate career, I want to expand to work on molecules that have relevance in that field.” Ali is poised for a career in industry research after their graduation. 

Several years after their SRI experience, Ali still sees their mentors and colleagues around campus and in the Crocker Science Center. “Josh [Steffen] says ‘hi’ every time he sees me and asks how I am doing,” they say. Whether it be science on a smaller scale, or the personal connections formed during one’s formative years, the little things truly matter.

When asked if they’d do it again, Ali Bouck says, “SRI set me on my academic and career path. Joining the program was the best decision I ever made.”

 

By Bianca Lyon

SRI Stories is a series by the College of Science, intended to share transformative experiences from students, alums, postdocs and faculty of the Science Research Initiative. To read more stories, visit the SRI Stories page.

‘Solving’ biology’s most important molecule

‘solving’ biology’s most important molecule

 

According to microbiologist “Venki” Ramakrishnan, “We all have imposter syndrome,” a phenomenon described as self-doubt of intellect, skills, or accomplishments among high-achieving individuals.

 

With Peter Trapa, dean of the College of Science

In a much-anticipated lecture at the College of Science’s Frontiers of Science September 27, Ramakrishnan detailed “My Adventures in the Ribosome.” With a warm reminder to the standing-room-only crowd at the Natural History Museum of Utah (NHMU) he explained that there were setbacks, re-directs and moments of doubt for the microbiologist who helped solve the structure of biology's most important molecule yet shrouded in mystery ever since the discovery of the double-helix structure of DNA fifty years earlier.  “Everything in the cell is either made by the ribosome or made by enzymes that are themselves made by the ribosome,” he says. The event was co-sponsored by the U's Department of Biochemistry, U Health and NHMU.

Whatever syndrome Ramakrishnan once suffered from, the Nobel Prize laureate learned to value change, whether it was pivoting from his early studies in physics — a discipline that dates back to Galileo in the 16th century — to that of biology, now in the midst of a resurgence, supercharged with the advent of genetics. (To the PhD physicist “lambda” was a wavelength, not a virus, he shared with the audience, garnering laughs.)

In his new life science digs, he soon gravitated to capturing the essence of an enormous molecular machine made up of a million atoms — wherein large, complex protein molecules are produced, turning the genetic code into organisms.

If you want to see the world

Finding the structure of the ribosome wasn’t easy. For one thing, it entailed uprooting his family. In his presentation, Ramakrishnan repeatedly displayed a travel map with dotted lines to illustrate how, if you want to see the world, study the ribosome. He and eventually his family traveled from his home in India to Ohio to San Diego before beginning his postdoctoral work with Peter Moore at Yale University in Connecticut, and then a sabbatical in Cambridge, England, to Utah, where he was on the biochemistry faculty for more than four years. (A U lab staff photo projected at the event prompted Ramakrishnan to refer to himself, heavily-bearded in the 1990s photo, as being his “bin Laden days.”)

From Utah he returned to Cambridge, England and the MRC Laboratory of Molecular Biology where he is currently group leader.

The race for solving the ribosome turned into a four-way contest of labs and turned on securing the right level of detail to see how the ribosome actually works–from x-ray technology to eventually crystallography facilitated by the U’s own Chris Hall and others determined to solve a fundamental problem regardless of the challenges.

Fifteen years after the first crystals and there was still no apparent progress towards determining the actual structure of the ribosome. In Utah, Ramakrishnan and his lab focused on what had earlier been identified as the smaller subunit of the ribosome, but it wasn’t until his return to the UK that the goal of bagging atomic resolution crystals of both ribosome units was accomplished. This with the help of electron microscopy as well as circular particle accelerators known as synchrotrons used by his team and his Yale colleagues.

Mission Accomplished

Finally, there was enough detail to hazard a “mission accomplished,” and in 2009 Ramakrishnan, now elected to The Royal Society, shared the Nobel prize in chemistry with Thomas A. Steitz and Ada Yonath for research on the structure and function of ribosomes. In 2012 he was knighted.

Not bad for someone who claims to be subject to sometimes crippling self-doubt, and he was eager to share some take-aways to the audience for not only scientific research success, but life success. In addition to his recurring refrain that we all suffer from imposter syndrome, Ramakrishnan referenced the late Max Perutz, the Austrian-born British molecular biologist who shared the 1962 Nobel Prize for Chemistry with John Kendrew, for their studies of the structures of hemoglobin and myoglobin. Perutz charted the variables at play for success in the scientific realm beyond just talent:  money, skill, patience and luck.

And Ramakrishnan's advice?

  • Keep your options open, even if it means learning completely new techniques, moving, or even changing fields
  • Never be afraid to ask for help or show your ignorance
  • Talk to people but not all the time

Of course, “success” is never final for a scientist, perhaps especially for one traversing the mysterious inner galaxies of molecules. And this is where Ramakrishnan brought his journey back to a recognizable metaphor for the uninitiated. In a series of slides, he showed the structure of this mighty molecular machine, including where antibiotics bind to the molecule which has advanced our understanding of how the ribosome works and how antibiotics inhibit it.

It took ten to fifteen years of taking snapshots of the ribosome to get a full complement of intricate, uniquely shaped moving images at an atomic resolution that could then be fitted together like a jigsaw puzzle. Finally, biologists could see and render the long-enigmatic process that takes place from the blueprint of DNA to protein: where exactly mRNA entered, how other proteins attached, and where the amino acid chain exited from the ribosome.

Each of the slides at the Tuesday night event presented a progressively more detailed model of the ribosome, until it was three-dimensional. In his visual piece de la resistance, Ramakrishnan put up an animation of the completed jigsaw puzzle designed by Janet Iwasa and the U’s animation lab. The frenetic choreography of multi-colored components wowed the audience, especially when the good scientist put it up to speed and the illustrated ribosome seemed to go kinetically cosmic before everyone’s very eyes.

Ribosome exhibit at Natural History Museum of Utah.

The animation is featured in a new exhibit dedicated to the ribosome on the fourth floor of the Natural History Museum of Utah.

It was a stirring finish for Venki Ramakrishnan who brought it all up to scale when he closed the evening by saying, “During the time you've been listening to me, the thousands of ribosomes in each of your cells have been churning out tens of thousands of proteins as we speak."

Read Michael Mozdy’s post about Dr. Ramakrishnan and the new Ribosome exhibit at the NHMU.

By David Pace

 

About Frontiers of Science

The College of Science Frontiers of Science lecture series was established in 1967 by University of Utah alumnus and Physics Professor Peter Gibbs. By 1970, the University had hosted 10 Nobel laureates for public Frontiers lectures. By 1993, when Gibbs retired, the Frontiers organizers had hosted another 20 laureates. Today, it is the longest continuously running lecture series at the U.

The next event in the series takes place March 19, 2024 and will feature Maureen Raymo, American paleoclimatologist and marine geologist.

Ribosome adventures

Venki Ramakrishnan, 'My adventures in the ribosome'

 

Venkataraman “Venki” Ramakrishnan’s story is the stuff of fiction. He went from an eager undergraduate student in India to a self-described “failed physicist” to a major player in the race to uncover one of biology’s biggest mysteries—the structure of the ribosome, the most important molecule that nobody’s heard of that earned him a Nobel Prize in chemistry in 2009.

The opportunity to research the ribosome drew Ramakrishnan to the University of Utah in the late ‘90s. The ancient molecule brings him back as a Nobel laureate to discuss his “Adventures in the Ribosome” at the College of Science’s Frontiers of Science Lecture Series on Sept. 26, at the Natural History Museum of Utah. The evening should be enthralling—his popular memoir Gene Machine reads like a thriller that navigates inspired collaborations, friendly rivalries, and cutthroat competition behind scientific discoveries and international accolades.

“Why did my career work out? I didn’t go to any famous schools for my undergrad or graduate school, and I was sort of an outsider most of my life. I think there’s some sort of general lessons there,” Ramakrishnan said. “One of them is if you find things don’t work out, you have to be open to change.”

Ramakrishnan has never been afraid of change. He earned a PhD in theoretical physics at the University of Ohio, but immediately realized that developing theories and mathematical calculations wasn’t for him. The field of biology grabbed his attention.

“Every issue of Scientific American when I was a grad student was full of big breakthroughs in biology. That was a time when the first sequences of DNA were being reported, Ramakrishnan said. “Biology was going through this huge revolution, and it hasn’t stopped.”

 

Read the full story by David Pace and Lisa Potter in @TheU.
Read more about the Ribosome exhibit, in conjunction with Ramakrishnan lecture, at the Natural History Museum of Utah. 

 

Matthew Sigman Receives The 2023 Patai-Rapport Lecture Award

Patai-Rapport Lecture: Matt Sigman

 

He received this award at the 22nd European Symposium on Organic Chemistry. According to www.esoc2023.org, the "European Symposium of Organic Chemistry" includes key scientific events that since the 70s have been organized every two years in different cities in Europe. Every edition had an attractive multidisciplinary scope and worldwide attendance from industry and academia.

The Patai - Rappoport Lecture celebrates the vision of Saul Patai and Zvi Rappoport in creating and advancing the book series "The Chemistry of Functional Groups," providing chemists with a highly valuable tool for advancing their research. Founded in 1964, the series has grown to over 150 volumes with 1,750 chapters on a wide range of functional groups and compound classes, contributed by expert authors from more than 50 countries. The current chief editor of the series is Professor Ilan Marek. The Patai – Rappoport Lecture is supported by John Wiley & Sons.

Read more about Sigman Research Group.

Originally posted at chem.utah.edu

Vahe Bandarian – 2023 ACS Fellow

Vahe Bandarian has been selected as one of the 2023 American Chemical Society (ACS) fellows.

Associate Dean for Student Affairs in the College of Science, Bandarian arrived at the University of Utah in 2015, and his work at the U currently centers on developing molecular level understanding of biosynthesis of complex natural products. Specifically, his lab has reconstituted the key steps in the biosynthesis of the modified transfer RNA base, queuosine, which is found in all kingdoms of life. Future directions in this area will include probing the biological role of this and other ubiquitous RNA modification. Additional new areas of research being initiated will focus on mechanistic studies of enzymes involved in complex radical-mediated transformations.

Bandarian graduated with a B.S. from California State University-Los Angeles in 1992 then went on to get his Ph.D. at the University of Wisconsin-Madison in 1998 followed by an NIH postdoctoral fellowship at the University of Michigan.

ACS began this fellowship tradition in 2009 as a way to recognize and honor ACS members for outstanding achievements and contributions to science. Read more about the American Chemical Society and the 42 selected fellows here.

Originally announced on chem.utah.edu.

Outstanding Undergrad Research Awards 2023

The University of Utah is one of the top research academic institutions in the Intermountain West, and it’s thanks in major part to the U’s undergraduate student researchers and the faculty who advise and mentor them.

Some of the university’s up-and-coming researchers and mentors were honored at the 2023 Office of Undergraduate Research (OUR) Awards, held virtually on April 3 due to a winter weather advisory in the Northern Utah area.

Every year, OUR recognizes one undergraduate student researcher from each college/school with the Outstanding Undergraduate Researcher Award, according to the office’s website. Partnering colleges and schools are responsible for selecting the awardee.

Dr. Annie Isabel Fukushima, director of the Office of Undergraduate Research and associate dean of Undergraduate Studies at the U, said the OUR recognizes that to foster a culture of future problem-solvers working in tandem with current premier researchers in their fields of study, they must also foster a culture of recognition and rewards.

This year, 16 undergraduate researchers were honored with the Outstanding Undergraduate Researcher Award, three of them from the College of Science:

Yexalen Barrera-Casas (left) Mentor: Professor Michael Morse, Dept. of Chemistry

Alison Wang (center) Mentor: Professor Caroline Saouma, Dept. of Chemistry

Nancy Sohlberg (right) Mentor: Professor Gannet Hallar, Dept. of Atmospheric Sciences

“The Outstanding Undergraduate Researcher Awards exemplify excellence in research at the University of Utah across the disciplines,” Fukushima said. “The awardees are creative thinkers, innovators, and solving pressing societal problems.”

Dr. Carena Frost, Associate Vice President for Research Integrity and Compliance at the University of Utah, gave opening remarks on behalf of the Office of the Vice President for Research (VPR). Frost told the audience there’s no doubt the student researchers will continue to innovate in science, medicine, technology and many more fields thanks to the work they do.

“Research is all about helping people,” she said. “Finding solutions for our society is what gets me most excited about the future of research at the U, and you are at the forefront of it.”

At the ceremony event, award recipients were able to thank their mentors, family and others for their support. Four students were honored for being Parent Fund Undergraduate Research Scholarship recipients.

For the first time in the event’s history, mentors were honored with the Outstanding Undergraduate Research Mentor Award. Nineteen mentors were recognized at this year’s event.

Fukushima, who is also an associate professor of Ethnic Studies, was one of the mentor award honorees. She said mentoring relationships are successful because of commitment, communication, and a culture — both within a department and university-wide — that is invested in research occurring at all stages of academic, from undergraduate to faculty.

“Student-faculty collaborations are successful because mentors invest the time, and mentees are willing to risk going into the unknown and the uncomfortable,” Fukushima said. “Doing research is hard, but it can be rewarding.”

More information and criteria for both awards can be found on the OUR’s website to see OUR awards program click here.