homenews

Retroviral Symposium

October 10, 2023

Developing HIV Anti-virals

The annual Retroviral Symposium held at Snowbird convened a wide-variety of scientists from many disciplines ... along with troupe of actors, a playwright and a dramaturge.

October 10, 2023

Infectious viral cores in the nuclei of infected cells are largely intact and uncoat near their integration sites just before integration. Illustration: The Animation Lab.

In September of 2023 the Department of Physics and Astronomy hosted the 12th International Retroviral Symposium at Snowbird Utah. The retroviral symposium is held bi-annually and is hosted alternatively in US or Europe. This symposium originally initiated from a group of NIH researchers which had strong collaborations with European scientists beginning in 1990’s.  

Fundamental mechanisms that ensure proper assembly, maturation and uncoating of retroviruses remain unclear. Understanding these mechanisms is critical for development of effective antivirals. While HIV antivirals now exists, the rapid evolution of HIV under antiviral selection requires new targets. The 12th Retroviral Symposium was focused on Assembly, Maturation and Uncoating and highlight fundamental biochemical, virological and biophysical mechanisms involved in these processes.

In a novel turn, this year’s symposium also featured a staged reading of an original play, “Emergence” by playwright Gretchen A. Case, professor at the U’s Department of Theatre and Associate Professor in the Division of Medical Ethics and Humanities at the U’s School of Medicine. Set “in the future, but not so far that it is unrecognizable,” the one-act has four characters: three scientists and an “AI,” as in artificial intelligence. The cast includes “Liv” who is saving her reproductive eggs in jars in a futuristic world where retroviral therapy in human reproduction is the norm. (Retroviruses, it turns out, are critical to the formation of the placenta.) The script is based on the book Discovering Retroviruses by Anna Marie Skalka, professor emerita at Fox Chase Cancer Center in Philadelphia. Skalka attended the symposium in a post-play discussion. 

 

 

Taking the leap

Also on-hand during the post-play discussion was Sydney Cheek-O’Donnell, chair of the U’s theater department, a long-time collaborator with symposium organizer and U professor of physics Saveez  Saffarian. Cheek-O’Donnell said that the project is an on-going attempt to understand and develop a way to work across multiple disciplines between science and arts /  humanities “so that others can take the leap… . Stories,” she says, “are one of the best ways to teach people complicated new ideas.” The Play was partially supported by a 1U4U award to Professors Case, Cheek-O’Donnell and Saffarian.

 

By David Pace

You can watch a video of the staged reading of “Emergence” below.

 

Putting the ‘fun’ in commutative algebra

October 9, 2023

the ‘fun’ in commutative algebra

 

The word “fun” is a subjective one, but that is how Anne Fayolle describes mathematics as a discipline.

A graduate student in mathematics at the University of Utah, Fayolle is a recent recipient of a multi-year scholarship from The Natural Sciences and Engineering Research Council  (NSERC) which is Canada’s equivalent of the National Science Foundation’s Graduate Student Fellowship in the U.S.

Math credentials

As a Ph.D. student working with Professor Karl Schwede, Fayolle, who was born in France and grew up in Canada, clearly has her mathematics credentials. Before coming to the U, she studied first at McGill University, one of Canada's best-known institutions of higher learning and one of the leading universities in the world. There, she quickly developed an affinity for the independent learning model in which one is paired with a professor in a one-on-one setting and in which both determine together what textbooks and papers they will study together. This conversational model of learning proved to be better than the lecture-and-classroom-style model for Fayolle and helped solidify her desire to go to graduate school.

Following her bachelor’s degree, Fayolle returned to Europe at École Polytechnique Fédérale de Lausanne (EPFL), one of the most celebrated public universities in Europe. As a master’s student, Fayolle studied with Dr. Carvajal-Rojas in commutative algebra. This involves working in modular arithmetic, a type of arithmetic in which addition works similar to time on a clock: 5 + 10 = 3. “The numbers working differently,” she says, “means one cannot use the traditional tools of calculus to study polynomial equations and the shapes they define. "For instance, since the numbers work differently, we can't draw graphs exactly like we would over the real numbers. So our intuition derived from those graphs doesn't always work here. One has to rely on the underlying algebraic structures."

This algebraic abstraction and the understanding it brings is one of Fayolle’s favorite parts of doing math, and it may speak to what Fayolle identifies as the “weird” aspect in commutative algebra, followed closely by the feeling of it being “fun.” The appeal is also philosophical “You can get to the heart of why something works the way it does. I really enjoy the abstraction that comes with [commutative algebra]––trying to find the structure in abstract things.”

Part of her enjoyment in doing math is that singular moment when someone (or “some ones”) in the math sector solves a persistent problem. “It’s [only] ‘hard’ until someone comes along and finds the right object or point of view of how things are working,” she says of breakthrough findings. “It’s suddenly less ‘weird’ because it makes more sense.” She explains that she’s been working in this positive characteristic realm for the past few years and is now used to it. Fayolle is especially interested in studying singularity theory, she says, in positive and mixed characteristics and, fortunately, in Schwede has found a principal investigator/mentor at the U who “does cool math.” 

Everyone can do math

The multi-year NSERC fellowship will free up more of Fayolle’s time for research. ​​Her ambition is to continue in academics as a post-doctoral researcher and then as a faculty, if possible. “I like having stuff that has more world impact independent from [just the study of] math. I think that pure math is intrinsically valuable, hard to justify by linking it to real world applications, but still necessary. ” This includes teaching.  

“I think math is very scary to a lot of people.  I personally think that everyone can do math. Everyone struggles, and I think that’s very important to emphasize when you’re teaching. I struggle in math. I don’t think struggling in math should be a barrier to doing math.”

 In the meantime, Anne Fayolle continues in graduate school, sharing mathematics by organizing BIKES, the student commutative algebra seminar here at the U as well as co-organizing an Association for Women in Mathematics conference later this year. She also skis on the weekends. “I was skeptical,” the Montreal native says, “when I first saw the [Utah “Greatest Snow on Earth”] license plates. But after I went skiing, I agreed.” It helps, she says, that it doesn’t get too cold and is not too icy. 

“I think the license plates might be right.”


by David Pace

‘Roving sentinels’ discover new air pollution sources

October 6, 2023

‘Roving sentinels’

 

In 2019, University of Utah atmospheric scientists, the Environmental Defense Fund and other partners added a new tool to their quiver of air quality monitors—two Google Street View cars, Salt Lake Valley’s roving sentinels that would detect hyper-local air pollution hotspots.

Jon Lin. Banner Photo: A Google Street Car loaded with air quality instrumentation. Credit: Logan Mitchell

In the ensuing months John Lin, professor of atmospheric sciences at the U, developed a new modeling approach that used modeled wind patterns and statistical analysis to trace pollution back to its source location to a scale previously missed by coarser scale monitoring projects that have traditionally characterized air quality averaged over an entire urban airshed.

In a U- and Environmental Defense Fund (EDF)-led study that was published in the October 2023 issue of the journal Atmospheric Environment, the results are in.

“With mobile vehicles, you can literally send them anywhere that they could drive to map out pollution, including sources that are off the road that previous monitoring missed,” said Lin, who also serves as associate director of the Wilkes Center for Climate Science & Policy. “I think the roving sentinel idea would be quite doable for a lot of cities.”

The researchers loaded the vehicles with air quality instrumentation and directed drivers to trawl through neighborhoods street by street, taking one air sample per second to create a massive dataset of air pollutant concentrations in the Salt Lake Valley from May 2019 to March 2020. The observations yielded the highest-resolution map yet of pollution hotspots at fine scales—the data captured variability within 200 meters or about two football fields.

“The big takeaway is that there is a lot of spatial variability of air pollution from one end of a block to another. There can be big differences in what people are breathing, and that scale is not captured by the typical regulatory monitors and the policy that the U.S. EPA uses to control air pollution,” said Tammy Thompson, senior air quality scientist for EDF and co-author of the study.

Read the full story by Lisa Potter in @TheU. 

 

Ring-of-fire eclipse: How to see it

October 6, 2023

Ring of Fire Eclipse

 

“It’s like when you make a circle with your fingers and close one
eye. When you move your hand closer to your face, the circle gets bigger. Move it away, and it appears smaller.”

Paul RIcketts. Credit: Sara Tabin/Park Record

This is what Paul Ricketts has to say about the upcoming eclipse on Saturday October 14. “This will be a cool event. You’ll still see the surroundings get darker, you’ll feel it get colder, but you won’t be able to look at the eclipse without protective glasses,” continued  Ricketts, the director of the University of Utah’s South Physics Observatory. “Plus, this will last way longer than the total eclipse.”

This is a front row seat for Utahns to an annular eclipse the morning of the 14th. The so-called ring-of-fire eclipse is different than the total eclipse of 2017 but will still be spectacular.

A solar eclipse occurs when the moon’s orbit moves between the sun and the earth so that it blocks out the sun’s light and casts a shadow on Earth’s surface. During an annular eclipse, the moon is at a farther distance from the Earth. The distance makes the moon appear smaller, and it fails to block out the entire sun. The moon looks like a large black disk in front of the bright sun disk. This results in a ‘ring of fire’ around the moon’s silhouette.

Every year the moon drifts slowly farther away from the Earth—around one inch farther per year. Ricketts said that’s one reason to take advantage of these astronomical events while you can.

“Right now, our Earth position with the moon and the sun, they appear the same size in the sky, which is why we can enjoy total eclipses. A few billion years down the road, the moon will appear too small and we’d only get these types of annular eclipses.” Ricketts said. “We’re lucky to be alive right now. In the future, we’d only able to see annular eclipses that look like a much smaller black dot crossing the sun’s surface.”

While many will enjoy viewing the solar spectacle, the event is sacred to local Indigenous tribes. For some Indigenous tribes, an eclipse is a time of renewal and reflection through cultural practices that include fasting and meditation. Diné (Navajo) and Ute Indian Tribes do not watch, or even look at images of the eclipse. When posting images on social media, be mindful of people who want to avoid such images. Consider using a filter so your followers can opt-in to view any multimedia of the eclipse.

 

Learn how to see the eclipse by reading the rest of the story by Lisa Potter in @TheU.

Fall’s flamboyance: The science of autumn leaves

October 6, 2023

Fall's Flamboyance

 

To many, Utah’s fall leaves are a dazzling display of nature’s beauty. To Eleinis Ávila-Lovera, the autumnal switch to reds, yellows, oranges and purples tells a chromatic story of survival.

Eleinis Ávila-Lovera. Banner photo: Archie enjoys the fall leaves changing in Millcreek Canyon. Credit: Jessica Taylor

“Whenever I see plants outside, I’m always thinking what’s going on at a cellular level and why they’re doing what they’re doing. It always goes back to what’s best for the plant through evolutionary time,” said Ávila-Lovera, assistant professor in the School of Biological Sciences. “We might think that they just want to put on a show for us, but the changing fall colors are part of a strategy that allows these plants to survive the climate they experience in their natural habitat.”

Ávila-Lovera is a plant ecophysiologist who researches how plants respond to and tolerate drought. She figures out the mechanisms and traits underlying plant strategies that allow vegetation to cope with extreme water limitations. For example, some desert plants drop their leaves during the hottest and driest months to preserve moisture. In the mountains, the psychedelic foliage works in much the same way—trees that are deciduous drop their leaves to preserve nutrients and prevent freezing over harsh cold winter months.

The science of autumn leaves

Fall officially begins after the autumnal equinox, when the Northern Hemisphere begins to slowly tilt away from the sun. The shortening daylight triggers the beginning of the changing colors.

“Deciduous trees want to drop their leaves in a controlled way to preserve some of their nutrients and sugars. This process is called leaf senescence,” Ávila-Lovera said.

Read the rest of the story by Lisa Poster on @TheU.

Mining and rare earth mineral extraction

October 4, 2023

Mining & rare earth mineral extraction

 

The growth in high-tech products, cell phones, computers, and electric vehicles brings with it the necessity for rare earth minerals, which requires more mining and extraction. Although mining can come with a high environmental price tag, consumers are increasing their demand for these products.

What exactly are rare earth minerals, and can their extraction become more efficient and less damaging? Featured on KPCW's COOL SCIENCE RADIO podcast, Pratt Rogers, assistant professor of mining engineering at the University of Utah, answers these questions and many others.

Listen to the podcast at KPCW.

‘Solving’ biology’s most important molecule

September 28, 2023

‘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.

Nada Math Anxiety Here

September 27, 2023

Nada Math Anxiety with Ken Golden

 

At this point, we have all heard of STEM education, that is Science, Technology, Engineering and Math. And there’s also STEAM education which includes the Arts.

Why is specifically math so important in STEM education and subsequent careers?

Featured on KPCW's COOL SCIENCE RADIO podcast, Professor Ken Golden, Distinguished Professor of Mathematics at the University of Utah, talks about the importance of STEM careers in the U.S. to meet the needs of our climate and the economy.

Listen to the podcast at KPCW.

Safe Landings Weather-wise

September 27, 2023

SAFE LANDINGS Weather-wise

 

Aviation meteorologists like 2008 atmospheric science alumnus Warren Weston connect the dots between severe weather and flight schedules by creating detailed forecasts to help planes and their travelers arrive at destinations safely.

From thunderstorms and limited visibility to scorching temperatures and turbulence, the weather dictates when and where planes can fly. Severe weather is the leading cause of air travel disruptions in the United States.

Aviation meteorologists plan for and around difficult conditions, crafting weather forecasts used to determine the nuances of flights, from altitude to optimal routes. They play an essential role in ensuring travelers get to their destinations safely and efficiently.

Several major domestic carriers, including Delta Air Lines, have in-house meteorologists who monitor global weather 24 hours a day. Delta has 28 meteorologists on staff — the largest team of any airline, it declares — who sit in the carrier’s Operations and Customer Center, alongside flight dispatchers, customer service agents and hundreds of other staffers, at its headquarters in Atlanta.

In this cavernous and screen-filled room, Warren Weston, Delta’s lead meteorologist, recently spoke about the importance of data, the difference between surface weather and upper-air hazards, and how even one degree of temperature can change a flight plan. The conversation has been edited and condensed for clarity.

Photo credit: Delta Air Lines

Read the full Q&A with Warren Weston conducted by journalist Christine Chung in the New York Times.

Ribosome adventures

September 25, 2023

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.