Revisiting the Coast Salish Woolly Dog

Revisiting the Coast Salish Woolly Dog

Researchers and Coast Salish people are analyzing a 160-year-old Indigenous dog pelt in the Smithsonian’s collection to pinpoint the origin and sudden disappearance of the culturally significant Coast Salish Woolly Dog.

 

Chris Stantis. Banner photo above: The reconstructed woolly dog shown at scale with Arctic dogs and spitz breeds in the background to compare scale and appearance; the portrayal does not imply a genetic relationship. Credit: Karen Carr.

Researchers from the Smithsonian’s National Museum of Natural History led a new analysis that sheds light on the ancestry and genetics of woolly dogs, a now extinct breed of dog that was a fixture of Indigenous Coast Salishcommunities in the Pacific Northwest for millennia. A team of researchers analyzed genetic clues preserved in the pelt of “Mutton,” the only known woolly dog fleece in the world, to pinpoint the genes responsible for their highly sought-after woolly fur.

The study’s findings, published Dec. 14, in the journal Science, include interviews contributed by several Coast Salish co-authors, including Elders, Knowledge Keepers and Master Weavers, who provided crucial context about the role woolly dogs played in Coast Salish society.

“This was one of the most exciting projects in my career as an archeologist and an isotopes expert because of the way that we were able to weave together these different types of knowledge,” said Chris Stantis, postdoctoral researcher in the Department of Geology & Geophysics at the University of Utah and co-author of the study.  “To work with geneticists, historians, and Indigenous Knowledge Keepers just makes better research to bring it all together.”

Read the full article by Lisa Potter in @TheU. 

2023 Catalyst Magazine

2023 Catalyst Magazine

 

Catalyst is the official magazine of the Department of Chemistry at the University of Utah


Read the full issue
here

Dear Friends of Chemistry:

It has been a while since we published our last issue of the Catalyst. Many things have changed since then–we have new colleagues, lost some of our friends, weathered the complexity of the pandemic, and continued to build the department. What has remained the same is the underlying passion, drive, and excellence that I observe day to day in our faculty, staff, graduate and undergraduate students, and postdoctoral researchers. I see this while advising and mentoring my own research team and working with my colleagues and our staff to address challenges.

Perhaps the clearest view of our culture was on display in October as we recognized our four 2023 Distinguished Alumni Awardees

(who will be highlighted in detail in the next issue!). Their message to our current faculty and students was the same: you are providing and receiving an outstanding education that will allow you to lead the next generation of scientists, managers, and students. Their message was inspiring and a grand reminder of why we do what we do every day.

In this issue we feature the culture of our department and bring you up to date on several highlights from the last two years. This includes some descriptions of our successful alumni, including the 2020 Distinguished Alumni–Rik Tykwinski, Carrie Wager, and Raymond Price. In addition, a previous Chemistry Distinguished Alumnus, Clifton Sanders, has been recognized in several Universitywide honors, including the 2023 U

Distinguished Alumni Award and the 2023 Hugo Rossi Lectureship. Finally, we do a deep dive into one of our more recent graduates, Rory “Ziggy” Uibel and his adventures in growing a highly successful local instrument company.

The issue also highlights faculty and students who have received prominent recognition and have had exciting research accomplishments. While there are many to acknowledge, I would like to give a shout-out to Cindy Burrows (Pauling Medal), Valeria Molinero (Irving Langmuir Award and induction into the National Academy of Sciences), Michael Morse (Distinguished Professorship), and Luisa Whittaker -Brooks (U Presidential Scholar, ACS-WCC 2024 Rising Star Award, and MRS Outstanding Early Career Investigator Award). It is always rewarding to see our colleagues honored for their excellence!

On a sad note, we lost several of our former colleagues, including Laya Kesner, Frank Harris, and Wes Bentrude. I was personally close with Wes as he retired soon after I arrived but remained present for several years while I was building my program. He was such a kind and giving person with an easy smile and great sense of humor. I will also note that his research on understanding the reactivity of unusual radicals has circled into the mainstream many years after his initial publications. The organic chemistry community is utilizing his insights as the use of radicals has had a renaissance in recent years.

As a final note, this is my last year as department chair. This has been a demanding job, and I look forward to passing the reins to my successor. However, I can say with all honesty that working with such an incredible group of people has been a pleasure. The culture of our department–collaboration, excellence in education and science, and a good sense of humor–has been a centering force through the challenges encountered.

Sincerely,

 


Chair Matt Sigman

Read the full issue here

Carrie Wager, Chemistry Alumna

U CHEMIST LEADS MATCHUP AGAINST GENETIC DISEASE

 

CARRIE WAGER, PHD’00, RECIPIENT OF CHEMISTRY’S 2020 DISTINGUISHED ALUMNI AWARD, HAS ALWAYS VALUED TEAMWORK WHETHER ON THE SOCCER PITCH OR IN THE LAB.

While studying at the U, she researched total synthesis of natural products in Gary Keck’s lab and played on an intramural soccer team where she met her husband.

Wager is a chemistry midfielder in her career, driven to cover a lot of ground by her passion for working in a fast-paced, team environment. After graduating from the U, she spent 17 years at Pfizer as Senior Principal Scientist, Director of Business Planning, Chief of Staff for Pfizer Medical, and Medical Strategy Lead in Oncology. Then she earned her MBA from MIT in 2017 before joining Ascidian Therapeutics. “I really found the place where my heart belongs, and that’s working in startups,” she says. “In those situations, it’s pretty high risk, but also high reward. The strength of the team is critical, and I really enjoy that part. I’ve always been into team sports. I love having a phenomenal team that I work with.”

EXON-EDITING IS THE NAME OF THE GAME

Carrie Wager

The team Wager currently works with at Ascidian is taking a new approach to gene therapy, influenced by the organisms that the company is named after. Wager says, “We were inspired by what happens with sea squirts or ascidians because they re-engineer the transcriptome. They start as creatures that are free-floating … but then they become these structures after they re-engineer their transcriptome and are fixed on the bottom [of the ocean].” As sea squirts (Ascidiacea) mature, they self-edit their messenger RNA to change the proteins that are expressed and, ultimately, their structure.

Ascidian’s strategy for fixing genetic diseases in humans is different from other existing methods of gene therapy because it works by editing RNA through a process that is already inherent to the cell. “DNA is transcribed into RNA in the nucleus,” Wager explains. “It’s initially transcribed into pre-messenger RNA (pre-mRNA) and pre-mRNA becomes mature RNA, which leaves the nucleus. But the process of going from pre-mRNA to mature RNA is the excision or the cutting out of introns.” The splicesome is the enzyme responsible for removing the introns and leaving the exons which are then joined to form the mature strand of RNA.

Ascidian designs molecules to target mutant exons and replace them with a wild-type version. “We use these molecules that are packaged in an adeno-associated virus to gain entry into the nucleus. Then those molecules are built to bind to specific locations in messenger RNA. … The spliceosome machinery comes along and flips-in our healthy exon that’s packaged in our molecules and removes the mutant components. Then that [corrected RNA] continues on outside of the nucleus into the ribosomes, and you generate the healthy protein.”

The procedure or process can sound convoluted and dicey–like a wellplaced strike by Spain’s Olga Carmona during the final of the recent FIFA Women’s World Cup. But the stakes are just as high (and even higher for its beneficiaries) for Wager and her team whose exon editing method has many advantages over other gene therapies. Since only the RNA is being edited, risks associated with DNA editing are reduced. Harnessing a natural cellular process prevents the need for bacterial enzymes, which pose an immunological threat, to be introduced to the cell.

The most impactful benefit is the amount of editing that can be done at one time. For example, Ascidian is currently focused on addressing Stargardt’s disease, a genetic retinal disease that causes blindness and stems from mutations in the ABCA4 gene which codes for the protein involved in clearing vitamin A from the retina. Without the healthy protein, toxic compounds begin to accumulate in the eye, destroying cells and impairing central vision function.

Rather than doing “point mutations or small base insertion,” Wager uses technology that replaces whole exons. “We can swap out up to 4,000 nucleotides. So that allows you to make a difference in diseases that have really big gene sizes and genes that have high mutational variants. With one drug we can cover the majority of patients.” If Ascidian’s exon editing idea passes human trials and FDA approval, the treatment is something any ophthalmologist could do during a half-day clinic.

No Magic Bullet

While RNA exon editing is an exciting new strategy for tackling genetic disease, that’s not to say that other tools like CRISPRCas9 aren’t useful. “I’ve been in drug discovery for twenty-three years now,” says Wager. “I don’t think that there is one type of way to ameliorate disease. [T]here’s lots of different ways. They all have their niche.”

In this way, the multi-faceted dynamic of the fight against genetic diseases mirrors that of the startup culture where Wager excels. “When you find a place where it’s not just that you enjoy what you’re doing, but you thrive, that’s what the startup environment for me is [with] super intelligent people [who are] super motivated to make a difference in patients’ lives.”

Each scientist brings something different to the startup, and Wager’s expertise along with her technical skills which she attributes to her time at the U makes her a valuable addition to the team. Through her training she “learned how to exquisitely design and execute research problems in this [startup] environment… .”

“I truly believe that my graduate training here [the U] has set me up to be able to do whatever I want. … I’ve had a bunch of twists and turns [in] my career… I didn’t stay in one kind of role for more than five years. The U just teaches you skills that carry over in everyday life and in your career, and I really am grateful for how we were set up [early] to do research.”

The extensive application of Wager’s education is a testament to the quality of the chemistry department’s graduate program, successfully preparing students for careers in academia, industry, and beyond. The Distinguished Alumni Award celebrates Wager’s impressive career since her time at the U, but really, she’s just getting started in her match against genetic disease. <

By Lauren Wigod

Life in the Gas Lane

life in the gas lane

 

Industrial chemist Ziggy Uibel performs at high octane.

Occasionally, one stumbles upon someone who convinces you, through a combination of training, tenacity and enthusiasm on an existential level, that they could do or be anything in this life.

Such is the case with Rory “Ziggy” Uibel, PhD ’03 who recently provided for a select group of non-chemists a tour of Process Instruments, Inc. Founded by Lee Smith, Process Instruments (PI) has pioneered Raman spectroscopy analysis for process control, primarily for refinery and petrochemical plants at sites that can be environmentally extreme, from arctic to desert and from tropical climates to off-shore locations.

If that sounds arcane, it becomes clearly grounded and articulated by the tour guide who leads an X Games-style stunt-double life as an extreme athlete. Even so, he’s categorically in his element as a chemist at the office and shop located in Research Park southeast of the University of Utah.

Uibel moves about the floor of PI with the wild-eyed energy of a kid in a candy shop. He might as well be on inline skates or skiing, two pastimes of his as a younger man. He is fond of picking up a dense spectrograph housed in something to the uninitiated that looks like kryptonite casing and dropping it with a satisfying thud on the bench to show how shockproof his product is.

It needs to be. A Raman analyzer uses a laser to excite a molecular vibration of molecules where a tiny portion of the incident radiation is shifted to a longer wavelength and produces a Stokes Raman scattering band. The wavelength-shifted Raman bands provide a structural fingerprint by which molecules in a sample can be identified. Process Instruments manufactures Raman instruments for not only extreme environments but for the rough handling of petroleum engineers. Its featured, online process monitoring provides updates in real time of up to seventeen different process streams per machine.

“We think of ourselves as more of an information company than an instrument company.” says Uibel. “A refinery with our real time information will be able to optimize stream blends and reduce giveaway of more expensive components,” such as octane.

PI’s optically fast spectrometer and low loss sequential optical multiplexer are paired with a set of fiber optic cables for exciting the sample and collecting the Raman scattering. At PI, the analysis and the machinery – from computers to the cooling apparatus and from the laser probes to the fiber optic conduits – can all be monitored and maintained remotely. Equipment includes back-up components and, if needed, are repaired or replaced on demand, by calling a certain mobile phone number at the other end of which is none other than Uibel (“Hi. This is Ziggy!”) who arranges to assess the situation and then often travels personally to the site to provide service.

This kind of customer service is legendary in the sector and has garnered the loyalty of clients who also benefit from rent-to-own set-ups that would otherwise run them $500,000. Most clients see a return on investment within two-to-four months, says Uibel with a grin. From a modest shop of five employees beginning in 1993, Process Instruments has grown to a staff of 16 and currently boasts a share of 20% of all U.S. refineries and 6% of the worldwide market.

But it isn’t just nerd-out technology that Ziggy’s team offers; it’s clearly encased in business acumen that is innovative and relentlessly hands-on with clients. “We are working on reaching approximately 60% total penetration with many of the individual refineries having multiple (5-10) instruments. The demand for instrumentation within the refinery markets has kept us quite busy and with the limited spare time we do have to continue to work on additional applications for our Raman instruments.”

Those applications are numerous — and always expanding. Petroleum products vary broadly from state to state, and nation to nation based on regulations related to clean air and other considerations. In addition to offering gasoline solutions such as reducing octane loss and the “giveaway” of Reid vapor pressure, (a common measure of and generic term for gasoline volatility), PI helps optimize jet and diesel fuel. The company also provides upstream solutions which optimize crude oil and offshore solutions. More than a dozen streams of samples can be analyzed with a single instrument/system. 

Uibel is also keen to talk about applications outside the fuel industry, including pharmacology packaging (using a unique Raman spectrometer to analyze each pill, for example) as well as food production and distribution. The petroleum industry may be the “low hanging fruit,” says Uibel, but the company’s Raman analyzers are also being used in tracing ppm sulfate detection in offshore waterflooding streams and direct determination of olefin concentrations in motor gasoline (US Patent No.7,973,926). Blood testing is already being done with handheld Ramen systems.

Bowling with brio on Grandeur Peak.

A Canadian by birth, Uibel has pretty much always had a dual life: one in the lab and one on the streets and the slopes where his athleticism really shines. In fact, chemistry did not appeal to him at all when he was an undergraduate at the University of Washington in Seattle. Instead, he was infatuated with aeronautics and while taking general chemistry courses researching a pressure sensitive paint for wind tunnel applications using a porphyrin molecule (water-soluble, nitrogenous biological pigment) Uibel worked with NASA and Boeing developing the paint and over time his interests shifted from aeronautics to spectroscopy.

Uibel wanted to continue his studies in spectroscopy for this purpose, and after asking around, discovered that Joel Harris’s name was at the top of everyone’s list. He decided that the University of Utah would be the ideal location for his graduate career. “I can easily say that coming to the U of U was one of the best decisions of my life,” he remarks.

That’s saying a lot, considering what Uibel’s life (and times) looks like these days, even as he’s entered middle age. What started as a seasonal gig as a “liftee” at Snowbird turned into a full “gap year” between his bachelor’s and graduate school at the U. Between skiing in the winter and rock climbing all summer near Elko, Nevada, he actually thought he would eventually find himself in a classroom teaching. That changed after earning his doctorate in analytical chemistry and landing a job at PI to design, assemble, test, calibrate and install Raman analyzers.

If this sounds like intensive work, it is. But Uibel is an intense man, and it seems to fit not only his inherent brio but also to play out and build on his activities outside of work. A globetrotter with clients from Canada to Singapore, and from Australia to off the coast of South America, Uibel has racked up a million-plus airline miles in no time (and without knowing he’d done so). This is an unassuming man who had to fetch his business card when asked what title he had at PI. (Turns out it’s Applications Manager or, maybe, Vice President of Technology.)

That’s not to say Uibel is a shrinking violet. As a youth he competed on MTV Sports as a stunt model. He recently completed the Rage Triathlon in the Lake Mead National Recreation Area, and he doesn’t stop at donning the Lycra for the swimming, bicycling and running competitions; he’s famous for summiting Grandeur Peak in Salt Lake Valley not once in a single day but a whopping five times (31 miles). The Peak has a special place in Uibel’s heart. Following the discovery of “misplaced” brick in his backpack compliments of his jokester friends, he started carrying a bowling ball and pins to the summit during the winter and bowling in carved-out lanes of snow “with an automatic return” (i.e., uphill). Stand-by participants who happen to be on-hand are awarded a tag for their backpacks emblazoned with “I Striked out on Grandeur Peak.”

“We try not to do it in the summer,” says Uibel. “Don’t want a bowling ball landing downhill on Interstate 80.”

Bowling on a mountain peak in the dead of winter? Why not? It’s consistent with Ziggy Uibel who has gone from his ambitions to be an aeronaut, a teacher, an academic and researcher, and purveyor of stunt double-inspired antics to, these days, an industrial chemist using the latest technologies and techniques to advance everything from petroleum refining to blood testing. 

By David Pace

CO2 changes over past 66 M years

CO2 Atmospheric changes

Carbon dioxide has not been as high as today's concentrations in 14 million years thanks to fossil fuel emissions now warming the planet.

 

Gabriel Bowen

Today atmospheric carbon dioxide is at its highest level in at least several million years thanks to widespread combustion of fossil fuels by humans over the past couple centuries.

But where does 419 parts per million (ppm) — the current concentration of the greenhouse gas in the atmosphere—fit in Earth’s history?

That’s a question an international community of scientists, featuring key contributions by University of Utah geologists, is sorting out by examining a plethora of markers in the geologic record that offer clues about the contents of ancient atmospheres. Their initial study was published this week in the journal Science, reconstructing CO2 concentrations going back through the Cenozoic, the era that began with the demise dinosaurs and rise of mammals 66 million years ago.

Glaciers contain air bubbles, providing scientists direct evidence of CO2 levels going back 800,000 years, according to U geology professor Gabe Bowen, one of the study’s corresponding authors. But this record does not extend very deep into the geological past.

“Once you lose the ice cores, you lose direct evidence. You no longer have samples of atmospheric gas that you can analyze,” Bowen said. “So you have to rely on indirect evidence, what we call proxies. And those proxies are tough to work with because they are indirect.”

Read the full article by Brian Maffly in @TheU.
Read more about Gabe Bowen, recipient of the College of Science's Excellence in Research award,  and his work with isotopes here.

Read related article "'Call to Action': CO2 Now at Levels Not Seen in 14 Million Years" in Common Dreams.

Solving Water Shortages by Lease

Solving Water shortages Through Lease

 

Booming growth is driving more demand for water, but climate change, aridification and an over-allocated system ensure a short supply.

Lily Bosworth. Banner Photo Credit: US National Park Service

 

State lawmakers have looked to farmers to solve Utah’s mounting water issues, hoping they’ll lease water to save the Colorado River and Great Salt Lake.

So far, almost no irrigators have signed up. Their reasons vary, but a pilot program on central Utah’s Price River shows farmers are willing to lease their water if it makes economic sense and if they trust the process. And the state has a lot of hurdles to overcome before water leasing makes a measurable difference.

“If we can generate the revenue we need with water versus putting something in the ground, it works,” said Kevin Cotner, a hay farmer near Price. “It’s yet another cash crop.”

Cotner just wrapped up his third season participating in the Upper Colorado Basin Commission’s water leasing project, called the System Conservation Pilot Program. He irrigated 450 acres this year and left 530 acres fallow. He got paid up to $650 per acre-foot left in-stream.

But Cotner’s participation in the pilot water leasing plan isn’t purely based on economics.

“This is a hard ag area to make a living. Things are pretty severe,” he said. “We’re transforming the desert. Water is one of the big issues.”

Cotner serves as the president of the Carbon Canal Co., and policing use is part of his daily life.

“I’m the bad cop,” he said. “I’m the water guy.”

Even after Utah saw record-breaking snowpack and runoff last winter, Cotner said drought is becoming the norm rather than an exception. Last year, his canal company could only deliver shareholders 38% of the water they’re entitled to on paper.

“That was a hard summer,” he said. “A lot of unhappy people.”

Booming growth in the West is driving more demand for water, but human-fueled climate change, aridification and an over-allocated system have ensured it remains in short supply.

The water leasing pilot is one strategy Upper Basin states identified to get demand back in sync with reality in the Colorado River system.

All the water Cotner conserved by fallowing his fields stayed in the Carbon Canal, making its way back to the Price River, eventually flowing to the Colorado River and Lake Powell reservoir. It will then flow to thirsty Lower Basin states like Arizona and California, helping the Upper Basin fulfill its obligations under the century-old Colorado River Compact.

At least that’s how it’s supposed to work. As of now, Utah and other Upper Basin states don’t have the ability to track where the saved water goes, or ensure another irrigator downstream doesn’t divert it away.

“We want to get there,” said Lily Bosworth, a U alumna from geology & geophysics and now a staff engineer with the Colorado River Authority of Utah. “That’s our goal.”

Read the full article in the Salt Lake Tribune (subscription required). 

 

More about Lily Bosworth BSG, HGE, '20

Bosworth is a Staff Engineer for the Colorado River Authority of Utah. Born and raised in Ogden, Utah, Lily has observed Utah's dynamic water systems throughout her life and developed an interest in water systems that combine natural and engineered elements with supporting water quality and quantity for all stakeholders. Lily completed bachelor's degrees in Honors Geological Engineering and Environmental Geoscience at the University of Utah, with a thesis on changes in hydrology when beaver dam analogs are installed during the riparian restoration. Lily also completed a master's degree in Hydrologic Science and Engineering at the Colorado School of Mines, with a thesis focusing on water treatment with engineered wetlands. Outside of work, Lily loves to mix and match birding, backpacking, water coloring, yoga, trail running, hiking, biking, and ballet with friends and family.

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.

You can listen to an interview of Jessica Swanson on Cool Science radio at KPCW.

Bio Faculty Retirees

Festschriften 

 

 

At the annual SBS Award Ceremony this past spring, three retiring faculty members, now emeritus status in the School, were recognized by their colleagues. 

Festschriften: a book honoring a respected person, especially an academic, presented during their lifetime and containing contributions from the honoree's colleagues, former pupils, and friends. 

Michael Bastiani 

On a clear night deep in the Wasatch the sky is painted by starlight – you can see about 5000 stars!  But that is only a tiniest fraction of their total number. There are 100 billion stars in our Milky Way Galaxy, that is 20 million times more stars than the ones you can see.  That unfathomable number is how many nerve cells are in your brain; your mind is as big and complex as the stars in Milky Way Galaxy.  Moreover, those neurons form connections, and are signaling to each other.  But the connections and networks must be correct for each of us to be the talented human beings that we are.

Mike Bastiani spent his career studying how the brain forms these connections in a reliable and correct manner among the number of those signaling neurons. The scale we are talking about here is worth mentioning. Nerve cells are only 30 micrometers in diameter but must send a thin process called an axon up to one meter away to form the correct connection to its target cell. Let's pretend that you're a nerve cell. That would be equivalent to your hand crawling on the ground for 85 miles – all the way from Salt Lake City to the Idaho state line.(That would be a pretty remarkable journey for a human hand).  

Mike first studied this process in grasshoppers, demonstrating that each of what he identified as sprouting growth cones on the end of the nerve’s axon follows a specific path, making contacts with particular cells along the way. His laboratory identified unique proteins on the surface of these tracts of axons that acted as guides for growth cones that followed along the established roadways, changing direction of migration – as if reading a map.

 With his labeled-pathways hypothesis in hand, Mike began to study growth cone behavior in intact (not dissected) transparent nematode worms. His lab was the first to characterize growth cones in an unperturbed environment and unexpected behaviors of growth cones, their collapse ­– a once discarded notion — and their re-creation of the growth cone on the other side once they’ve successfully navigated a barrier.

Using this assay, his laboratory then discovered an entirely new process in nervous system development. By continuing to observe the nervous system after wiring was complete, he and his team identified genes that stabilized it. These genes “told” neurons to set aside their youth, to stop sprouting growth cones, and to stabilize the existing network. 

Initially, Mike observed in yet another subject model, C. elegans, what most believed: that damaged axons could not regrow and shut down. But then seven hours following the damage done to axons by a laser, he saw that growth cones sprouted from the stump and regrew to their target, though admittedly not perfectly. He then screened for mutants that could not regrow axons and discovered a protein called DLK-1 that was required for the reappearance of a new growth cone. Importantly, if he caused the neuron to make DLK-1 before the axon was damaged, the growth cone sprouted immediately after being cut and was able to find its correct target.

Subsequently, these experiments have been validated in mammals.  It turns out, the nervous system can heal itself, and if the neurons can be prodded to respond to damage earlier, can regrow, and re-establish functional synaptic contacts. These experiments have led the neuroscience community to explore repair of damaged nervous systems such as spinal cord injuries that result in patient paralysis.

Mike Bastiani retired from the School of Biological Sciences this past May, but as of 11 am this morning can still be seen at his microscope room repairing the laser. Apparently, there’s more work to be done.   ~ Erik Jorgensen

Don Feener

Don Feener has retired from the School of Biology, joining the ranks of the emeriti. His lively wit and penetrating questions have been an integral part of the intellectual and social life of our School since 1989. I first met Don when we were both at the University of Texas at Austin in the late 1970s. I was just starting my PhD program and Don had just finished his PhD on the community ecology of ants. Don was famous as one of the most well read of all the students, exhibiting a remarkable breadth of ecological knowledge and being up to date on all the latest publications. He inspired me as I pursued my own career in insect ecology. Also, that lively wit was on full display, making for awesome parties at Don's. In 1981, Don published a ground-breaking paper in Science, showing how parasitic flies affect ant behavior, mediating and altering competitive interactions among ant species. This simple and elegant field experiment had a large impact on thinking in community ecology. To this day I use that paper in my teaching, as an example where the discovery did not rely on new or sophisticated technology, but simply asking the right question. Great science can be done with a pencil, a notebook, a stopwatch, and a prepared mind. Don went on to establish a prominent career as a community ecologist, using ants and their parasitoid flies as a model system for understanding how ecological communities are structured and function.

 Beyond focused research, Don has always been a conscientious contributor to the teaching and administrative components of our academic enterprise. Don is a dedicated and empathetic teacher and has shepherded countless students through a broad range of topics: general biology, ecology, evolution, tropical biology, entomology, and quantitative methods. He has advised and launched sixteen graduate students and served on innumerable graduate committees. Always a good citizen, Don was a regular and reliable member of administrative committees, doing the necessary but generally thankless work.

 But Don is more than his professional life. He has always been a consummate "curious naturalist," observing and pondering nature in all its beauty and complexity. He has also been a consummate human being, deeply caring for others and alert to their needs. I have been a colleague of Don's for 40 decades, a great experience. I have also been a friend, an equally important honor. In his new role, we lose his teaching and administrative service, but luckily we still get the scientist, the curious naturalist, and the friend.
~ Jack Longino

Jon Seger 

As a scientist, Jon brings rigorous scholarship, creativity, and a "no barriers" approach.  He defined bet-hedging in classic work, worked with Hamilton on parasites and sex, and was inspired by his wife Vicky Rowntree's right whale system to appreciate the power of being boring.  Whale lice, that we hoped would tell us something about whale movement, turned out to tell us absolutely nothing. Jon had the vision to appreciate how their dull environment and mind-numbing population dynamics provide the perfect system to measure the chilly draft of deleterious alleles that makes each of us rather less than perfect. 

Unlike some theorists I can think of, Jon knows how to run a lab, and can be found sequencing whale lice at odd hours of the day and night to extract the interesting from the boring.

 We've had fun running Theory Lunch since I arrived, making up witty posters, maybe helping a few people, and learning a lot along the way. As I see it, I come up with the "right way" to address the question, and Jon presents an alternative. He finds the holes in the logic, and by creating even bigger holes, finds the deeper questions lurking beneath a seemingly simple facade.  

Soon after my arrival, we were discussing some problem, and I made an off-hand comment about "pointy-headed molecular biologists."  Jon swiftly set me straight, that biology is biology and that head shape is uncorrelated with subdiscipline. That short conversation was part of the long conversation that set me on the path of my own increasingly pointy-headed research and perhaps even to the role I find myself in today.  For everything but that, Jon, thanks. I hope and trust that your retirement is the opportunity for us to keep our conversation going. It's in our genes after all… .  ~ Fred Adler

Cold Fog & Complex Terrain

Cold fog & Complex Terrain

 

You might not initially think of fog as a form of severe weather, but when fog sets in and visibility plummets, transportation becomes dangerous.

Zhaoxia Pu

Fog is the second-most-likely cause of aircraft accidents after strong winds, but despite the high impact of fog events and a long history of research, fog prediction remains a long-standing challenge for weather prediction because of complex interactions among the land surface, water, and atmosphere. There’s still a lot of fundamental things about fog that we don’t know.

Zhaoxia Pu, University of Utah professor of atmospheric sciences and Eric Pardyjak, professor of mechanical engineering, hope to change that through a field campaign and scientific research using Utah’s Heber Valley as the laboratory.

For about six weeks, from 7 January to 24 February 2022, Pu, Pardyjak and their colleagues, including scientists from the National Center for Atmospheric Research (NCAR) and the Environment and Climate Change Canada as well as graduate students and undergraduate students from atmospheric sciences and mechanical engineering at the University of Utah, watched a network of sensors on the ground in the Heber Valley along with comprehensive sets of instruments from the NCAR's Erath Observing Laboratory and satellite observations. The valley is bounded by mountains, relatively flat in the basin and features two lakes — Jordanelle and Deer Creek reservoirs. Its conditions, Pu says, are representative of mountain valleys around the world.

On winter nights, cold air pools on the valley floor and creates favorable conditions for several forms of fog, including cold-air pool fog, ephemeral mountain valley cold fog and radiative ice fog. By observing how these different kinds of fog form and dissipate, the researchers are continuing to learn about the meteorological conditions and physical processes governing the formation of fog and improve fog prediction.

The study is funded by a $1.17 million grant from the National Science Foundation.

Now, in a recent paper in the Bulletin of the American Meteorological Society, Pu and her colleagues have published findings via The Cold Fog Amongst Complex Terrain (CFACT) project, conceived to investigate the life cycle of cold fog in mountain valleys.

The overarching goals of the CFACT project, according to the paper’s abstract, are to 1) investigate the life cycle of cold-fog events over complex terrain with the latest observation technology, 2) improve microphysical parameterizations and visibility algorithms used in numerical weather prediction (NWP) models, and 3) develop data assimilation and analysis methods for current and next-generation (e.g., sub kilometer scale) NWP models.

Field observations, NWP forecasts, and large-eddy simulations provided unprecedented data sources to help understand the mechanisms associated with cold-fog weather and to identify and mitigate numerical model deficiencies in simulating winter weather over mountainous terrain. The paper summarizes the CFACT field campaign, its observations, and challenges during the field campaign, including real-time fog prediction issues and future analysis.

Comprehensive measurements

A network of ground-based and aerial in situ instruments and remote sensing platforms were used to obtain comprehensive measurements of thermodynamic profiles, cloud microphysics, aerosol properties and environmental dynamics. Over its seven-week course, the CFACT field campaign collected a diverse and extensive dataset, including high-frequency radiosonde profiles, tethered balloon profiles, remotely sensed thermodynamic and wind profiles, numerous surface meteorological observations, and microphysical and aerosol measurements. Nine intensive observation periods (IOPs) explored various mountainous weather and cold fog conditions.

Despite the drought in the western United States in 2022, which limited the occurrence of persistent deep fog events associated with persistent cold-air pools that regularly form in higher-elevation Intermountain West basins, the campaign observed highly spatially heterogeneous ephemeral fog and ice fog events. Since ephemeral fog and ice fog are extremely difficult to detect, model, and forecast, CFACT provided unprecedented datasets to understand both types of fog and validate the NWP model.

Meanwhile, the variety of non-fog IOPs provided valuable observations for understanding near-surface inversion, ice crystal formation, moisture advection and transportation, and stable boundary layers over complex terrain, all of which are essential factors related to fog formation. Comprehensive studies are ongoing for an improved understanding of cold fog over complex terrain.

Critical high resolution observations

The CFACT campaign observations, complemented by model simulations, have been instrumental in studying the lifecycle of fog and the behavior of the stable boundary layer. More importantly, since Heber Valley is a small-scale valley, the observations from the two CFACT supersites, eight low-cost stations and nine satellite sites provide critical high-resolution observations to validate and improve current and next-generation (i.e., sub-kilometer scale) NWP models.

Moreover, the available CFACT high-resolution meteorological observations, along with the soil and snow observations during CFACT, are helpful for developing fine-scale atmospheric data assimilation and the coupled land–atmosphere data assimilation (e.g., Lin and Pu 2019, 2020; Zhang and Pu 2019) for improved near-surface weather prediction, including cold-fog forecasting.

Various comprehensive studies are presently underway for numerical model validation, improvement and data assimilation to improve cold-fog prediction.

First author of the paper, Zhaoxia Pu is a member of the NOAA Science Advisory Board. She is an elected fellow of the American Meteorological Society and Royal Meteorological Society.

This story is adapted from an earlier announcement on this project by Paul Gabrielsen in @TheU.

UPDATE (Dec.19, 2023): With the persistent "inversion" now occurring in the Salt Lake Valley and beyond,
additional coverage from FOX 13 of Dr. Pu's research has been broadcasted / posted.
Listen to the story here.

UPDATE (Feb. 13, 2024): The EOS newsletter of American Geophysical Union  (AGU)
featured the CFACT project here.

UPDATE: (January 9, 2025): This study and story are featured in the National Science Foundation stories.


Remembering Marta Weeks

Remembering Marta Weeks

 

With husband Karelton Wulf.

A longtime Associate Trustee of the Association of American Petroleum Engineers Foundation she embodied legendary civic promotion as well as historic philanthropic support to the Foundation as well as to the Department of Geology & Geophysics and the College of Mines & Earth Sciences at the University of Utah which honored her in 2010 with the Founder's Day Distinguished Alumna Award.

The daughter of a petroleum geologist and the wife and daughter-in-law of world-renowned petroleum geologists, Weeks generously and continuously supported the AAPG Foundation as well as a host of other cultural and humanitarian causes around the world.

Weeks had many careers (often publicly praised as a “Renaissance Woman”) and remained active and passionate about her roles well after the usual retirement age – she was ordained an Episcopal priest in 1992 – directly impacting thousands of lives through her involvement with a host of groups and organizations.

The world knew of her great and lasting work; friends and those close knew that she was, in the words of past Foundation Trustee Chairman William L. Fisher, “as modest as she is generous.”

With AAPG, she had been a Foundation Trustee Associate since 1976. For her, philanthropic engagement with AAPG was her opportunity of “giving back,” she said, and it was a lifetime pleasure.

“I give to AAPG to honor my father, my husband and my father-in-law,’ she said, “all of whom were involved in petroleum geology.”

For Weeks, advancing opportunities in education for new generations of geoscientists was an especially significant part of her life.

Her most recent gift to the Foundation was bequeathed just last year – a $5 million annuity that will be distributed through 2029, impacting geoscientists for decades to come.

Indeed, she and her family made many donations to the AAPG Foundation throughout its history, including a $10 million bequest in 2006, the largest gift ever received by AAPG.

A Life of Excellence

Marta Weeks receives AAPG Foundation's inaugural highest honor, the L. Austin Weeks Memorial Medal, at the 2008 Annual Convention & Exhibition in San Antonio, Texas.

Marta Joan Sutton Weeks was born in Buenos Aires, Argentina, where her father Fredrick Sutton worked as a petroleum geologist. She was raised in both North and South America, and petroleum geology was a constant in her life.

Her first job – at age 13, while residing with her family in Maracaibo, Venezuela – came as she started a small popcorn business for the outdoor oil camp moviegoers.

She attended high school in Salt Lake City, Utah before attending Beloit College in Wisconsin, then graduated with a degree in political science from Stanford University.

Her career then started with summers spent teaching English for the Mene Grande Oil Co. and the Centro-Venezolano Americano in Caracas, Venezuela. Again, the oil business was a regular part of her life.

She then married petroleum geologist Lewis Austin Weeks in 1951, who was the son of famed petroleum geologist Lewis Weeks, and subsequently resided with him in Utah, Colorado, California and Maryland before moving to Miami, Fla., in 1967.

In 1988 she returned to graduate school in Austin, Texas, earned a master’s degree in theology and in 1992 was ordained an Episcopal priest. Her ministry included chaplaincies at Jackson Memorial Hospital in Panama, the Bahamas, the American Cathedral in Paris, France, and ultimately the Diocese of Southern Florida.

In 2008 she was the first recipient of the L. Austin Weeks Memorial Medal, intended to recognize “extraordinary philanthropy and service directed to advance the mission of the AAPG Foundation.”

In addition to the geosciences, she was passionate in her support of the University of Miami, where she was an advocate for academics, the arts, health care and research.

A complete listing of all her connections, honors and activities would be exhaustive, but a partial listing includes:

  • Director of Weeks Petroleum Ltd., Omni-Lift Corp. and the Weeks Air Museum
  • University of Miami Board of Trustees (their first woman chairperson, 2007-09)
  • Founding member and president of the Stanford Club of Florida
  • A member of St. Andrew’s Episcopal Church Foundation, board member of the SE Episcopal Foundation and a trustee of Beloit College and Bishop Gray Inns
  • A member of the National Advisory Council-University of Utah and the Order of St. John of Jerusalem (both as a chaplain and a Dame)
  • Supporter of the Center for Sexuality and Religion
  • Her name graces the YMCA building in Miami, a music school building at the University of Miami and the center at the Episcopal Theological Seminary of the Southwest
  • Chairs and scholarships are named for her and exist because of her generosity at numerous schools

And Foundation TAs know very well of her passion for golf and active participation at TA annual meetings – a plethora of stories of her exploits on the links will keep that part of her legacy alive for years to come. In addition to being a legendary philanthropist and woman of vision, she was a friend.

After Lewis Austin Weeks passed in 2005, Marta married Karleton Wulf in 2009. Wulf passed in 2020, and Marta spent her final years residing with her daughter, Leslie Anne Davies, on Jupiter Island.

In addition to her daughter, Marta Weeks is survived by her son, Kermit Austin Weeks; granddaughter, Katie Weeks; and grandsons, Bryce and Cole Davies.

A version of this memorial was first published in American Association of Petroleum Geologists (AAPG)'s Explorer where you can read more about Weeks and her impact on the industry. Watch a video of Week's receiving the AAPG's top honor, the inaugural 2008 L. Austin Weeks Medal.