bio-news
Kona Coffee Lawsuit
James Ehleringer
Those farmers recently won a series of settlements — totaling more than $41 million — after a nearly five-year legal battle with distributors and retailers that were accused of using the Kona name in a misleading way.
In 2019, Bruce Corker, who owns the Rancho Aloha coffee farm in the Kona district, filed a lawsuit on behalf of Kona farmers against more than 20 companies. At the center of the complaint was a chemical analysis performed at a private lab in Salt Lake City by James Ehleringer, Distinguished Professor in the School of Biological Sciences at the University of Utah who ran the analysis and who said that standard tests depended on the amount of water in each sample. That wouldn’t have worked on the variety of Kona products at issue.
“As you go from green beans to roasted beans, you’re changing the water content,” says Ehleringer. So he borrowed an approach from geology that instead looked at the relative concentrations of rare, inorganic minerals in the beans. These ratios, he said, stay constant even at roasting temperatures.
After testing coffee samples from around the world as well as more than 150 samples from Kona farms, Dr. Ehleringer’s team identified several element ratios — strontium to zinc, for example, and barium to nickel — that distinguished Kona from non-Kona samples. “We were able to establish a fingerprint for Kona,” said Dr. Ehleringer, who described the general method in a 2020 study. “It’s the characteristics of the volcanic rock.”
Those chemical signatures, he found, were largely absent from samples of coffee labeled “Kona” sold by the defendants.
Read the full article in the New York Times by Virgina Hughes here.
SRI Stories: Irvane Nelson
A study of ‘magic mushrooms’
Alexander Bradshaw, PhD'22, now postdoctoral researcher at the U and lead author of the study. Credit: Bryn Dentinger
They captured the wider world’s attention as a psychedelic staple in the 60s and 70s. Now, these infamous organisms are at the forefront of a mental health revolution. Psilocybin and psilocin, the psychoactive compounds found in nearly all species of Psilocybe, have shown promise as a treatment for conditions including PTSD, depression, and for easing end-of-life care.
To utilize psilocybin as a therapeutic, scientists need an extensive roadmap of the compound’s underlying genetics and evolution, information that doesn’t exist. Our limited knowledge comes from research on just a fraction of the ~165 known species of Psilocybe. Most psilocybin-producing mushrooms haven’t been studied since they were first discovered—until now.
A team of researchers led by the University of Utah and the Natural History Museum of Utah (NHMU) has completed the largest genomic diversity study for the genus Psilocybe. Their genomic analysis of 52 Psilocybe specimens includes 39 species that have never been sequenced.
Bryn Dentinger, principal investigator. Credit: B. Dentinger
The authors found that Psilocybe arose much earlier than previously thought—about 65 million years ago, right around when the dinosaur-killing asteroid caused a mass extinction event. They established that psilocybin was first synthesized in mushrooms in the genus Psilocybe, with four to five possible horizontal gene transfers to other mushrooms from 40 up to 9 million years ago.
Their analysis revealed two distinct gene orders within the gene cluster that produces psilocybin. The two gene patterns correspond to an ancient split in the genus, suggesting two independent acquisitions of psilocybin in its evolutionary history. The study is the first to reveal such a strong evolutionary pattern within the gene sequences underpinning the psychoactive proteins synthesis.
“If psilocybin does turn out to be this kind of wonder drug, there’s going to be a need to develop therapeutics to improve its efficacy. What if it already exists in nature?” said Bryn Dentinger, curator of mycology at NHMU and senior author of the study. “There’s a wealth of diversity of these compounds out there. To understand where they are and how they’re made, we need to do this kind of molecular work to use biodiversity to our advantage.”
M.A.D. about Skeeters
Chris Bibbs, Great Salt Lake
Yes. Harassment, regardless of how you pronounce the word, will get you in trouble by your local mosquito abatement district (appropriately acronym-ed as “MAD”). It turns out that the pest in “pesky” can actually have a deleterious effect on lifestyle, kids walking to and from school, vacationers and can even, eventually, impact the local economy.
Whether it’s dodging dengue or out-maneuvering the little dogfighting Red Barons as you try to conduct business, Salt Lake Valley has one of the first MADs in the country, predating the Center for Disease Control and Prevention known for its recent flurry of COVID-19 mandates by more than twenty years.
And Salt Lake City MAD (SLCMAD), located north of the airport down on the floodplain by the Great Salt Lake, is also the catalyst for one of the Science Research Initiative’s (SRI’s) celebrated research streams that science students can participate in.
Ready to get bitten by the bug of composite biology research? You’ll be in good hands. Toxicologist and behavioralist Christopher Bibbs, SLCMAD’s laboratory director, and SRI stream leader with his colleague Nate Byers and others can take you the distance into the fascinating world of mosquitos as they interface with public health and environmental concerns.
“Although our job is to deal with the mosquitoes, we coexist with this entire system,” says Chris, meaning that scientists don't just survey only those of us with a blood-flush target on us. “We look at non-targets; we look at migratory bird pathways; we look at invasives; we look at general composite biology.” To work in abatement doesn’t just mean you’re a mosquito murderer–fly swatter in hand or the wielder of broad-spectrum pesticides, which do not discriminate what they kill; you have to be concerned about the types of interventions you experiment with.
“If you introduce this into the system, does it cause harm?” Chris is quick to ask. “If we use a pesticide? Does it create a pollution build–up? If we use a trap, does this give a reasonable inference on what's going on in the area? We do all these types of exploratory projects, because again, the goal is to help track and control mosquitoes. So, any discipline that we can use, whether that's biochemistry, bioinformatics, spatial modeling, whatever — engineering — it's a tool for us.”
Under the direction of molecular biologist Nate who sets up the traps — 60 at a time — team members do viral surveillance looking for viruses in field-caught mosquitoes. This is followed by collating and analyzing data. Research at SLCMAD presents a field as well as a lab component to the experience. And the work is not only ultimately a public service but the process sets up an exploratory site emblematic of the kind of pure science inquiries that undergraduates are asked (and encouraged) to do at the University of Utah.
Indubitably, sheer curiosity drives the research.
Past students during the spring semester (2023) stream were not just dodging bites by female mosquitoes (the ones who need a blood meal to produce eggs). No, these SRI students were asking questions and setting up experiments that helped vector the SLCMAD team in different but productive research directions, something SLCMAD is eternally grateful for.
“The stuff that we're doing isn't just some fundamentalisms about the fields,” says Chris, who has a lot to say about his work as SRI stream leader and preceptor with the U students and other interns. “It's stuff that can actually help people, maybe change a process, maybe improve the way you look at data. Maybe it's just a new method of doing something, designing equipment, new traps, or something like that. So, this is the kind of stuff that's actually very easy to get out there. Because it's tangible and useful to people. So that's something I can pretty reliably offer.”
Chris and his team are relatively regimented in their mentoring. “I try to figure out what you like,” says Chris, referring to his mentees. “It's not even what you've been trained in. What do you like, right now? What are you interested in? What do you want to do? And I try to take those interests and piece them together with stuff that we have already talked about that we would like to do.” This is followed by a review of the research literature and then, says Chris, “I kind of turn you loose.”
The result has been gratifying. Students have come to him with ideas–sometimes that make him raise an eyebrow–but that ends up productive, like looking at how common synthetic sugar additives trigger forceful hypoglycemic reactions that are toxic to mosquitoes. Or, like the freshman student who kept bringing up the component of vision in the animal which is typically thought to be olfactory driven. “He was absolutely right,” says Chris, of the student whose findings from bio assays were eventually paired with research being done by biology professor Neil Vickers who is on the SLCMAD board.
“On top of that,” continues Chris, “for us as a district, you know, [this student’s work] pertained to a mosquito that actively harasses people all year long.” Now, the District is planning on using this information to attempt better surveillance on the species which, if left unchecked, can cause heart-worm disease in domestic animals like cats and dogs.
But wait. There’s more!
Both of these research questions led to experiments, data, conclusions and eventually a paper–more than one. (Not a bad thing to publish papers as an undergraduate.)
“I'm super proud of the SRI involvement with this, because I kind of went into this not knowing what to expect, but I feel like with their unique creativity, and how they look at stuff, they really contributed a lot to this whole equation. It's kind of funny [the process], but it's like now … you were on the money!”
There’s something infectious, no pun intended, about Chris and Nate’s animated descriptions of what might appear as an unlikely marriage of an entity whose main goal is public health with an auxiliary function of research with an SRI teaching lab at the U. Part of that elevated feeling is likely that, to do their mission-driven job, MAD deploys every aspect of biology, ecology, chemistry, physics, and “every nuance and subdiscipline” to get the job of mosquito abatement done.
It’s a model for targeted, real-work experience connected with academics and research, and — except for the mosquitoes — everyone, especially SRI students, seem to benefit.
Nematode proteins shed light on infertility
Nematode proteins shed light on infertility
We have two copies of each chromosome in every cell in our bodies except in our reproductive cells.
The Rog Lab
Sperm and egg cells contain a single copy of each chromosome with a unique mix of genes from our parents, an evolutionary trick to give our offspring genetic variability. The sperm and egg are made during meiosis, the process by which cells with two chromosome copies reduce their chromosome numbers to one. For meiosis to work, the two chromosomes must align perfectly and exchange the correct amount of genetic information. Any deviation puts fertility at risk.
Enter the synaptonemal complex (SC), a zipper-like protein structure that lines up and anchors the two parental chromosomes together, end-to-end, to facilitate successful genetic exchanges. Failure to regulate this exchange is a leading cause of age-related infertility in humans and could compromise fertility across the tree of life. Humans, fungi, plants, worms and anything that reproduces sexually uses the SC to make reproductive cells, known as gametes. Despite its importance, we don’t understand how proteins within the SC regulate chromosomal interactions because this multi-step process happens in internal organs and has been impossible to recreate in a lab.
“This is a way to lock in on systems in cells that are too ‘loosie-goosey’ to use methods that rely on crystallization,” said Ofer Rog, associate professor of biology at the U and senior author of the study. “A lot of the interactions in cells are loosely bonded together. The problem is that you can’t look at it under an electron microscope because nothing is stable enough—everything is constantly moving. Our approach allows you to study even the interactions that are relatively weak or transient.”
Read the full article by Lisa Potter in @TheU.
Presidential Scholar Award
Bio Faculty Retirees
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