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

Presidential Scholar Award

Associate Professor of biology Sophie Caron is a 2023 awardee. The University of Utah Presidential Scholar Award supports the work of exceptionally promising mid-career faculty in academic units across campus by providing $10,000 in funding each year for three years to the award winners.

 

In addition to Caron, an internationally prominent neuroscientist, other awardees include a top researcher in prosthetics, an expert in environmental health and public health challenges and a distinguished leader in the field of chronic diseases in vulnerable populations have been selected as the 2023 cohort of Presidential Scholars. The associate professors will receive this designation for three years.

The Presidential Scholar award supports the work of exceptionally promising mid-career faculty in academic units across campus by providing $10,000 in funding each year for three years to the award winners. The funds — made possible by support from a private donor — may be used to support scholarly, teaching and outreach activities. Up to four new Presidential Scholar Awards are made each year.

Former Mario Capecchi Endowed Chair, Caron uses cutting-edge techniques to tackle fundamental questions about perception. In order to understand how brains are built to learn, she uses the Drosophila mushroom body as a model system. She built an interdisciplinary research program by drawing on computational models, species-comparative studies and various anatomical, functional and behavioral techniques to elucidate the structural, functional and evolutionary pressures that shape the mushroom’s learning function. For her work, Caron has received an NSF CAREER award and two NIH R01 awards, totaling $4.5 million. In addition to her research, Caron designed and regularly teaches the popular cellular neurobiology class (BIOL 3240) which regularly attracts nearly 100 enrollments per semester. Her work has been described as “stunning” and “breathtaking” by colleagues at outside institutions.

In addition to Caron, the 2023 winners include Nancy Allen, associate professor in the College of Nursing; Tommaso Lenzi, associate professor in the Department of Mechanical Engineering in the John and Marcia Price College of Engineering; and Neng Wan, associate professor in the Department of Geography in the College of Social and Behavioral Science.

“These educators represent the cutting-edge work on this campus that can impact our world for the better,” said Mitzi Montoya, senior vice president for academic affairs. “I’m grateful for their contributions and pleased to recognize their research.”

 

Read the full article about all four awardees in @TheU

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

$7M to build better life sciences workforce

$7Mto build bigger, better life sciences workforce

 

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

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

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

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

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

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

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

Read the full article in @theU.

SRI Stories

SRI stories:  From the lab to Costa Rica

 

Despite being over three thousand miles away from her lab back in Salt Lake City, Sylvia Lee was still able to sequence the DNA of the species she is studying.

While doing field work in Costa Rica, Sylvia continued her research by using Oxford Nanopore’s MinION, a portable technology that allows for DNA and RNA sequencing wherever you are.

Sylvia works in an SRI research stream that focuses on using Next Generation Sequencing (NGS) technologies to barcode and sequence DNA. This allows her lab to uncover new species and their phylogenetics. NGS allows in-house sequencing within the lab, rather than having to send it off to a company or lab. Or with the portable MinIOn, on a Costa Rican beach.

Sylvia’s main project is focused on ant-plant symbioses. She works to identify a third party within that symbiosis which is a crucial piece of the mutualistic interactions between ants and plants. The ants can’t get certain nutrients from their host plant, so the third party, mealybugs, are essential for this mutualistic relationship. She’s identifying the species of mealybugs involved, and after that, will look more closely at the nitrogen-fixing microbiome surrounding this entire process.

Sylvia is planning to go to graduate school, pursuing research in the biotech field. She’s a Social Justice Advocate, connecting U housing residents to resources and creating safe communities where they feel like they belong. She’s also part of the U’s undergraduate chapter of SACNAS, designed to support Chicano, Hispanic and Native American STEM students. 

“My parents are my heroes,” she said. “I look up to them because I have seen how much they’ve gone through, raising two children in a foreign country, far away from what’s familiar and far from where they called home. They did all of this just to make sure their kids would have a good life and a good future.”

Sylvia was born in Cheongju, South Korea, but at a young age moved overseas with her family. She traveled many places, but spent a lot of time in Mexico, and came to the U as an international student. Sequencing DNA has not only proven “portable” for Sylvia Lee; when she graduates with BS in biology and minor in chemistry, they’ll be infinitely “portable” as well. 

By CJ Siebeneck

Mechanisms of plant microbes

Mechanisms of Plant microbes

 

'Plants do have immune systems or immune responses, and a lot of people don’t realize that,' explains Efthymia ‘Effie’ Symeondi. 

“They have a pretty complicated and well-defined system for responding to pathogens.”

The post-doctoral researcher in the School of Biological Sciences is this year’s recipient of the College of Science Outstanding Post-Doc Award. 

Symeondi's fascination with genetics has led her to research an impressive variety of topics, eventually bringing her to Talia Karasov’s Lab at the University of Utah in 2020. 

Her research is focused on investigating the complex interactions between plants and microbes, particularly the effectiveness of certain microbes as pathogens, and plants’ unique immune responses to them: 

Because microbial pathogens have the ability to evolve very quickly, the research on them must be dynamic as well. One of the powerful implications of these studies applies to agricultural crops, which can be particularly vulnerable to infection. “When a farmer grows a crop that is a monoculture, it's a single genotype,” says Symeondi. “So the moment there is a microbe that can cause disease in this culture, it wipes out the whole field.” 

In order to understand these outbreaks, it is critical to decipher the mechanisms of these microbes, especially why they are pathogenic in one genotype versus another. In the future, Symeondi hopes to expand this research in order to inform farmers about how best to protect their crops: “We would like to utilize agricultural data and collaborate with different labs to see if we can predict outbreaks, and use different genotypes to prevent pathogen spread” she says. 

Presently, Symeondi is grateful to have the lab running smoothly post-pandemic (she arrived in Utah in October 2020 when Covid-19 was still wreaking havoc) and is excited to be expanding the scope of her studies. When she isn’t busy exploring plant genetics, Symeondi loves to be in the outdoors, hiking, visiting national parks, and spending time with her dog, Muninn. 

By Julia St. Andre

SRI Stories

SRI Stories: hands-on learning during COVID

 

 

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

 

 

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

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

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

 

 

 

 

 

 

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

 

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

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

zebrafish (Danio rerio)

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

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

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

 

by Lauren Wigod
Science Writer Intern

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

Read more College of Science stories by Lauren Wigod here.

SRI Stories

SRI Stories: Gap-Year Buzz

 

“I joined the beekeepers club my first semester of college,” says Claudia Wiese, a recent graduate from the U and an alum of the Science Research Initiative (SRI). She became very interested in bees — both honeybees and native bees. “So when an opportunity arose to do research on bees, I was very excited.”

Not as excited, perhaps, as bees get when they’re being looked at and managed by an eager student researcher. Little do they know, they are in good (and ambitious) hands. The Missoula, Montana native graduated with no fewer than three degrees: two BS honors degrees, one in biology and the other in Environmental and Sustainability Studies as well as a BA in Latin American Studies.

But wait. There’s more. She also graduated with Honors Ecology and Legacy Integrated Minor which offers students a guided pathway through Honors, one where they can dive into environmental and ecological thinking in an interdisciplinary manner.

Busy as a bee, it would appear.

SRI experience

No wonder today, Claudia is taking a gap-year break before she heads back to academia for a graduate degree. In the meantime, she spends “a lot of time outside and work[ing] as a ski instructor and river guide. It’s also a priority of mine to be active in local organizations that work on protecting public lands.”

Bzzzzz . . .

“Honeybees,” she reminds us, “are only about eight species of 20,000+ bee species in the world! In other words, the vast majority of bees on earth do not make honey.” This isn’t your average backyard beekeeper. In her research, she explains, “I sequence the DNA of pollen from honeybees to understand what plants they are visiting. Specifically, I am using this approach to understand the effect of a mite treatment that is commonly used. Do bees visit different flowers due to the treatment?,” she asks.

Her SRI experience in the program's Pollen Metagenomics research stream was a definite introduction and asset to her field of study. And gap-year or not, she regularly leaves Snowbird during the winter where she works as a ski instructor to continue working in her SRI stream “with the goal to finalize my research and mentor other students.”

“I am very thankful for the opportunities that SRI has provided me,” says Claudia Wiese, the recent graduate, poised to take on the next hive of scientific inquiry. “They have been an incredible launchpad to culture my passion for research and [to demonstrate how to balance it with my other interests.”

 

By David Pace

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

Nadkarni Named NatGeo Explorer at Large

Nadkarni named NatGeo Explorer at Large

 

The National Geographic Society has appointed famed University of Utah forest canopy researcher Nalini Nadkarni as a National Geographic Explorer at Large.

A Professor Emerita at the School of Biological Sciences, Nadkarni, an ecologist who pioneered the study of Costa Rican rainforest canopies and an avid science communicator, will serve as an ambassador for the National Geographic Society. As an Explorer at Large, Nadkarni will receive support for her research and in bringing accessibility to science and nature across communities.

Explorers at Large hold the highest distinction within the organization. They are preeminent leaders in their field who also serve as mentors to other National Geographic Explorers. The title is bestowed upon a few select global changemakers, including Explorers like storyteller Shahidul Alam, oceanographers Bob Ballard and Sylvia Earle, artist Maya Lin and ecologist Rodrigo Medellín.

“At the National Geographic Society, we often say science and exploration are our foundation, and storytelling and education are our superpowers. Nalini’s career embodies this sentiment,” said Jill Tiefenthaler, chief executive officer, National Geographic Society. “Nalini is passionate about sharing her work with people of all backgrounds to foster a greater understanding of and care for the natural world. This is key to our mission and among the many reasons we’re thrilled to name her a National Geographic Explorer at Large.”

Read the full press release dated Wednesday, Oct. 18, 2023 at National Geographic.

Epiphytes face growing threats

Epiphytes face growing threats

 

Orchids, mosses, ferns—or epiphytes, defined as nonparasitic plants that grow on other plants—are crucial for Earth’s biodiversity and play essential roles in forests around the world, building habitat in trees for myriad other life forms, from bacteria and insects to birds and reptiles.

However, the very attributes that have enabled epiphytes to thrive in forest canopies are now making them vulnerable to both natural and human-caused disturbances, according to Nalini Nadkarni, the University of Utah biologist renowned for her pioneering work studying and conserving treetop ecosystems.

Nalini Nadkarni, professor emerita of biology

In a study published this month, Nadkarni found these vital plants are under more and more pressure as a result of rapid environmental change, and proposes specific actions for preserving these fascinating plants.

“This synthesis revealed the exceptional vulnerability to the increasing levels of disturbances—such as climate change and deforestation—on the abundance diversity and connectivity of canopy-dwelling plants around the globe,” she said. “Although we categorize the disturbances with greatest negative effects on canopy plants as ‘natural,’ as hurricanes and wildfire, human activities are increasing the severity and frequency of those in the USA and around the world.”

Nadkarni’s latest paper reviews the available science on epiphyte communities and categorizes the drivers and consequences of and societal responses to drought, wind, insects, wildfire, logging and other disturbances. Her findings should serve as a wake-up call to land managers and others interested in preserving the health of the world’s woodlands.

Read the full story by Brian Maffly in @TheU.