Institute of Arctic Biology

Yin Hsieh, PhD
Murie Auditorium
Friday, 28 Mar 2025 @ 3:00PM

Title:

Prediction of protein interaction sites: Lessons learned from exploration of ALPHAFOLD 2 capabilities on selected mTORC1 regulatory proteins

Abstract:

In this talk, we take a deep dive into the current landscape of protein structural bioinformatics – particularly into protein-protein interaction prediction, one of the biggest challenges in modeling biological pathways. I examine several proteins of the mTOR network, a master regulator of cell growth in eukaryotic cells, which is a large and complex network that cancer researchers worldwide have been working to piece together for the last several decades. Experimental structure and interaction data is sparse for this network, and in some cases very hard to obtain. The proteins I target in this network have been shown to form transient complexes with each other, governed by fine-tuned competition for interaction sites. Using these proteins, I test out AlphaFold2, an algorithm originally developed to predict protein structures of single proteins, which, since its release in 2021, has shown a very high accuracy to predict protein structures not only for single proteins but also for protein complexes. I therefore use this approach for de novo prediction of protein complexes and their interaction sites, focusing in the latter on AlphaFold2 capabilities to predict stably-bound and transiently-bound complexes known to form in the mTOR network. AI approaches such as AlphaFold2 (and 3!) are rapidly being adopted across many fields in science, not just within bioinformatics. My goal with this talk is to show how an attempt to benchmark and use a rising computational neural-network-based tool is less straight-forward than assumed. The lesson I wish to convey is that there's a lot happening behind the AI hype, and it’s essential to delve into this to increase interpretability and confidence in the tools we develop and use.

About the Speaker:

Yin Hsieh is currently a postdoc in the Glass Lab of UAF College of Fisheries and Ocean Sciences, working on a project detecting ice-binding protein production and mapping their distribution in Arctic and subarctic intertidal invertebrates, specifically echinoderms. She completed her undergraduate in mathematics at the Universiteit van Amsterdam in the Netherlands, focusing on applied mathematics within biology, and for her graduate studies shifted to bioinformatics, completing a masters (Wageningen University & Research, Wageningen), and recently finished her PhD (UiT Arctic University of Norway, Tromsø) within this field. Her research centers around protein bioinformatics, specifically developing and\r\napplying computational techniques to analyze evolution and co-evolution of protein-protein interactions for the prediction of interaction sites. She has applied this to address a variety of questions in computational biology, plant ribosome physiology, environmental microbiology, and human protein biology.

Joseph Bump
Murie Auditorium
Friday, 25 Apr 2025 @ 3:00PM

Title:

Voyageurs Wolf Project: insights from a decade of research in northern Minnesota, USA

Abstract:

This seminar will present research and outreach efforts to better understand and share the ecology of wolves along the United States-Canadian border in north-central Minnesota, USA. These efforts were coined the Voyageurs Wolf Project at the University of Minnesota to denote a sustained, collaborative study of the predation behavior, reproductive ecology, and functional role of wolves in this system. This presentation will detail the key insights from this project to date, including wolf predation of beaver and freshwater fish, wolf predation personalities, indirect effects of wolves on wetlands and forests, how humans shape wolf predation, and public commentary that informs the debate about the impact of wolves on deer. 

About the Speaker:

Bump holds the Gordon W. Gullion Endowed Chair in Wildlife Research and Education and is Director of Graduate Studies for the Conservation Science Program at the University of Minnesota. Bump’s focus is on the functional role wildlife species play—alive and dead—in ecosystems and how that applies to biodiversity conservation. He currently leads research projects in Voyageurs, Isle Royale, and Yellowstone National Parks, across Minnesota, and in Switzerland, Kenya, and India. Bump’s curiosity in the natural world began with a childhood spent mucking around the Hudson River and Tivoli Bays in New York. He earned most of his college tuition by catching salmon as a commercial fisherman on the northside of Kodiak Island, Alaska, which was a formative experience in the natural world. Undergraduate field courses at the University of Michigan’s Biological Station confirmed Bump’s interest in animal ecology and he finished a biology degree in just a little over four years. Jobless at the turn of the century, Bump followed a woman west to Wyoming and through much luck, support, and steady effort he bounced between the Great Lakes and the Rockies, earning degrees and positions until now. He lives in St. Paul, Minnesota with two sons, a cat, a dog, and the same love that led him west.