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Jill Johnson Publishes Paper on Heat Shock Proteins in Nature Communications

Professor Jill Johnson, in collaboration with researchers at the University of Alberta and the University of Würzburg, recently published a paper in Nature Communications titled: “The conserved NxNNWHW Motif in Aha1-type co-chaperones modulates the kinetics of Hsp90 ATPase stimulation and is essential for in vivo function.” This research seeks to understand how Hsp90 partners with interacting cochaperones to help 10-15% of cellular proteins fold properly. As part of an IBEST pilot grant award to Dr. Johnson, she identified a version of Hsp90 that increases the requirement for specific cochaperones, allowing more detailed analysis of their function. Hsp90 binds and hydrolyzes ATP, but the link between this activity and function remains unclear. This work suggests that one type of cochaperone regulates a critical step that occurs after ATP hydrolysis. Future collaborative efforts will lead to a greater understanding of Hsp90 function, with the eventual goal of learning how changes in nucleotide release affect the ability of Hsp90 to interact with misfolded proteins.

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BCB PhD student Clint Elg awarded NSF graduate research fellowship program (GRFP) award

Clint Elg is one of only 2,050 students country-wide who is receiving the prestigious and very competitive NSF graduate research fellowship this year! Elg is a Ph.D. student in the Bioinformatics and Computational Biology (BCB) program and is in the lab of Dr. Eva Top in Biological Sciences. There is only one other U of I student this year who is offered the same fellowship. The NSF Graduate Research Fellowship Program recognizes and supports outstanding graduate students in NSF-supported science, technology, engineering, and mathematics disciplines who are pursuing research-based masters and doctoral degrees at accredited United States institutions.

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Polymorphic Games Interns Win Big at the North Idaho Science & Engineering Fair

Emily Ball and Ari Carter, high school interns in the University of Idaho’s Polymorphic Games studio, had a resoundingly successful day at the North Idaho Science & Engineering Fair in early March; leaving the event with three major awards and two special ones. Their educational video game Bees & Flowers, entered in the math/computer science/ integrated systems category, received a gold medal, a best-in-category, and was the second runner up project for the entire fair out of 83 entries. Ari and Emily’s game also received two special awards including the Outstanding Research Project award from the Idaho Academy of Science and the Intel Excellence in Computer Science award. Bees & Flowers is a video game made to explain evolutionary concepts to elementary and middle school-aged children by showing the coevolutionary relationship between honey bees and flowers. Working in the Polymorphic Games studio in IRIC 107, Emily created the art and 3D models, while Ari programmed the mechanics of the game and the evolutionary model.

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It is strange that only extraordinary men make the discoveries, which later appear so easy and simple.

Georg Lichtenberg
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Diana Mitchell and the GRC published in Scientific Reports - Nature

Assistant Professor Diana Mitchell, in collaboration with Professor Deb Stenkamp of the Dept. of Biological Sciences and the IBEST GRC, recently published a paper in the Scientific Reports - Nature journal titled: “Regeneration associated transcriptional signature of retinal microglia and macrophages.” Funding for this work was provided by Idaho INBRE through a Technology Access Grant awarded to Dr. Mitchell and an NIH R21 awarded to Dr. Stenkamp. Their research seeks to understand the remarkable capacity in which zebrafish can regenerate retinal neurons, in this case with a focus on immune cell populations present during retinal repair. This manuscript is the first work of its kind to use RNA sequencing to probe macrophage populations isolated from tissue in a regenerative state. This work has increased the knowledge of macrophage functions during zebrafish retinal regeneration and provides a wealth of candidate pathways towards understanding macrophage functions in this context.

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U of I Drone Experts to Hold Immersive Half-Day Workshop in Lewiston

Jennifer Hinds and Gina Wilson at the Northwest Knowledge Network and the Institute for Bioinformatics and Evolutionary Studies will lead a drone workshop titled "Rising to New Heights: Drones, Data and Science” Wednesday, March 27, among a series of events over three days at the Northwest Science Association's 90th annual meeting at Lewis-Clark State College in Lewiston. The introductory workshop will cover a broad range of topics on the use of drones in natural resources and will include a combination of lecture and hands-on activities for flight planning and processing drone captured data. Registration is required and one-day passes are available.

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Dept of Fish and Wildlife Sciences Researcher Ryan Long Published in Science

Assistant Professor Ryan Long from the Department of Fish and Wildlife Sciences published in Science. Working in Gorongosa National Park, Mozambique, Long and his colleagues found that bushbuck, a forest-dwelling antelope, began to graze the plains after the country's civil war exterminated large predators. In a domino effect, this change in bushbuck foraging behavior altered plant growth on the plain. However, when the researchers mimicked the smell and sounds of predators, bushbuck reversed this behavior, suggesting that the effects of human-caused extermination of big predators can also be reversed if predators are restored.

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I seem to have been only like a boy playing on the seashore, and diverting myself in now and then finding a smoother pebble or a prettier shell than ordinary, whilst the great ocean of truth lay all undiscovered before me.

Isaac Newton
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Dr. Eva Top was recently featured by KIVI Boise

Dept. of Biology faculty Dr. Eva Top was recently featured by KIVI Boise for her research on antibiotic-resistant bacteria. Dr. Top’s research plays a major part in preventing a growing, worldwide public health crisis.

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Polymorphic Games Releases Newest Game, Project Hastur

Polymorphic Games has just released their newest game "Project Hastur" on Steam in honor of #DarwinDay. PROJECT HASTUR creates a unique challenge by combining elements of 3D tower defense and real-time strategy with biological evolution. Fight against alien Proteans that evolve - using biologically accurate models of evolution - to overcome the player’s defenses. Each creature you will face has its own unique genome controlling its abilities, behaviors, and appearance. Those that make it the furthest and do the most damage to your defenses have the most offspring you will have to defeat in the next generation. The result? Evolution responds to the player’s strategy and makes every playthrough a unique experience.

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Nothing in life is to be feared, it is only to be understood. Now is the time to understand more, so that we may fear less.

Marie Curie
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U of I Researchers Investigate the Snail Rainbow

Department of Biological Sciences' Christine Parent, Andrew Kraemer, and BCB student Andrew Rankin published a paper on Galápagos snails in the Proceedings of The Royal Society B. They found mockingbirds were less likely to feed on snails that matched the color of their backgrounds than conspicuous snails. They think this food selection process may have led to the variation in snail color across the island chain. In addition, it seems the snails in the sunniest locations have evolved to reflect more light than shade-dwelling snails, an adaptation that would help them avoid overheating.

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IBEST Researchers Create New Method to Study Viruses in Fungi

Department of Biological Sciences' Paul Rowley, Angela Crabtree, Emily Kizer and James Van Leuven, as well as Samuel Hunter, Daniel New and Matthew Fagnan with the Institute for Bioinformatics and Evolutionary Studies (IBEST) Genomics Resources Core published a study in the journal Viruses. Brewer's and Baker's yeast play host to many viruses that have genomes made of double-stranded RNA. This type of genetic material is labor-intensive and time-consuming to analyze. The team created a new method to purify and sequence the double-stranded RNAs of two mycoviruses in yeast. They discovered new mutations in the RNA that increased the toxicity of an antifungal drug produced by yeast.

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The nice part about being a pessimist is that you are constantly being either proven right or pleasantly surprised.

George Will
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Cameron Perry: Animating a Hero

At age 6, Cameron Perry began playing a video game that featured a world undergoing industrialization. The consequences were environmental degradation and the exploitation of labor. Perry didn’t understand the themes at the time. He was more concerned with helping his character escape a meat packing plant and join a band of revolutionaries. Over time, the game’s motif started to sink in. “There’s plenty of issues in fiction where you have a prominent social issue and it’s an analog for what’s going on in the real world,” said Perry, a virtual technology and design student graduating in fall 2018 from the University of Idaho College of Art and Architecture. “Abstracting things like that lets us examine social issues that might otherwise be uncomfortable.” Perry worked for Polymorphic Games at U of I and created animations for Project Hastur, a video game where users try to protect humanity from invading aliens that evolve in response to users’ defenses. He also worked for the university’s Institute for Bioinformatics and Evolutionary Studies, designing a mobile app prototype to teach kids about snail biology, evolution and conservation. A native of Boise and Bonners Ferry, Perry, 26, already has a job lined up creating virtual reality environments as a more engaging and less costly aid for workplace training. Someday, though, Perry would like to return to the realm of video games, creating “oppressive worlds that people are fighting back against.”

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The optimist proclaims that we live in the best of all possible worlds; and the pessimist fears this is true.

J. Robert Oppenheimer
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U of I Study Predicts Increase in Global List of Threatened Plant Species

MOSCOW, Idaho — Dec. 3, 2018 — More than 15,000 plant species have a high probability of being considered threatened or near-threatened under a new model used to predict conservation status. The model, which shows the predicted levels of risk to plants worldwide, was published as part of a study to help governments and resource managers evaluate where conservation resources are most needed. Findings from the model, built by a research team from the University of Idaho, University of Maryland, Radford University and The Ohio State University, were published today in the Proceedings of the National Academy of Sciences. The International Union for Conservation of Nature’s (IUCN) Red List of Threatened Species is a powerful tool for researchers and policymakers working to limit species loss across the globe. A new approach developed at U of I and The Ohio State University uses the power of machine learning and open-access data to predict plant species that could be eligible for at-risk status on the IUCN Red List. Adding even a single species to IUCN’s Red List demands hours of expensive, rigorous and highly specialized research. As a result, many known species have not been formally assessed by the IUCN and ranked from least concern to critically endangered; only about 5 percent of all currently known plant species appear on IUCN’s Red List in any capacity. The research team created and trained a machine learning algorithm to assess more than 150,000 species of plants from all corners of the world, making their project among the largest assessments of conservation risk to date. The researchers trained the model using open-access data from the relatively small group of plant species already on the IUCN Red List, and then applied the model to the many thousands of plant species that remain unlisted by IUCN. “Our method isn’t meant to replace formal assessments using IUCN protocols. It’s a tool that can help prioritize the process, by calculating the probability that a given species is at risk,” said Anahí Espíndola, who worked on the project as a U of I postdoctoral researcher and now is an assistant professor at the University of Maryland. “Ultimately, we hope it will help governments and resource managers decide where to devote their limited resources for conservation. This could be especially useful in regions that are understudied.” The model predicted roughly 10 percent of the total plants assessed by the team have a high probability of qualifying as near-threatened or worse. Maps of the data indicate at-risk species tend to cluster in areas already known for their high native biodiversity, such as the Central American rainforests and southwestern Australia. The model also flagged regions such as California and the Southeastern United States, which are home to a large number of endemic species not naturally occurring anywhere else on Earth. “Although our primary goal was to help prioritize the process for ranking species, identifying geographic areas with high concentrations of potentially at-risk species was an added bonus,” said David Tank, associate professor in U of I’s Department of Biological Sciences. The model also flagged a few surprising areas not typically known for their biodiversity, such as the southern coast of the Arabian Peninsula, as having a high number of at-risk species, according to the study. Some of the most imperiled regions have not received enough attention from researchers, Espíndola said. She hopes the study method can help to fill in some of these knowledge gaps by identifying regions and species in need of further study. “We’re in an era in which large-scale public databases contain massive amounts of information,” said Jack Sullivan, a professor in U of I’s Department of Biological Sciences. “This paper demonstrates that machine learning approaches can yield important conclusions in biodiversity studies by detecting signals and patterns in big data.” Media note: An image associated with the study’s findings is attached to the press release. Image caption: This map shows the predicted levels of risk to more than 150,000 species of plants located worldwide. Warmer colors denote areas with larger numbers of potentially at-risk species, while cooler colors denote areas with low overall predicted risk. Image credit: Anahí Espíndola and Tara Pelletier. This project was funded under National Science Foundation grant No. DEB-1457726. The total amount of federal funds for the project is $622,609 of which 100 percent is the federal share.

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Whoever is careless with the truth in small matters cannot be trusted with important matters.

Albert Einstein