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Exploring the Algorithms of Life

Exploring the Algorithms of Life

Thanks to Phil Bogdan, Marketing and Communications Manager for the Office of Research and Economic Development, for helping us tell our story. This article was published in the November 2019 Scholars and Researchers newsletter. Tawny is just one of the amazing students we have working on the various research projects within IMCI. Professor Marty Yterberg is the Associate Director of IMCI and PI on the RII Track-2 FEC: Using Biophysical Protein Models to Map Genetic Variation to Phenotypes.

Scientists call proteins coded by DNA ‘the building blocks of life.’ For Tawny Gonzalez, these proteins became building blocks for her education.

Gonzalez, an alumna of the College of Science and first-year WWAMI medical student, plays a key role in a molecular modeling study using complex math to plot out the genetic changes affecting the health and structure of living things.

Gonzalez indirectly found her interest in molecular modeling while shadowing an infectious disease physician at Kootenai Health in Coeur d’Alene.

“That was the coolest shadow job, true Sherlock Holmes stuff,” Gonzalez said. “To diagnose culprits for infection, you have to follow clues in the patient’s body and history to figure out when and where they were exposed,” Gonzalez said.

Gonzalez began exploring ways to research viruses and infectious diseases at U of I. While looking into projects in the physics department, she learned about Marty Ytreberg, professor of physics and an associate director of U of I’s Institute for Modeling Collaboration and Innovation (IMCI), a highly collaborative center that teams up with researchers to integrate more modeling into their projects.

Ytreberg, a biophysicist by training, recently published a paper with colleagues about using computational methods to help predict whether mutations in the Ebola virus could weaken treatment efforts.

“I was fascinated by the idea that physics could be so deeply involved in biology,” Gonzalez said. “I had no idea what molecular modeling was, how computational methods worked, or how I would fit into his research group; but I thought it would be interesting. I decided to see if Marty would let me join the group despite my lack of knowledge.”

Even with the steep learning curve, Gonzalez joined Ytreberg’s IMCI working group, using molecular modeling to benefit human health. She quickly picked up the basics and found herself exploring the complex math and algorithms that can make research more efficient and less costly.

“It was cool to see how physics could be used to predict biological interactions that could then assist people on the experimental side,” Gonzalez said.

As Gonzalez’s interest and knowledge in molecular modeling grew, Ytreberg brought her in to a project to understand how amino acid mutations in proteins change the way proteins fold and bind and in turn how this changes plant and animal characteristics. The project, led by Ytreberg, involved researchers from Idaho, Rhode Island and Vermont.

“Using computational methods to narrow down the number of mutations a research group should study can be very beneficial, but it’s difficult; there are a bunch of models out there using different algorithms, and it’s not always clear which one would best suit a researcher’s needs,” Gonzalez said.

Gonzalez used special databases to thoroughly document the structure and binding strengths of various proteins, including those that result in notorious ailments like HIV, cancers and plagues. She used this database to test the speed and accuracy of eight computational methods that predict protein binding strength after mutations. In all, she tested 16 protein complexes involving two or more proteins interacting with each other.

Gonzalez originally believed that the more advanced calculations would be better at predicting final outcomes, but that wasn’t always the case.

“Many models did well at predicting how simpler proteins would bind and fold with other proteins,” Gonzalez said. “But some didn’t do as well, particularly in more complicated scenarios, like when viruses interact with antibodies.

Gonzalez and Ytreberg expanded their study to look at these more complex cases.

“We wanted to be able to suggest, ‘If you need a basic method for predicting a simple mutation, use this one. If you want to make predictions for a more complex scenario involving certain viral proteins and antibodies, this other method can work well.’”

Gonzalez’s work will be featured in a research paper that she and Ytreberg will soon submit for publication in a scientific journal.

“Tawny will be the first author on this paper, which is very unusual for an undergraduate student,” said Ytreberg. “She’s driven, motivated, self-sufficient, and capable of tackling tough projects alone. She’s really done the brunt of the work, and that’s very impressive for an undergrad working a handful of hours a week.”

Gonzalez graduated in May 2019 with a B.S. in chemistry and biochemistry, as well as a minor in physics. She plans to continue pursuing her interest in infectious disease through U of I’s WWAMI Medical Education Program. She also plans to earn a Master of Public Health degree before practicing medicine in Moscow.

“I want to be a real driver of public health in Idaho,” Gonzalez said. “Having an M.D. and a Master of Public Health degree can really help me do that!”

Answering Questions with Keystrokes

Answering Questions with Keystrokes

A special thanks to U of I science writer Leigh Cooper in Communications and Marketing for helping us celebrate IMCI molecular modeler, Dr. Jagdish Patel! View the original article in the College of Science’s feature section. Some of Jagdish’s work was recently published in Science Magazine. He is an accomplished researcher and we’re proud to have him on our team.

IMCI’s Jagdish Patel Uses Computer Models to Probe Microscopic Worlds

photo of Jagdish Patel
Jagdish Patel, Research Assistant Professor

The word “model” evokes many images such as a woman strutting down a Fashion Week runway or a model home. For scientists, a model represents a complex system such as the ocean’s currents or the economy. Scientists construct computer models to analyze, explain and simulate situations too multifaceted to study in the real world.

When molecular modeler Jagdish Patel sits down at his keyboard, he doesn’t model global markets or fancy homes. Instead, the University of Idaho research assistant professor focuses on how microscopic biomolecules interact.

“It’s all about creating a computer-generated world that mimics reality,” Patel said. “A good model helps answer real-world questions.”

A Microscopic World

Patel and U of I developmental biologist and vision scientist Deb Stenkamp wanted to understand the relationship between proteins and color vision. As members of the Institute for Modeling Collaboration and Innovation (IMCI) — U of I’s multidisciplinary, collaborative research program that houses biomedical research modeling experts — they began studying opsin proteins, which are light-sensitive proteins in the eye. IMCI’s Modeling Access Grant funded their work.

Jagdish Patel stands in front of a number of the deep-sea fish they used in their opsin experiment.

“If we succeeded, we could ask questions about the evolution of sight and afflictions of the eye that would be too expensive or time consuming to test using lab-based experiments,” said Patel, who is in the Department of Biological Sciences.

To achieve this goal, Patel first generated a 3D model of the opsin protein from its amino acids, the building blocks of a protein. Although complex at the molecular scale, the basic shape of an opsin is simple — it’s a cage. Patel then brought the cellular environment to life by adding the movements resulting from being in eye fluid.

During his research, Patel was specifically interested in asking questions about a chemical called retinal, which sits within the opsin. The retinal is basically a bird in an opsin cage, Patel said.

Depending on little differences in the sequence of amino acids that form the opsin cage, the shape of the retinal may change. Changes to retinal configuration can result in an animal seeing a greater range of colors. For instance, a mutation within a species that sees only green light may tweak the conformation of retinal enough that the species can see green and blue light.

Previous research documented the relationship between specific retinal conformations and opsin configurations and the color an animal sees. Knowing this relationship, Patel can, within his model, alter an opsin amino acid sequence, identify resulting changes to retinal conformation and make predictions about the colors the animal can see.

The task Patel and the rest of the team attempted was very difficult, and none of them were sure it would succeed. But it did, said Holly Wichman, director of IMCI, and it has led to multiple publications and two international collaborations.

“This demonstrates the power of interdisciplinary teams and reinforces the IMCI motto — modeling improves research at every stage,” said Wichman.

Bring in the Modeler

Patel is now tackling a wide variety of questions related to eyesight. He helped an international group of researchers investigate vision in deep-sea fish using his modeling approach. The deep-sea fish had opsins in light-sensitive cells called rods, which are usually used for night vision, not color vision. Using Patel’s approach, the study concluded some deep-sea fish species may have highly sensitive, rod-based color vision, likely green and blue.

Patel is also working with Chinese and British collaborators to study bats that have lost the ability to see ultraviolet light. In addition, Patel is a project director on an IMCI pilot grant to develop a tool that predicts how small changes in the amino acids that make up opsin affect the colors the opsin detects. Patel hopes his findings will be a steppingstone toward engineering opsins suitable for optogenetics — using light and genetic engineering to control brain cells — or developing targeted therapeutic strategies for eye diseases.

“Molecular models can solve such different problems,” Patel said. “On one hand, I’m currently using models to design anti-depressant and anti-cancer drugs. But I’m also helping a team from U of I’s Virtual Technology and Design build an educational tool for interacting with proteins in virtual reality.”

In addition, modeling has led Patel into pharmaceutical research involving the devastating Ebola virus. He screened thousands of computer-simulated molecules against a 3D model of Ebola virus protein to identify the molecules that might block Ebola virus’ ability to attach to humans. Currently, Patel is looking into patenting the most promising molecules.

“With a molecular model, you see things that you can’t see even with a microscope,” Patel said. “It’s a privilege to be the first one to see these events taking place at a molecular level.”

Article by Leigh Cooper, University Communications and Marketing

Photos by Melissa Hartley, University Communications and Marketing

Published November 2019.

This project was funded under National Science Foundation award 1736253. The total project funding is $6 million, of which 100% is the federal share. This project was funded under the National Institutes of Health National Institute of General Medical Sciences award P20GM104420. The total project funding is $10,572,579, of which 100% is the federal share.

Our Look

Our Look

A new look, or graphic treatment, is part of our transition from a center (CMCI) to an institute (IMCI).

In October, Creative Services attended a Brown Bag Lunch to talk about the U of I brand. They also collected input and ideas from participants for an IMCI graphic.

All of it is so that we can communicate effectively and consistently. View the pdf version of Creative Services’ presentation.

University Communications & Marketing also offer the following resources for your use and reference:

Visual Style Guide
How to represent U of I

Brand Toolkit
Contains templates, downloadable logos, font links,
photo assets, email signature, etc.

Sample Work
Samples of marketing pieces created
within the U of I brand guidelines

Stay tuned for more information!

Seamon Joins IMCI

Seamon Joins IMCI

IMCI is pleased to welcome Erich Seamon, a quantitative climatologist and data scientist, to the postdoctoral team. Seamon holds a MS in geological sciences from Bowling Green State University and a Ph.D. in Natural Resources from the University of Idaho. He has worked on several research team collaborations throughout the Pacific Northwest and thrives in this synergistic environment of dynamic, multi-disciplinary science research.

Seamon is the second postdoc to join us in as many months, which is reflective of our current geospatial modeling core initiative.

“Understanding the interactions and changing importance of model inputs can often times be just as valuable as the final predictive outcome,” said Seamon. “IMCI’s collaborative, team approach to complex systems is exactly the type of research I want to be engaged in.”

Eye of the Storm

Outside of his life full of numbers and quantitative research, Seamon is an artist. He paints abstract pieces that represent the intersection of chaos and organization – which is similar to the chaotic relationships of the climatic and atmospheric worlds he studies. “I’ve found that music and art are a nice offset to my research,” he said.

Geospatial Modeling Postdoc Joins IMCI

Geospatial Modeling Postdoc Joins IMCI

Welcome, Hui (William) Wang to Idaho, the University of Idaho and to the Institute for Modeling Collaboration and Innovation!

Geospatial Modeling is a current Core Initiative, or unique research area for ICMI. We are excited to add a talented postdoctoral fellow to the team with this focus and look forward to establishing new collaborations.

William has been in the US for five years and just finished his PhD in Geography at the University of Connecticut. He made the drive to Moscow by himself, crossing 12 states and enjoying the diverse landscape along the way.

So far he’s discovered Moscow’s Farmer’s Market and many friendly people. Soccer is William’s sport of choice and he also enjoys fishing and hiking. He’s excited about the move. “Idaho is the right state for me!” he stated.