The tube-eye (Stylephorus chordatus) is one of several species of deep-sea fish to have expanded its repertoire of rhodopsin genes to maximize visual sensitivity and, possibly, color detection. In the deep sea, multicolored bioluminescence replaces surface illumination as the main source of light. Many fishes that reside at great depths have evolved a visual system for recognizing bioluminescent signals and perceiving color in the dark. See pages 520 and 588. Photo: Danté Fenolio/DEEPEND/Gulf of Mexico Research Initiative
The cover of Science Magazine currently features an important discovery made by an international research team: deep-sea fish can see more than just one color.
When a Switzerland- and Australia-based research team recently needed to validate their findings regarding what colors of light a deep-sea fish species could see at up to 1500 meters below the surface, they turned to scientists at the University of Idaho. Biological Sciences Research Assistant Professor and CMCI Modeling Fellow Jagdish Patel and Biological Sciences Professors Deborah Stenkamp and Celeste Brown used Patel’s newly developed computational molecular simulation based approach to generate a mathematical model to predict color sensitivity.
Deep-sea fish rhodopisn within the lipid bilayer. Image created by Jagdish Patel.
The team was able to successfully predict the maximum wavelength of light, or color, absorbed by light sensitive proteins, called opsins, in the eye. In the case of deep-sea fish, these opsins are present in rod photoreceptors. In other species rods are not used for color vision. Thus, the research team was able to conclude that certain species of deep-sea fish may have highly sensitive, rod-based color vision. The range of sensitivity matches the dim light conditions present in the deep sea due to bioluminescence.
Blue and green dancing proteins
Movies showing molecular simulations of blue- and green-light sensitive opsin models created by Jagdish.
“This discovery is both exciting and unexpected,” said College of Science Dean Ginger E. Carney. “We are pleased that groundbreaking discoveries by U of I researchers continue to be featured in premier research journals such as Science.”
Yesterday, the University of Idaho took delivery of a just-released, state-of-the-art DNA sequencer: PacBio Sequel II. This instrument is one of the very first of its kind in the entire world. And because we are one of the first organizations to acquire the machine, it also means that we will be one of the very first organizations to have access to an immense amount of quality data, the likes of which has never been available on campus before. This creates a tremendous opportunity for researchers at the University of Idaho to innovate and leverage this new type of data, creating major impacts in their fields and doing things people have not yet even thought of.
Vice President Nelson asks President Staben if he knows how much it cost and how long it took to sequence the first human genome.
Also significant is the fact that 23 different people and organizations across campus came together in just 3 weeks to collaboratively purchase the sequencer. No one department or faculty researcher could make such a large purchase on their own. But with everyone contributing bits and pieces of funding, a momentous opportunity unfolded.
Funding organizations and individuals include:
Center for Modeling Complex Interactions (CMCI) Institute for Bioinformatics and Evolutionary Studies (IBEST) BEACON Center for the Study of Evolution in Action GEM 3 Genes by Environment Office of the President Office of the Provost & Executive Vice President Office of Research and Economic Development College of Agricultural and Life Sciences College of Engineering College of Natural Resources College of Science Dr. Kenneth Cain Dr. Chris Caudill Dr. Larry Forney Dr. James Foster Dr. Paul Hohenlohe Dr. Alan Kolok Dr. Chris Marx Dr. Craig Miller Dr. Ben Ridenhour Dr. Paul Rowley Dr. Eva Top Dr. Lisette Waits Dr. Holly Wichman Dr. Marty Ytreberg
Vice President for Research and Economic Development Janet Nelson announced the arrival of the Sequel II at the SAS Talks yesterday in the IRIC:
How long do you think it took and how much do you think it cost to generate the first sequence of a human genome? It took 13 years and $3 billion! Tonight’s theme is public impact research, and from that perspective this was one of the most important scientific achievements of its time. Like many important milestones in science, the technological by-products of the quest are as important at the achievement itself. The moon landing gave us Velcro; deciphering the human genome gave us next-generation sequencing technology. Today the University of Idaho took delivery on the just-released, state-of-the-art, DNA sequencer—PacBio Sequel II.
Why is this important for Idaho?
First, this is a game changer in the field of genomics and will allow us to continue our tradition of high impact research. With this instrument it will take less than a week and cost about $5000 to sequence a human genome, and the quality of both the sequence and the assembly will be vastly superior to the $3 billion genome released 16 years ago. The new PacBio will have applications in many fields, including medicine, natural resources, and agriculture, to name a few.
Second, the University of Idaho is one of the first institutions in the world to take delivery of this new instrument, putting us on the cutting edge of genomic sequencing technology. This will allow our Genomics Resources Core to continue to provide the value-added service for which it so well known. It will improve research at the University of Idaho and across the state, creating a tremendous opportunity for our researchers to lead the world in integrating this new type of data into our research programs.
Finally, this purchase is concrete evidence of what we can achieve by working together. In just over a month, we brought together 23 contributors to purchase this machine and an extended service contract. This is the largest number of contributors to come together so quickly for a purchase of this type– at least that I am aware of. Let’s take a moment to celebrate what we can do through cooperation and collaboration.
Congratulations to James (JT) Van Leuven, who was recently awarded the U of I’s Outstanding Post-Doctoral Scholar/Fellow Award!
JT has been a postdoc at the Center for Modeling Complex
Interactions (CMCI) for 3 years. CMCI is a highly collaborative and
interdisciplinary endeavor where JT successfully utilizes his wide breadth of
scientific skills. He is a member of several working groups, has given numerous
oral presentations and is frequently involved in writing grant proposals and
research publications. JT also coordinates CMCI’s weekly Brown Bag Lunch events
and helps schedule seminar speakers.
“He is an important contributor to both the hands-on research / data analysis and the intellectual design and interpretation of experiments,” says Holly Wichman, CMCI Director. “A next-gen scientist.”
In addition to scholarly research, JT contributes to the
university community by sitting on Staff Council and co-chairing the University
of Idaho Postdoc Association.
The University Awards for Excellence recognize and encourage excellence in all forms at the academic level. Recently, the 2019 Interdisciplinary Award was presented to the Flow Ventilators Team for their collaborative efforts for working to improve treatments for asthma and other lung diseases.
Provost & Executive Vice President John Wiencek (center) poses with the 2019 University Awards for Excellence Interdisciplinary Award recipients.
Team members include 4 researchers from 2 colleges: Tao Xing, associate professor of mechanical engineering, Gordon Murdoch, associate professor of physiology in animal and veterinary science, Gabriel Potirniche, associate professor of mechanical engineering, and Nathan Schiele, assistant professor of biological engineering.
The Flow Ventilators Team aims to significantly improve the fundamental understanding of mechanics of respiration and physiological mechanisms of ventilation through interdisciplinary research. Their goal is to use research to promote respiratory health through the development of next-generation flow ventilators for better prevention and treatment of various lung diseases. This will improve the quality of life and extend the lives of those with lung diseases. The team began in 2016 with Xing, Murdoch and a Center for Modeling Complex Interactions pilot grant for a multiscale model of interaction between lung and pulmonary ventilation. They then realized the importance of performing fluid-structure interaction computer simulations that required the knowledge of not only fluid but also solid mechanics and accurate tissue properties, which are the expertise of Potirniche and Schiele, respectively. The team’s success in its interdisciplinary and collaborative efforts was shown not only by the amount of funding it secured in a short amount of time, but also by its strong publications, number of citations and number of post-graduate and graduate students that have been involved in the enterprise. The interdisciplinary team and the industry partner network that the team has been developing have the potential to grow even further as they energize a wider circle of collaborators across campus, and as they continue to attract the interest as well as the respect of external constituents.
Spring means we’re nearing the end of the school year – and various award banquets and receptions. We’re proud that so many CMCI participants received awards this year.
2019 College of Science Staff, Faculty, and Graduate Student Awards
Nominations for the staff and faculty awards were made by members of the College of Science executive board, and nominations for the graduate student awards were made by each academic department or program.
Early Career Faculty Award: Chris Remien (Mathematics)
2019 College of Science Undergraduate Student Awards
Casey Beard – graduating with a major in Physics
Tawny Gonzalez – graduating with a major in Chemistry (Pre-Medical option)
John B. George Award
The outstanding graduating senior in the College of Science; given by the dean.
Tawny Gonzalez
University Awards for Excellence
The University Awards for Excellence recognize and encourage excellence in all forms at the academic level.
Excellence in Research and Creative Activity Award: Deb Stenkamp (Biological Sciences)
Outstanding Post-Doctoral Scholar/Fellow Award: James Van Leuven (CMCI)
Interdisciplinary Award: Flow Ventilators Team. Tao Xing* (Mechanical Engineering, College of Engineering), Gordon Murdoch (Animal and Veterinary Science, College of Agricultural & Life Sciences), Gabriel Potirniche (Mechanical Engineering, College of Engineering), Nathan Schiele (Biological Engineering, College of Engineering
Left to right: Dr. Gordon Murdoch, Dr. Tao Xing, Dr. Gabriel Potirniche, and Dr. Nathan Schiele. Dr. Xing is holding a 3D printed model for a human lung upper airway.
