Cutting-edge SHERLOCK app will make fish sleuthing a snap
Starting this September, scientists from Michigan State University, Texas A&M University-Corpus Christi and St. Anselm College, New Hampshire, will harness the power of genomics and artificial intelligence to make waves in global, sustainable seafood harvests.
The researchers received a $749,255 grant from the National Science Foundation’s (NSF) newest and most unique structure, the Convergence Accelerator, to begin Phase 1 development of a user-friendly, fish species identification tool. In the right hands, the app will significantly reduce illegal, unregulated and unreported fishing. Next year, the team will be up for an additional two years and $5 million in funding.
“Our project combines the CRISPR-Cas13a Specific High-sensitivity Enzymatic Reporter unLOCKing system, or SHERLOCK, and artificial intelligence capabilities to develop low-cost, rapid field-deployable species identification tools,” said Mariah Meek, assistant professor in the Department of Integrative Biology in the College of Natural Science and lead investigator on the grant. “During Phase I of this project, we will develop SHERLOCK assays paired with an artificial intelligence smartphone app for species identification between three pairs: Carolina vs Scalloped Hammerhead, Atlantic salmon vs the Pacific salmonids, and bigeye vs yellowfin tuna.”
In the past 30 years, sustainable harvest of global fish stocks has plummeted from 90 percent to 66 percent, according to the Food and Agricultural Organization of the United Nations. Regulation, monitoring and enforcement of sustainable harvest is difficult and hinges on the ability to correctly identify species that, on the surface, look extremely similar. Some species are almost impossible to distinguish based on their appearance, such as the two species of sharks, while at other times customs officials may only have a fin to go on.
That’s where Meek believes SHERLOCK—one that Arthur Conan Doyle could never have imagined—will give fishers, fisheries managers, agency biologists, customs officials and seafood venders the power to become their own piscatorial gumshoes. By snapping a picture with their phone and wiping the fish in question with a swab, the tools will enable them to correctly identify which fish is which.
“This app will improve seafood traceability by enabling verification of species at each level of the supply chain, as well as improve monitoring of conservation status and enforcement of protective regulations,” Meek said. The app will be the latest genomics tool helping to improve humans’ ability to conserve biodiversity under development in the Meek Lab.
Dave Portnoy, associate professor, and Chris Hollenbeck, assistant professor, both from Texas A&M University-Corpus Christi’s Marine Genomics Lab, as well as Shannon O’Leary, assistant professor from St. Anselm College, are co-PIs on the project. Nihar Mahapatra, associate professor in MSU’s Department of Electrical and Computer Engineering in the College of Engineering, is co-PI on the project and the lead for the computational and artificial intelligence aspects of the project.
“This project represents an excellent example of diverse disciplinary approaches working together to address a significant societal challenge,” said Mahapatra, whose data-driven AI software will be paired with the smartphone app and SHERLOCK assays to enable cost-effective, high-throughput testing to identify large-scale patterns in fish species mislabeling. “Though more than 90% of seafood consumed in the U.S. is imported, less than 1 percent of those imports are inspected for compliance with existing regulations due to large volume, limited resources and time constraints.”
“Our goal is that these tools will also help smaller, sustainable fisheries as it will provide a path for verifying the labeling and sustainability of their products and may allow them to sell their products at a higher price point and gain access to retailers with sustainability commitments,” Meek added.
The team is one of 28 phase 1 teams chosen for the NSF Convergence Accelerator’s 2021 cohort and one of 16 teams focused on the Networked Blue Economy (Track E) that aims to produce products, processes and resources that will allow the United States to engage more sustainably with the ocean both environmentally and economically. Fueled by cutting-edge convergent research and human-centered project design, the Convergence Accelerator format seeks to collapse the time and distance between research, problem-solving and deliverables designed to benefit society on a massive scale, and fast.
“Collaboration with researchers, government and non-government agencies and industry are vital to this project as our tools are only as good as they are useful and useable,” Meek said. “That’s why our team includes experts in fisheries policy and decision making, the social sciences of ocean sustainability, public outreach and education and members of the seafood marketing and retail community.”
Nadya Mamoozadeh, senior personnel on the grant and MSU postdoc, is a key researcher helping to design the SHERLOCK assays and to bring people into the project that can provide valuable perspectives on how the tools they design can be as user-friendly as possible.
“The SHERLOCK and AI technologies leveraged in this project provide a really great example of recent technological advances that can be applied in a new way to combat long-standing challenges to sustainable fisheries management,” Mamoozadeh said. “Our main goal is for the tools we develop in this project to better equip diverse end users for protecting our oceans.”
As the number of people in the world who eat fish increases while sustainable harvesting decreases, the speed with which the team’s app goes live will be key to preventing the illegal harvest of millions of fish and helping the seafood-eating public avoid purchasing unregulated and overfished species.
“The simplicity of the genomic test kits and smartphone app integration will make information on fisheries practices and seafood supply chains accessible to the general public, equipping consumers to make informed decisions about seafood consumption,” Meek said. “These public education efforts will be furthered by collaborations with prominent U.S. aquariums for educational outreach in dedicated exhibitions.”
For more information on about the NSF Convergence Accelerator 2021 cohort Phase 1 awards, including the SHERLOCK app, visit https://www.nsf.gov/news/special_reports/announcements/092221.jsp.
Banner image: Cases of mistaken identity are at the root of increasingly unsustainable seafood harvest. Different species of hammerhead sharks can be hard to identify as individuals or fins, making it particularly challenging to combat illegal harvest and trade, so scientists at MSU and collaborating institutions are pairing genomic test kits with a smartphone app to create rapid, field-deployable identification tools to allow accurate species indentification of whole fish, fins and fillets. Credit: Marko Dimitrijevic, Wikimedia commons https://www.flickr.com/photos/189433751@N04/50350835563/
