Four Projects Selected for Funding from the Risk to Resilience Research and Innovation Roundtable

Susan McNicholl, Office of the Vice President for Research

Posted Jun 20, 2025

The spring 2025 Research and Innovation Roundtable (RIR) resulted in four projects being selected for seed funding support from the Office of the President. All RIR projects are considered critical investments in the future of Iowa State University, as outlined in the 2022-2031 Strategic Plan.

Iowa State University’s Office of the Vice President for Research (OVPR) launched the RIR program in the 2022 fiscal year as a platform to bring together diverse voices across campus. The program fosters the exchange of ideas, leading to the self-assembly of multidisciplinary teams competing for Strategic Plan success funding.

The spring RIR focused on the theme of Risk to Resilience: Combatting Endemic and Zoonotic Microbial Threats and offered Iowa State researchers a unique opportunity to collaborate with colleagues from the U.S. Department of Agriculture (USDA) Agricultural Research Service (ARS) National Animal Disease Center and the Commonwealth Scientific and Industrial Research Organisation (CSIRO), an agency of the Australian government. Self-assembled teams submitted proposals following the March 2 event, with four ultimately selected for support. Proposals—evaluated by program facilitators— were required to meet specific criteria, including alignment with the Iowa State Strategic Plan and inclusion of team members from diverse disciplines using varied research methods and approaches.

“The RIR program continues to spark innovative, high-impact research at Iowa State,” said Vice President for Research, Peter Dorhout. “With the addition of partners like USDA-ARS and CSIRO in the process, we’ve extended the reach of these efforts to develop practical solutions with global relevance and lasting value.”

“The Research and Innovation Roundtable with Iowa State University and USDA is a testament to the power of global collaboration,” added Jon Spaits, Program Development and Innovation Lead at CSIRO. “We’re proud to bring our expertise in biosecurity and zoonotic disease research to the table, working alongside brilliant minds to turn bold ideas into actionable solutions for a resilient future.”

Deciphering Genetic Determinants of HPAIV Resistance in Avian Hosts Using Genome-Wide CRISPR-Activation Screening Technologies

Principal Investigator: Silvia Carnaccini, assistant professor, Veterinary Diagnostic and Production Animal Medicine, Iowa State University

Co-PIs:
Arjun Challagulla, research scientist, CSIRO
C. Joaquin Caceres, assistant professor, Veterinary Microbiology and Preventative Medicine, Iowa State

Collaborator:
Debolina Majumdar, CSIRO

Proposed project summary
This project addresses the growing threat of highly pathogenic avian influenza (HPAI) and aims to uncover the genetic factors that make some birds more resistant to infection. The project focuses on the H5Nx HPAIV strain, which has had devastating effects on poultry, wildlife, and food supply chains. Current control methods—such as strict biosecurity and eradication programs—have proven insufficient, and trade restrictions prevent the use of vaccines. With recent advances in precision breeding, the team sees new opportunities to develop poultry that are genetically resistant to the virus, but doing so requires a deeper understanding of the host’s genetic response to infection.

Researchers will compare chickens, which are highly vulnerable to the disease, with ducks, which typically resist symptoms despite being infected. By developing and studying newly developed immortalized cell lines from both species, the team will use CRISPR-based screening to identify the genes that help block viral replication. The goal is to discover what makes some birds resist the virus—and use that knowledge to develop treatments or breed stronger, virus-resistant poultry for the future.

“This exciting project marks a significant step forward in understanding host resistance to HPAIV through genome-wide CRISPR screening, while also strengthening the research collaboration between ISU and CSIRO (Australia),” said PI Silvia Carnaccini. “The RIR process offered a valuable opportunity to connect with researchers who share similar interests and bring complementary expertise, fostering collaborations that will enhance and accelerate our work. What I look forward to the most is seeing this new partnership in action, advancing scientific discovery and opening doors to future opportunities.”

University Strategic Plan aspirational statement this project advances
To be the trusted partner for proactive and innovative solutions.

Potential external funding partners and opportunities
Future funding opportunities at the federal level with National Institutes of Health (NIH), USDA National Institute of Food and Agriculture (NIFA), and the National Science Foundation (NSF) as well as foundations such as the Foundation for Food and Agriculture Research (FFAR).

A PLUM Job: Protein LangUage Models for Engineering Antimicrobial Peptides as Feed Additives to Ameliorate Enteric Pathogens in Poultry

Principal Investigator: Britta Rued, assistant professor, Veterinary Microbiology and Preventive Medicine, Iowa State University

Co-PIs:
Iddo Friedber, associate professor, Veterinary Microbiology and Preventive Medicine, Iowa State
Brett VanVeller, associate professor, Chemistry, Iowa State
Christopher Anderson, research microbiologist, USDA-ARS
Torey Looft, research microbiologist, USDA-ARS

Proposed project summary
Food safety has improved exponentially over the past several decades. Still, millions of people in the U.S. get sick each year from foodborne illnesses that are often severe enough to require hospitalization or even lead to death. Poultry products, especially chicken, are a common source of these illnesses because they are frequently contaminated with harmful bacteria like Salmonella and Campylobacter, which are responsible for many outbreaks.

This project aims to explore a more effective way to reduce these bacteria in poultry before the birds are processed for food. Instead of relying solely on traditional methods like cleaning environments or identifying contaminated meat, the team will use artificial intelligence to design new antimicrobial peptides (AMPs)—tiny proteins that can kill bacteria. These AMPs will be tested as feed additives to see how well they prevent bacterial growth, how stable they are in poultry feed, and whether they could affect the birds’ gut health. If successful, this approach could lead to safer poultry products and fewer cases of foodborne illness.

“Poultry products such as chicken represent an important food source – and using antimicrobial peptides to inhibit bacterial growth instead of current techniques such as chlorine washing would make U.S. poultry products much more competitive in trade markets across the world,” explained PI Britta Rued. “Currently, some U.S. poultry products are restricted from use in the European Union and other countries due to bans on methods such as chlorine washing. Our team is particularly excited to use this approach to make U.S. based poultry products more competitive in international markets and safer for consumption.”

University Strategic Plan aspirational statements this project advances
To be the university that creates opportunities and forges new frontiers, and to be the trusted partner for proactive and innovative solutions.

Potential external funding partners and opportunities
Potential sponsors for continued support include the U.S. Poultry and Egg Association and the Cobb Research Initiative.

Discovery of On-Farm Biomarkers to Predict Vaccine Response

Principal Investigator: Annaleise Wilson, research scientist, CSIRO

Co-PIs:
Mark Lyte, professor and W.E. Lloyd Endowed Chair, Veterinary Microbiology and Preventive Medicine, Iowa State University
Marina Alexander, research scientist, CSIRO

Proposed project summary
Even with widespread vaccination, poultry—especially layer hens—still show a wide range of responses, leaving flocks vulnerable to diseases like avian influenza and Salmonella. This project, led by researchers in both the U.S. and Australia, will use metabolomics (the study of small molecules in the body), microbiome analysis, and neurochemical profiling to better understand what makes some birds respond better to vaccines than others. By combining this data with machine learning tools, the team hopes to build a model that can predict vaccine effectiveness based on a bird’s gut bacteria, metabolic markers, and neurochemical signals such as dopamine.

The goal is to create on-farm diagnostic tools that help breeders and farmers select birds with stronger immune systems, paving the way for more targeted breeding and vaccination strategies. This could significantly reduce the need for mass antibiotic use or culling during disease outbreaks and strengthen biosecurity in both countries.

“The Research Innovation Roundtable has enabled a truly international and multidisciplinary collaboration to advance poultry health,” said PI Annaleise Wilson. “By identifying biological predictors of vaccine responsiveness, we aim to develop practical tools that help producers make smarter, data-driven decisions to optimize flock health and disease resilience.”

Potential external funding partners and opportunities
Companies that could be targeted for future funding include breeders Aviagen, Hendrix, and OmnisOva; vaccine companies Bioproperties, Zoetis, Boehringer Ingelheim, Elanco Animal Health, and MSD; animal nutrition groups Lallemand Animal Health, Lucta, and Metex Noovistago; Agrifutures and PoutryHub in Australia, and USDA and US Poultry in the United States.

Viral Databases, Algorithms, and Statistical Models for Rapid Pathogen-Agnostic Metagenomic Surveillance and Phylodynamics

Principal Investigator: Michael Zeller, assistant professor, Veterinary Diagnostic and Production Animal Medicine, Iowa State University

Research team:
Oliver Eulenstein, professor, Computer Science, Iowa State
Sriram Vijendran, graduate student, Computer Science, Iowa State
Karin Dorman, professor, Statistics and Gene, Development, and Cell Biology, Iowa State
Tavis Anderson, research biologist, USDA-ARS
Alexy Markin, research biologist, USDA-ARS
Jackie Mahar, research scientist, CSIRO
Matthew Neave, team leader, CSIRO
Rebecca Grimwood, postdoctoral fellow, CSIRO

Proposed project summary
As outbreaks of animal and zoonotic diseases become more frequent and complex, there is a growing and increasingly urgent need for more scalable detection tools. A collaborative team of virologists, bioinformaticians, statisticians, and computer scientists are developing a novel tool for an infectious disease early warning system. This project will transform animal health intervention efforts by integrating pathogen-agnostic sequencing platforms with next-generation statistical models for pathogen detection and identification.

The outcome of this international collaboration between Iowa State, USDA-ARS, and CSIRO will be an empirical system that generates information to inform veterinarians, animal health practitioners, and producers on the likelihood of disease outbreaks, improving the range of response options. With its emphasis on speed, sensitivity, and ease of use, the platform aims to transform how we track, understand, and respond to viral threats, strengthening animal health systems and global biosecurity alike.

“Our team is working to turn a promising idea into a tool that can truly transform viral disease detection in an animal diagnostic setting. By simplifying the process of detecting and classifying pathogens, this project will help bring next-generation sequencing closer to becoming a routine part of diagnostic practice,” explained PI Michael Zeller. “This change from the precedent will open new avenues for research, as we gain unparalleled insight into disease genomes.”

Potential external funding partners and opportunities
Future funding sources could include USDA-NIFA-AFRI grant program (Agricultural Biosecurity, and Data Science for Food and Agricultural Systems), the FFAR Rapid Outcomes from Agricultural Research program, the NSF/NIK/USDA Ecology and Evolution of Infectious Disease program, and the NSF Infrastructure Innovation for Biological Research program. The team will also apply for funding from the National Pork Board, Swine Health Information Center, and the NIH Centers of Excellence for Influenza Research and Response.