Network-of-Networks International Collaboration & Contributions
Building on existing collaborations, the AI2EAR network represents an unparalleled opportunity to deeply integrate the research efforts of 14 networks working at the frontier of food safety and security. These collaborations are at different stages of maturity, ranging from years of scientific and educational collaboration with written agreements and protocols to nascent relationships with huge potential. Through the catalytic grant, we are building a road map for all of the networks to mature into a larger, sustainable Network-of-Networks, building strong linkages that will support the overall mission of the entire team.
Rapid Innovations in SystEms Engineering and Agricultural Sustainability
The RiseEnAg Network, directed by Dr. Williams, is a research consortium whose vision is to enable personalized crop system solutions through innovations in sensor science, multiscale modeling, and data analytics. These solutions allow stakeholders, at various economic and agricultural levels, to respond and adapt to the environmental, ecological, and biological variability seen and expected in 21st-century agriculture. RiseEnAg is composed of an interdisciplinary team of experts from NC State, UC Davis, Univ. of Florida, NC A&T State Univ., UC Santa Barbara, and Univ. of Maryland Baltimore County. RiseEnAg’s goal is to drive fundamental advances in data sciences, developing new tools for data acquisition, data integration, and data mining. Currently, two RiseEnAg workshops have been organized with the objectives to: 1) Explore and identify unique and common challenges across all stakeholders that, if addressed, accelerate us toward the common goal of agricultural sustainability; and 2) Identify novel areas of engineering that can contribute to addressing these problems and the potential roadblocks where innovation is needed. Although RiseEnAg provides an example of a unifying network centered around the common goal of diverse stakeholders, the AI2EAR Network-of-Networks provides the resources needed to bring different and more parties together in an effort to identify actionable outcomes that will ultimately benefit all involved. RiseEnAg, within AI2EAR, is functioning as a catalyst for reshaping agricultural research, providing the tools of discovery that will be used for enhancing global food security, improving environmental safety, and improving human health.
Autonomous Cooperative Control of Emergent Systems of Systems
Autonomous Cooperative Control of Emergent Systems of Systems (ACCESS), NC A&T State University, USA. ACCESS Network, directed by Dr. Ali Karimoddini, aims to address fundamental problems in modeling, analysis, control, and improvement of complex systems. The approach of researchers at ACCESS to systematically develop tools and techniques for analysis and synthesis of complex systems. ACCESS formulates such complex systems as “Systems of Systems,” which are composed of a collection of (many) task-oriented components that together create a new and more complex system that offers more functionality and performance through sharing the resources and capabilities. Relevant to AI2EAR Network-of-Networks, ACCESS research includes “Cyber-physical systems,” “Cooperative and distributed control of multi-agent systems,” “Testing, evaluation, analysis, control, and decision making for large-scale complex systems.” The research at ACCESS has been funded over $15M by government agencies (NSF, DOD, AFRL, ARO, AFRL, DOT) and industry (GM, Intel, LM, FCA, GD) on different applications of autonomous vehicles. For example, ACCESS has been investigating the application of autonomous vehicles and sensor networks in agricultural problems. In a recent project, funded by NSF, ACCESS is investigating the use of multiple UAVs to form a distributed sensing network to survey a farm and detect problem spots in a farm. To explore the application of robotic systems and AI-driven solutions to agricultural problems, ACCESS has expanded the collaborations within NCA&T (the nation’s largest HBCU) and has created a network of researchers from NC State to take a multidisciplinary approach to agricultural problems. As part of AI2EAR, ACCESS is further expanding the network of collaborations with other universities and international groups. Throughout these collaborations, a Network-of-Networks of researchers is l providing resources that are making teams more capable to target larger problems in order to respond to new (funding) opportunities, helping the overall network to fill the gaps and grow in long-term and impactful research directions.
Root Phenotyping and Topological Data Analysis
Root Phenotyping and Topological Data Analysis Network, Donald Danforth Plant Science Center (DDPSC), Saint Louis University (SLU), and Washington University in Saint Louis (WUSTL). As the interface with soil, and the conduit for all water and nutrient resources, root systems are the foundation of plant health and productivity. Yet due to their complexity and difficulty of observation, roots have been largely ignored and arguably compromised during plant domestication and improvement, especially during and since the Green Revolution. New breeding and biotechnology-enabled breeding strategies that incorporate whole-plant structure and physiology are warranted across the spectrum of agricultural crops to simultaneously maximize resource use efficiency and yield. Under an NSF-funded proposal, a team of plant geneticists, physiologists, computer vision and AI experts, and applied mathematicians, led by Dr. Topp, have been working on X-ray based imaging and analysis of thousands of maize and sorghum root systems grown at multiple field sites over multiple years, and from temporally-resolved imaging in controlled environments. Deep Learning algorithms have been developed and employed to segment roots from the soil in 3D volumes. Major challenges are the lack of an open-source cyberinfrastructure capable of transmitting, processing, and storing very large datasets as well as linking our work to larger phenotyping efforts in these key crops to gain a comprehensive view of plant structure and function. In joining AI2EAR, RT-TDA is sharing lessons learned from interdisciplinary research, sharing our data and models and thus increasing the impact of our efforts, and in return linking up with a large collaborative network where existing solutions can be found and new ones developed. Furthermore, the impact on career development and the opportunity of our team members to be greatly enhanced.
Brazilian Synchrotron Light Lab Network
To address challenges in areas such as energy, health, and the environment, the new Sirius synchrotron in Brazil hosts a network of scientists conducting basic and applied research in agriculture, biology, geosciences, physics, materials science, and engineering. A network encompassing researchers at the National Center for Research in Energy and Materials (CNPEM) in Campinas, together with agricultural scientists at leading agricultural universities throughout Brazil, including the Federal University of Viçosa, Federal University of Lavras, the University of Saõ Paulo, Saõ Paulo State University, the Federal University Rural of Pernambuco, and the Federal University of Paraná use a variety of techniques, including 3-D chemical imaging of nutrient transport at the root-soil interface and through plants as well as nanometric coherent diffraction imaging of biogeochemical matrices and cellular substructures important for plant health and productivity. Dr. Hesterberg, crop and soil scientist at NC State, is part of the Sirius Network. Because Brazil is a leading producer and exporter of a wide variety of agricultural crops; including sugar cane, soybeans, coffee, oranges, and maize; agriculture is considered a critical scientific research area at Sirius. With a strong foundation of applied research to support the economically important agricultural sector, the network of scientists that are forming around Sirius are creating mechanistic knowledge needed to solve some of Brazil’s most vexing agricultural problems that are common in tropical regions globally. A key strength of the Brazilian Sirius network for AI2EAR is its combination of strong applied science coupled with emerging basic science conducted at one of the most advanced scientific facilities in the world. This expertise is contributing toward ensuring that the AI approaches used to bridge the essential, but diverse Network-of-Networks within AI2EAR is done in a quantitative and scientifically meaningful way.
The Agricultural Microbiomes Research Coordination Network
The Agricultural Microbiomes Research Coordination Network (RCN) is led by Linda Kinkel (Co-Scientists JP Dundore-Arias, Posy Busby, Jude Maul, Dan Tomso, and Jan Leach). The scientific focus of this RCN is to foster collaborative, synthetic, and cross-disciplinary research and analyses, advance the development of complex data analytics for microbiome research, and accelerate microbiome science and its applications to sustainable global crop production. Through 2020, the RCN has sponsored or co-sponsored 4 workshops, 9 sessions at national or international meetings, and one 2-day symposium. Of particular importance, we led the development of a novel hybrid in-person/virtual all small-group breakouts. By using this hybrid model, we were successful in democratizing our meeting, and especially facilitating the participation of early-career participants who may have lacked resources or time to travel to participate in-person. This provided an outstanding means for enhancing the diversity of participants in our workshop, and the deliberate construction of virtual communities to maximize disciplinary diversity to generate an extraordinarily rich record of discussions. The RCN is transporting this model to the AI2EAR Network-of-Networks to enhance participation and build bridges among scientists from diverse fields. There is substantial value in weaving together the AM RCN with the AI2EAR, specifically in facilitating efforts to build publicly-accessible databases, integrating the latest in engineering and AI with microbiome `big data’, and building our collective capacity to tackle big challenges. Being part of a larger network is expanding our potential for thinking beyond our own discipline or subdiscipline and inspires us to find both the complementarity and common ground needed to create new thinking in agriculture. The network-of-networks is helping to build a more expansive research vision while providing critical exposure and training to the next generation of scientists. We welcome our Ag Microbiomes research community into this network-of-networks.
Collaborative Crop Resilience Program
The grand challenge of providing food security for an ever-growing population can be addressed in part by harnessing interactions of plants, soil, and microbes for enhancing crop resilience. Recently researchers from the University of Copenhagen, Aarhus University, the Technical University of Denmark and NC State have been funded by the Novo Nordisk Foundation to help close the knowledge gaps of plant-microbe interactions to the degree that we could accurately and predictively model and manage plant-microbe communities to enhance crop resiliency and productivity in the face of increasingly challenging environmental stresses while reducing chemical and water inputs at the same time. CCRP research is building a robust agri-omics pipeline that supports meaningful network analyses and enables across-project comparisons as well as providing a state-of-the-art platform that can be leveraged by other groups to even further inform our understanding of critical plant-microbe interactions for enhanced plant resilience on a truly global scale, and as such is benefiting from serving as a network hub. Specifically, interaction through the AI2EAR is affording the opportunity for NNF students, postdocs, and faculty to engage in collaborative research and training visitations across the networks and more effectively engage stakeholder partners (e.g. NC Small Grain Growers Association, NC Soybean Producers Association), outreach partners (e.g. Natural History Museum of Denmark, NC Natural History Museum), and industry partners (e.g. Novozymes, Chr. Hansen).
PIRE Sub- Saharan Africa Network
This NSF funded PIRE grant created an international collaboration/network between universities in the US and Sub-saharan Africa. PIRE includes collaborations with institutions in the US that span bioinformatics, virology, entomology, and others. It includes East Carolina State University and North Carolina A&T Rutgers University and Auburn University. The collaboration with African Institutions includes the BeCA-ILRI hub and Jomo Kenyatta University of Agriculture and Technology in Kenya and the TARI-Mikocheni and TARI-Selian research centers in Tanzania. The BeCA-ILRI hub is a center that aims to secure food in Africa, does capacity building and empowers African scientists, together with technology and research and product development for advancing agriculture. It is also a networking hub for all of Africa. TARI is part of the national network of agriculture research centers in Tanzania and we have direct contact with two of the centers. We work on the diagnostics, control, and evolution of viruses and their vector transmission. PIRE's main focus is cassava but expands to other crops and systems. PIRE is bringing the experience in international collaboration and student training to the AI2EAR network and in return is using the AI2EAR to sustain the PIRE initiative and build on its legacy.
Foundation for Food and Agricultural Research Network
USDA- NC State- VIB (Belgium): Extreme weather negatively affects yield and seed nutritional content, making it imperative that researchers determine how to increase crop resilience to climate change. Through a project funded by the Foundation for Food and Agriculture Research, USDA-ARS is partnering with NC State University and the Flanders Institute for Biotechnology (VIB) in Ghent, Belgium, to apply advanced machine learning algorithms and leverage the existing genetic diversity of plants and improve the sustainability of crops. To accelerate the translation of basic biological knowledge to applied food crop breeding, the FFAR Network is critically leveraging a network of industry and nonprofit partners, including Benson Hill, BASF, and the North Carolina Soybean Producers Association. The FFAR Network is providing unique insights and lessons learned from their academic-industry-nonprofit relationships that are being shared during the AI2EAR activities.
Plant & Food Research LTD. (a Crown Research Institute)
Plant & Food Research (PFR) Ltd., New Zealand- USA: NC State collaborations with PFR institutes located in Palmerston North, Mt Albert, and Lincoln, NZ are primarily in the arena of functional foods, genomics, and metabolomics of health-protective foods, food strategies to i) combat escalating incidence of metabolic diseases; and ii) stabilization of the bioactive properties of food components to permit delivery to rural communities. Dr. Lila has collaborated on new food concepts and prototypes as well as technologies and formulations that deliver health benefits. The PFR Network, a wider audience, valuable scientific collaborations, and potential for more robust training opportunities for our students. In return, we are sharing our robust scientific resources on the development of functional ingredients and edible plant proteins, including phytoactive plant flavonoids.
Nagoya AgBiotech Network
Nagoya University is an educational and research hub in central Japan that, in 2007, founded the Technology Partnership of Nagoya University, Inc. (NU Tech), a non-profit organization, located in the Research Triangle Park (RTP) of North Carolina. NU Tech promotes technology transfer between Nagoya University and US companies primarily in the life sciences as well as it facilitates student and researcher exchange and collaborations between Nagoya University and North Carolina universities. In addition, NU Tech organizes an annual technology roundtable in RTP by partnering with NC State University, UNC-Chapel Hill and Duke University as a venue to share research innovations in agriculture and biotechnology areas. NU Tech, Nagoya University and their corporate partner, Gifu University, are working tirelessly to expand collaborative opportunities beyond the RTP. Through mutually beneficial research collaborations and roundtable-workshop coordination within the AI2EAR Network-of-Networks, the NU Tech-Nagoya-Gifu Network is leveraging our network-of-networks to indeed look beyond just NC State, UNC, Duke, and RTP companies partnerships but to welcome additional corporate, institutional, and academic partners thus creating new models and a common language to address complicated research questions to accelerate development and commercialization of technologies. The NU Tech is also continuing to offer a variety of short-term and long-term programs to which AI2EAR students and postdocs have access to, thus strengthening networks and relations among university researchers and transferring cutting edge technologies from Nagoya University and Gifu University in the USA.
University of Tokyo and RIKEN
Rikagaku Kenkyūjo (RIKEN) is a designated National Research and Development Institute with seven campuses and roughly 3000 scientists. Multiple ongoing collaborations between RIKEN investigators, including Drs. Sugimoto and Sozzani, benefit from NSF East Asia and Pacific Summer Institute (EAPSI) fellowships to graduate students and promote knowledge transfer and skill sharing. The strong plant molecular and plant-pathogen expertise at RIKEN is well suited to the AI2EAR interdisciplinary focus on applying engineering, AI, and data analytics to improve plant science. By coordinating new training and collaborations via the AI2EAR Network-of-Networks cutting-edge techniques such as those developed in the Higashiyama ITbM Live-Holonics Institute (soon moving to U. of Tokyo), will are shared with and applied by the greater scientific community at an efficient and widespread level. Correspondingly, RIKEN-Tokyo plant research groups benefit from reciprocal knowledge sharing with other AI2EAR networks.
Arabidopsis Research and Training for the 21st Century
The ART-21 Research Coordination Network is a mature network administered by present and former elected members of the North American Arabidopsis Steering Committee (NAASC). The project had several main goals including: 1) Identify emerging technologies where using Arabidopsis as a model organism will provide fundamental discoveries and enable translational research in crop species; 2) Enhance interdisciplinary training of scientists for academic and extra-academic careers; 3) Increase the diversity of research scientists using targeted mechanisms. Progress toward each of these goals involve community workshops and/or courses at our international annual meeting, targeted focus groups and production of commentary papers regarding our findings and recommendations, as well as providing funding and career development activities for early career researchers and underrepresented minorities. The ART-21 Steering Committee and project focus groups include relevant international partners and networks to provide a more global perspective. ART-21 is providing expertise and perspective into several critical areas underpinning the AccelNet Collaboration: execution of activities with a large group of members; insights into the best means and mechanisms to create meaningful scientific communication; and efforts to increase diversity and impact within larger communities. The AI2EAR Network-of-Networks is helping to disseminate ART-21 results and ensure that activities are continuing to have a broad impact.
RCN Urbanization Network
TomorrowNow is a collaborative project led by four universities in North Carolina focused on developing a serious game that can help a greater number, and a greater diversity of people affect decisions that impact the places where they live and work. TomorrowNow is using real spatial data and developing interactive technologies that can help build a common understanding of challenges in the Triangle, and figure out how to address them. This RCN Network unites government officials, academic researchers, industry leaders and members of community groups and other organizations to co-develop a serious game that will tackle challenges related to rapid urbanization and stormwater management in the Triangle region of North Carolina. As part of AI2EAR Network-of-Networks, TomorrowNow is gathering all the needed information to start assessing how people affect decisions that impact agriculture and transfer aspects of food production, supply chain movement and transportation to participating networks.
A Research Experience for Undergraduates in Bioinformatics, Genetics, and Genomic (BiGG) Sciences
Training the Next Generation of Women Bioinformatics, Genetics, & Genome Scientists: The BiGG FACTS program is a network of researchers who provide research and Extension training in big data analysis for undergraduates in agriculture or allied disciplines. The goal is to prepare women for the workforce and academic challenges in agricultural careers. Research teams, composed of students and faculty mentors, focus on: 1) Plant and animal sectors of One Health; and 2) Analysis and interpretation of big data. BiGG FACTS is an important educational network that is providing lessons learned to inform the preparation of underrepresented audiences in engineering, AI, and data analytics.
The Science and Technologies for Phosphorus Sustainability (STEPS) Center
The Science and Technologies for Phosphorus Sustainability (STEPS) Center is a convergence research network of diverse and leading scientists that addresses the complex challenges in phosphorus sustainability by integrating disciplinary contributions across the physical, life, social, and economic sciences. Nine institutions comprise STEPS: North Carolina State University, Arizona State University, University of Florida, RTI International, Appalachian State University, Marquette University, University of Illinois at Urbana-Champaign, North Carolina A&T State University, and University of North Carolina at Greensboro. STEPS draws from atomic and molecular insights to develop materials and technologies that are deployed at the human scale while considering supply-chain logistics, life cycle, and other regional and global issues. STEPS further leverages disciplinary contributions that transcend length scales and serve as integration mechanisms within the Center. One of these integration mechanisms is Convergence Informatics (CI). CI builds upon a materials informatics-based approach in which process-structure-properties-performance relations are designed by analyzing large materials data sets with machine learning algorithms. Through CI work, STEPS will integrate data sets across diverse research disciplines, projects, and themes. STEPS will provide its expertise in integration and CI to AI2EAR to strengthen network collaboration and data integration.
Transcription Regulation Initiative in Plants
Transcription factors (TFs) modulate genetic programs to drive plant growth, development, and response to environmental stimuli. TFs have two major roles: 1- to bind DNA directly through a DNA Binding Domain (DBD) or indirectly through interaction with another DBD-containing protein and 2- to recruit transcriptional machinery. Although DBDs have been well characterized, little is known about how TFs recruit a diverse set of coactivator and corepressor complexes. The protein domains that recruit co-activators, known as Activation Domains (ADs) are also ill-defined. When a genome is sequenced, putative TFs can be predicted based on the presence of a DBD, but due to a lack of predictive models, we have limited ability to predict whether these TFs are repressors or activators. TRIIP aims to fill this large knowledge gap by leveraging new experimental and computational technologies developed by our labs. We will begin our systematic search using well-defined Arabidopsis TFs and develop computational tools to predict ADs in all angiosperms. Our design and validation of tuned ADs will expand the synthetic biology toolbox for modulating transcriptional programs in development and in response to signals. This platform provides the necessary tuned AD components for engineering regulatory networks, advancing agriculture and contributing to solutions that could address environmental problems. In joining AI2EAR,the TRIIP Network will expand on and share data and modules through collaborative research, workshops, and seminars, thus propelling the possibilities of understanding TF and AD activity.
Evolution of Genetic Network Required for Fruit and Fruit-like Structures Development of Land Plants
Human and animal nutritional needs depend mainly on the intake of seeds and fruits, which are also a source of other priceless products useful for human well-being. For the plants themselves, seeds and fruits are key for their dispersal in nature and to ensure the future of the next generations. Although across flowering plants fruits, and to a lower extend also seeds, show diverse morphologies and functions related to these structural differences, it seems that all species share common networks controlling fruit and seed development.
This European Union funded research project, including partners from Italy, Germany, The Netherlands, Spain, USA, Colombia, Mexico, Australia and Brazil, builds an intercontinental and interdisciplinary network with the aim to deepen our understanding of the evolution of the molecular signaling and crosstalk among different players that regulate the development of fruit and fruit-like structures.
To build the Fruit evolutionary conserved Genetic Regulatory Network (FGRN) we use core eudicots to investigate: a) hormonal signaling involved in the coordination and synchronization of the phases in fruit/fruit-like development; b) cell wall related pathways involved in pectin maturation and cellulose deposition required for fruit development; c) cross talk between sporophytic and gametophytic tissues leading to successful sexual reproduction. We use a broad set of approaches such as molecular genetics, evolutionary genomics, biochemical and biophysical analyses. The consortium will be engaged in a program of communication and dissemination of these topics with the involvement and outreach efforts of three Botanical Gardens.