NANOSENSORS AND ARTIFICIAL INTELLIGENCE FOR RAPID DIAGNOSTICS IN FOOD, AGRICULTURE AND ENVIRONMENT.

• Sponsoring Institution: National Institute of Food and Agriculture
• Project Status: COMPLETE
• Funding Source: HATCH
• Reporting Frequency: Annual
• Accession No.: 1016484
• Project Start Date: Oct 1, 2018
• Project End Date: Sep 30, 2023
• Program Code: [(N/A)]- (N/A)

Recipient Organization
UNIV OF MINNESOTA
(N/A)
ST PAUL,MN 55108

Performing Department
Bioproducts & Biosystems Engineering

Non Technical Summary
The development of rapid diagnostic technologies is at the forefront of many challenges facing the global community today, including food poisoning, crop epidemics, animal diseases, antibiotic resistance, and terrestrial and aquatic invasive species. Rapid microbial detection (in less than 1 h) can provide actionable results to prevent disease outbreaks, mitigate inappropriate use of broad-spectrum antibiotics, and inform evidence-based medicine. Furthermore, rapid diagnostics to ensure the safety of manufactured products in less than 2 h would largely accelerate the production cycle and reduce risks and costs in healthcare, food, pharmaceutical and agricultural industries.While the diverse applications of this research can range from microbial detection in food safety, crop disease detection to terrestrial and aquatic invasive species identification, the main focus of the proposal is to make diagnostic technologies rapid and affordable and adapted to field use. To achieve this goal, we will combine some fundamental research related to biosensing transduction methods with new technologies such as nanomaterials and artificial intelligence. This transdisciplinary approach will be based on a strong collaborative effort to overcome current limitations in the field and help translate research into commercially viable products.

Animal Health Component

30%

Research Effort Categories

Basic

10%

Applied

30%

Developmental

60%

Classification

Knowledge Area (KA)	Subject of Investigation (SOI)	Field of Science (FOS)	Percent
402	5010	2020	40%
402	2499	2020	20%
402	4099	2020	40%

Knowledge Area
402 - Engineering Systems and Equipment;

Subject Of Investigation
4099 - Microorganisms, general/other; 5010 - Food; 2499 - Plant research, general;

Field Of Science
2020 - Engineering;

Keywords

nanotechnology

biosensors

microbial detection

rapid diagnsotic technologies

artificial intelligence

food safety testing

invasive species

Goals / Objectives
The proposed research integrates nanotechnology, biosensing techniques and artificial intelligence to address current challenges in food safety testing and precision agriculture. Over the next five years, we seek to achieve the following objectives:Foodborne Safety Testing:Investigate and develop new biosensing transduction concepts where the food sample matrix is optically, electrically or magnetically inactive, and thus appears "transparent" to the detection system. We will also research a biomimetic chemo-mechanical transduction system where the food sample is physically isolated from the transducer. Such developments would overcome the need of sample purification or pretreatment and enable direct rapid microbial detection in complex matrices from sample to results.Establish the Center for Rapid Diagnostic Technologies with the purpose of developing rapid and early diagnostics enabled by artificial intelligence (machine leaning). The Center for Rapid Diagnostic Technologies (CRDT) seeks to address these challenges by developing a core facility with shared resources and expertise, and a platform for academic-industrial collaborations with a focus on advancing rapid detection technologies using artificial intelligence.?Food Security and Precision Agriculture:Develop an intelligent mobile spectrophotometer capable of learning and rapidly identifying invasive plants from native plant species in the field and detection of crop diseases. The mobile spectrophotometer will include a smartphone with or without a hand-help spectrometer to collect images and/or spectral signatures invisible to the naked eye and subsequently identify the species using deep learning. Deep learning is an artificial intelligence technology for image analysis.Develop a novel aquatic eDNA collection and concentration technology for more efficient, reliable and cost-effective screening for not only invasive aquatic organisms and pathogens but also native and endangered species. The technology would significantly enable and empower aquatic ecosystem survey and management programs in Minnesota.

Project Methods
Novel transduction concepts for food safety testing: The development of new biosensing transduction systems will be achieved in three major tasks:- Study and develop gold-coated magnetic nanaoparticles (Au@MNPs) capable of interacting with the target microorganisms and capable of generating a nuclear magnetic resonance (NMR) signal. The aggregation of the nanoparticles leads to changes in the NMR signal, specifically the magnetic relaxation switching or T2 relaxation measurements. Such variations can be directly detected without any interference with the spectroscopic noise generated by the matrix. The Au@MNPs will synthesized by a modified solvothermal method, and functionalized with amine groups via polyethyleneimine self-assembly under sonication. Mucor circinelloides in yogurt samples will be used as a model microorganism/sample combination. The principal of our detection mechanism is the ability to distinguish between target-induced aggregation or disaggregation of MNP which are used to detect the interaction with biomolecules or specific biomarker. By measuring the change of spin-spin relaxation time (T2) of the water proton in sample solution. Under external uniform magnetic field, the existence of target in the samples will result in the state change of MNP in the sample solution (i.e. from a dispersed state to an aggregated state), leading to change the local magnetic field around target sample. The local magnetic field alters the spin-spin (transverse) relaxation time (T2) of the surrounding water molecules and the change of T2 value (DT2) is related to the degree of aggregation of MNP which is correlated to the concentration of target in the sample.- Study and develop nanoparticles (gold nanostars) that are optically active in the near-infrared (NIR) region of the EM spectrum, where biological samples are optically inactive (transparent). The aggregation of the nanoparticles in presence of the target microorganisms leads to changes in the NIR signal that can be directly detected without any interference with the spectroscopic noise generated by the matrix. Applications of new biosensors and assays in food safety testing are limited due to the strong absorption of the food matrix in the visible wavelength. Most food and biological samples have strong absorption in the visible range. Food samples and plant extracts contain large amount of components with a strong absorption at wavelengths below 600 nm and above 1300 nm. Chlorophyll contained in vegetables also give strong light absorption in the red and blue regions. We seek to develop new nanomaterials with strong adsorption properties in the near infrared region (700 - 1300 nm) for the development of biosensor and immunoassay for direct detection of microbes in food samples. The gold nanostar will be synthesized based on two-step procedure of seed and growth from gold nanoparticle described in literature.- Investigate a new biomimetic transduction concept, inspired by the chemo-mechanical transduction of biochemical signals across cell membranes, where the target recognition and signal transduction occur in separate environments. We will particularly study the intracellular transduction of antibodies and olfactory sensors using nuclear magnetic resonance analysis on artificial membrane.Center for Rapid Diagnostic Technologies: The Center will complement existing facilities by offering innovative solutions for the University laboratories that provide diagnostic services for the detection of human, animal, plant and food borne diseases. Hence, the diagnostic laboratories will be involved in testing and evaluation of new technologies as a major step towards certification and commercialization. Furthermore, the Center has the ambition to advance this effort at the national and international levels.The mission of the Center is to: 1) promote transdisciplinary and intercollegiate collaborations in the fundamental and applied aspects of rapid diagnostic technologies, and 2) Advance academic research and innovations towards commercialization, with a focus on three major products rapid and early diagnostics enabled by artificial intelligence (machine learning).Field Detection of Invasive Plant Species and Crop Diseases: Artificial Intelligence-Enabled Mobile Spectrophotometry for Field Detection of Invasive Plant Species and Crop DiseasesThe proposed intelligent imaging system will be developed through 3 major phases: 1) Establish a database of images and spectroscopic signatures: A database of photographs and spectroscopic signatures will be obtained for leaves and seed for Palmer Amaranth and for other native pigweed. Specific structural features of Palmer will be classified (absence of hair on the leaves, long petioles, long seed head, diamond-shaped leaves). Other spectral features will be obtained from the leaves and seed. 2) Develop and evaluate a Deep learning algorithm for invasive plant detection of Palmer amarant.Detection of Aquatic Invasive Species: A Novel Technology for eDNA Collection and Concentration: The proposed eDNA aquatic sampling technology will be developed and tested in three major steps:- Development of the eDNA nanofilter: In order to use AgNPs or MgNPs for eDNA capture, the nanoparticles need to be integrated into a filter or membrane with pore size ranging from 3 µm to 20 µm to allow large water flow rates without clogging.- In situ filtering of large volumes of water: After water filtration, the nanofilters will be immersed in a preservation buffer and stored in sterile conditions at -20 °C in the dark until used. The DNA will be retrieved from the filter using a recovery solution designed to break the bond between the nanoparticles and the eDNA without damaging the genetic material. Quantitative PCR (qPCR) will be performed to amplify and quantify DNA sequences related to target species described in the next section. S

Progress 10/01/19 to 09/30/20

Outputs
Target Audience:- Food industry - Environmental industry and public agencies - Healthcare industry - General public Changes/Problems:Despite working without interuption as Essemtial Workers since the beginning of the pandemic, we had to temporarily change ourresearch focus to develop RNA extraction kits for SARS-COV-2 for the diagnsotics of COVID-19, in collaboration of the School of Medicine. What opportunities for training and professional development has the project provided?- Training of 3 postdoctral resarch asssociates, one in food virology, one in the detection and analysis of volatie organic compounds for diagnosytic purposes, and one in machine learning applied to agricultural problems. - Training of two graduate students, one in environ,ental nanotechnology and one in food safety testing technologies. - Training of 4 undergraduate students in the same reserach topics addressed by the gradauate studentsand postocs. How have the results been disseminated to communities of interest?The research results have been dessiminated through two scientificpublications, 4 conferences and one news article (see below): - A feature article in The Furrow:"Finding Phosphorus, Reclaiming what was once lost". February 2020. Page 34-35 - An article in Legacy Magazine: "More than a mask, can fabric kill viruses", Fall 2020. (https://legacy.umn.edu/stories/more-than-a-mask?) - A College news article: "CFANS scientists innovate to fight COVID-19: Abbas Research Lab"(https://cfans.umn.edu/news/covid-series-story-1) What do you plan to do during the next reporting period to accomplish the goals?- Develop a rapidkit for microbial detection in food matrices, using T2-NMR. - Finalize a new extraction kit for eDNA and viruses for aquaculture and early detection of aqautic invasive species. This work should lead to a patent and a license. - Finalize the rapid diagnostic kit for the detection of oak wilt and other tree diseases, -Lauch the Center for volatolomics and rapid diagnostic technologies.

Impacts
What was accomplished under these goals? 1- Raised $1.2 million for the Center for Volatolomics and Rapid Diahnostic Technologes: $600,000 were used to purchase a PTR-MS for rapid analysis of volatile organic compounds, and hire two postdocs. 2- Received 400,000 from the Foundation for Foodand Agricultural Research (FFAR) as a winner of the Phase I EggTech Challenge. The EggTech challenge is an international competition that funds the development of In Ovo gender identification of chicken eggs to prevent male culling by the farmingindustry. We are using artificial intelligence fto enablerapid identification. 3- Published two papers and attended 4 conferences 4- Developed and validated a rapid RNA extraction kit for coronavirus SARS-CoV-2 5- Developped an extraction kit for environmental DNA to monitor invasice species 6- Started a second technology company on June 2020, focused rapid microbial diagnostic technoogies (www.frontlinebiotech.com). The first comnpany founded on 2018, is focused on clean water technologies. The new company has very recently obtained an SBIR grant from the USDA to move our technologies to the market.

Publications

• Type: Journal Articles Status: Published Year Published: 2020 Citation: John W. Brockgreitens, Fatemeh Heidari, and Abdennour Abbas, "Versatile Process for the Preparation of Nanocomposite Sorbents: Phosphorus and Arsenic Removal" Removal", Environmental Science and Technolology, 2020, 54, 14, 90349043.
• Type: Theses/Dissertations Status: Awaiting Publication Year Published: 2020 Citation: John Brockgreitens, "Environmental Nanotechnology: A Universal, Green Process for the Synthesis of Functional Nanocomposites", September 1st, 2020.
• Type: Conference Papers and Presentations Status: Other Year Published: 2019 Citation: Vinni Thekkudan Novi, Minh-Phuong Ngoc Bui, and Abdennour Abbas* "Magnetic relaxation switching (MRS) assay for direct detection of microbes in complex food matrices", BBE Showcase, Saint Paul, UMN, October 23, 2019.
• Type: Conference Papers and Presentations Status: Other Year Published: 2019 Citation: Qiuchen Dong, Akli Zarouri, Abdennour Abbas, "Enhancing fish surveys: A novel technology for environmental DNA capture", Minnesota Aquatic Invasive Species Conference, Sep. 18th, 2019.
• Type: Conference Papers and Presentations Status: Published Year Published: 2019 Citation: John Brockgreitens, Snober Ahmed, and Abdennour Abbas. "Novel Sorbent Technology for Simultaneous Removal and Degradation of Waterborne PFAS" WaterSmart Innovations Conference and Exposition 2019. October 2-3, 2019. Las Vegas, NV. Best Poster Award.
• Type: Journal Articles Status: Under Review Year Published: 2021 Citation: Andrew Gonzalez, Hamada A. Aboubakr , Sagar M. Goyal, Abdennour Abbas, "Process for the Preparation of Nanocomposite Face Masks to Inactivate Coronaviruses", Under Review,

Progress 10/01/18 to 09/30/19

Outputs
Target Audience:- Food industry - Food and agricultural research organizations - Environmental protection agency - Department of Defense - Natural resource conservation agencies Changes/Problems: Nothing Reported What opportunities for training and professional development has the project provided?The PI hired and trained - 1 postdoctral research associate in machine learning applied to biodiagnostic problems. - 1postdoctral research associate in rapid disease detection for forest pathogens - 1 graduate student for food safety diagnostics. The student received the Schwann Food graduatefellowship. - 4 undegraduate students in food safety diagnostics. The students received the Schwann Food undergraduate fellowship. How have the results been disseminated to communities of interest?The research results have been presented at two conferences: 1- "Rapid and PCR-free DNA Detection of Invasive Species by Nanoaggregation-Enhanced Chemiluminescence", North American Invasive Species Management Association (NAISMA) conference, September 30th - October 3rd. 2- Akli Zarouri, Abdennour Abbas, Loren Miller, "A Novel Technology for Environmental DNA Collection and Concentration", The Wildlife Society and American Fisheries Society Conference, Reno,Nevada, October 2nd, 2019. What do you plan to do during the next reporting period to accomplish the goals?- Continue the development of the Center for Volatolomics/Rapid diagnostic technologies by seeking more industrial partners. - Seek funding to start the project on the transparent matric for rapid microbial diagnostcs (Objective # 1) - Focus on research for the Egg Tech Challenge (two year project) and compete for phase II. - Integrate more machine learning to address problems in food and agricultural disease detection.

Impacts
What was accomplished under these goals? Three objectives have seen significant accomplishments: 1- A new center for volatolomics is under development, that will include rapid diagnostic technologies. The PI received funding from the Universityy of Minnesota and purchased the first equipment for the Center: a PTR-MS for the detection and analysis of volatile organic compounds for diagnostic purposes. 2- A new eDNA filter was developed and funding was received from the Minnesota Aqautic Invasive Species Center. 3- The PI won the Phase 1 of the Egg Technology Challenge and was fundd by the Food and AgriculturalResearch Foundation to develop a new platform for egg sex indetification using artificial intelligence.

Publications

• Type: Journal Articles Status: Submitted Year Published: 2020 Citation: Melanie Moore, Jennifer Juzwik, Snober Ahmed, Olga Saiapina, Abdenour Abbas,"Rapid Oak Wilt Detection using sodium hydroxide DNA extraction and nested PCR"
• Type: Journal Articles Status: Under Review Year Published: 2020 Citation: John W. Brockgreitens, Fatemeh Heidari, Abdennour Abbas, "Versatile process for the preparation of nanocomposite sorbents: phosphorus and arsenic". removal
• Type: Conference Papers and Presentations Status: Accepted Year Published: 2019 Citation: Rapid and PCR-free DNA Detection of Invasive Species by Nanoaggregation-Enhanced Chemiluminescence, North American Invasive Species Management Association (NAISMA) conference, September 30th  October 3rd.
• Type: Conference Papers and Presentations Status: Accepted Year Published: 2019 Citation: Akli Zarouri, Abdennour Abbas, Loren Miller, "A Novel Technology for Environmental DNA Collection and Concentration", The Wildlife Society and American Fisheries Society Conference, Reno,Nevada, October 2nd, 2019.