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Fruitomics

Integrazione di piattaforme high-throughput applicate all'agricoltura, alla nutrizione e all'ambiente: raccogliere i frutti delle tecnologie "omiche"

Image: FESR (1)

FRUITOMICS represents one of the most important bioeconomy infrastructures in Trentino, supporting the FOOD, AGRO-ZOOTECHNICAL and ENVIRONMENTAL sectors. It will generate new knowledge to valorize agri-food and territorial products and create new business opportunities.
The platform, which has already been identified in the Multiannual Research Program of PAT, has the aim to integrate and strengthen existing infrastructure at the Fondazione Edmund Mach (FEM) and link FEM to other national and international research infrastructure and clusters (e.g. Elixir, ESFRI EMPHASIS, cluster agrifood). It works on the priority research areas agro-food, quality of life, energy and environment by establishing on one site access to specialist skills and advanced high-throughput omics in synergy with other FEM and STAR (Trentino High Education and Research System) research infrastructures.

FRUITOMICS will generate new knowledge and enlarge both national and international research and industrial collaborations . It will also allow STAR researchers to submit innovative research proposals based on the most advanced enabling technologies necessary to compete internationally for both public (Horizon2020/2030, etc) and private research investment. It will provide companies with tools to support industrial research and develop knowledge-based innovative business ideas in line with the new international research strategies in the agri-food and environment sectors.

FRUITOMICS will translate into practice the Smart Specialization Strategy objectives, integrating the major existing FEM infrastructure with new and renewed instrumental lines to further enhance the capacity to generate knowledge and innovation in collaboration with the stakeholders in agriculture, environment, health and wellbeing under a framework of sustainable development and higher education.

Funding: Fondo europeo di sviluppo regionale (FESR) in Trentino
Asse: 1 - Rafforzare la ricerca, lo sviluppo tecnologico e l'innovazione
Action: 1.1.1. - Sostegno alle infrastrutture della ricerca considerate critiche/cruciali per i sistemi regionali
FESR Agreement: n. 05/2017
PAT Call: n. 29/21 February 2018
CUP number: C49H18000000001
Total project cost: 4.537.400 Euro
Coordinator: Urska Vrhovsek
Timeframe: 21.02.2018-20.02.2021 (postponed)
University/Department: Fondazione Edmund Mach

Image: lab-316553_1920

WP1 Metabolomics and traceability

It is intended to significantly extend research in metabolomics and traceability by coupling powerful analytical techniques based on mass spectrometry (MS) with complementary approaches based on nuclear magnetic resonance (NMR) spectroscopy.

The NMR system dedicated to SNIF-NMR measurement in the field of traceability operates 24/7 to check the authenticity of food products, with 100% level of use. The high molecular complexity and diversity of biological samples (food, biofluids, environmental samples) requires a spectrometer with i) significantly better sensitivity and resolution ii) autosampler iii) updated H/W and S/W for the application of modern NMR profiling methods in the agriculture, food, pharmaceutical and environmental research.
Reinforcement of MS has two objectives i) to maintain capacity, by replacing the 2 spectrometers for untargeted analysis, of which one operating 24/7 with >80% level of use, the other obsolete and decommissioned , and ii) to grasp opportunities for development by installing two new systems to support increased demand for targeted analysis from human nutrition studies.

WP2 Nutrition and nutrigenomics

The Nutrition and nutrigenomics unit will expand FEM research capabilities by developing a new on-site facility for human feeding studies. FNU will provide a a dedicated nutrition facility for studying how foods, especially fruit, vegetables and fermented foods, are metabolized by the human body and in turn help protect against human disease and promote health ageing.

The FNU objectives are:

  • To provide the analytical infrastructure to support a human nutrition and dietary intervention studies focused on food and function in healthy people.
  • To generate critical mass in terms of human nutrition, complementing existing expertise in gut microbiota and functional food design.
  • To provide a stimulus for attracting significant external financial support for nutrition research from both public and private sectors at national and international levels.
  • To provide the scientific infrastructure needed to attract the best nutrition researchers to FEM thereby boosting nutrition research capabilities, research output, and scientific competitiveness in attracting significant external research funding.

WP3 Computational Biology

The project aims to create an infrastructure for the conservation, analysis and display of omics data obtained within the RI. The infrastructure must satisfy the following requirements:

it must have a modular structure suitable for updating/expansion;
it must provide for an integrated traceability system capable of managing the whole lifecycle of experimental data, in line with the best standardisation practices established at European level;
it must be capable of managing a wide spectrum of computational tasks, both massively parallel and when a large amount of dedicated RAM is required.
The system will be based on a bipolar structure, with reinforcement of the “Kore” parallel computing cluster managed in collaboration with FBK, alongside a private cloud system for unstructured computing tasks, obtained by reinforcing and updating the infrastructures already present in FEM. The infrastructure will be served by mass storage for the archiving of data and parallel storage capable of guaranteeing high I/O intensity workloads. The file system will guarantee transparent accessibility to data from all computing resources.

WP4 Phenotyping

This part of the RI project aims to create a phenotyping platform for the quantitative and semi-automatic acquisition of morphological and functional data of apple, grape and soft fruits.

The collected phenotypic data relate to the physiological, phytopathological, production and qualitative parameters of the crops and are of interest both for the characterization of the new genotypes obtained in the breeding activity and for functional genomic studies. Non-invasive measures will be conducted with optical sensors operating in the visible, infrared and near infrared range, as well as in the hyperspectral region and through fluorescence measurements.

The project aims to realize both field and laboratory systems (different scales). In the first case, remote sensing of the characteristics of a large number of plants will be carried out at the production site under non-controlled conditions using transportable passive sensors (eg. Drone) for acquisition of fluorescence and hyperspectral readings.
The laboratory system will measure precisely and under controlled conditions (light, T, humidity) the differences between genotypes or plants treated by the 3D reconstruction of the foliage and the mapping of active fluorescence readings, infrared and the rest of the non-visible spectrum.