14TSB_ESAP Improved risk prediction for precision agriculture: automated monitoring of pathogen movement

该项目旨在开发一种创新的自动化现场仪器，用于对小麦中空气传播的真菌病原体进行综合孢子采样和测试，目前英国每年花费超过1.2亿英镑来控制真菌病原体。该仪器将构成一个分布式检测网络的基础，提供有关接种物运动的实时信息，使杀菌剂控制的时间和目标更加有效。这将有助于作物科学行业进一步研究风险预测和开发/改进真菌病原体的决策支持系统，首先使谷物行业受益，而且通过帮助确保食品行业的长期未来，也使英国社会总体受益。这项工作包括使用环介导等温扩增（LAMP）方法进行旋风空气采样，自动流体处理和DNA分析的集成，以直接检测和鉴定真菌种类。赫特福德大学（UoH）的主要参与，因此我们的核心目标是在该单元内开发颗粒捕获和运输机制。特别是，主要目标是开发用于孢子收集的旋风分离器（黑穗病菌，黑穗病菌和条纹状芽孢），以及随后的流体处理和样品处理平台开发。旋风分离器形成收集单元的初始阶段，收集单元还将包括颗粒保留室和机械/流体界面。后者包括毫流和微流控系统，将收集的分析物转移到处理模块，为检测室准备样品，其中检测将基于对目标DNA的敏感实时荧光检测。将开发一种工程解决方案来集成空气采样、流体处理和检测平台。该系统将定期取样，将收集到的分析物分批分析。我们在这里提出的方法将为远程分布的现场仪器收集的样品提供快速准确的分析。为了实现我们的目标，UoH的工作计划如下：里程碑（MS） 1.1旋风收集器和进气组件的设计与开发MS 1.2流体处理和处理模块的设计与开发MS 1.3原型旋风收集器和进气组件的制造与评估MS 1.4旋风气溶胶收集特性与干孢子模拟物性能测试MS 1.5原型流体处理和处理模块的制造与评估MS 1.6制造与评估流体处理和处理模块评估目标2：真菌孢子样品处理（铅Fera）MS 2.2样品制备程序与流体处理和处理模块的集成目标是促进精准农业工具的核心开发，以提高作物资源的有效利用，最大限度地提高产量，并最大限度地减少与粮食生产相关的潜在负面环境影响，符合竞争范围。该提案汇集了一个跨学科团队的知识和技能，包括科学仪器的设计师和工程师（Optisense和赫特福德郡大学）、作物保护行业的代表（拜耳）和植物病理学/检测专家（Fera）。因此，最终的工具将得到广泛的作物科学利益相关者的投入。然而，开发这些新技术只是挑战的一部分。还必须确保这些新方法符合目的，并以满足最终用户（包括研究科学家、食品生产者和农用化学品专家）需求的方式发挥作用。为了实现这一点，核心终端用户在该联盟的开发工作中有代表。

The project seeks to develop an innovative automated in-field instrument for integrated spore-sampling and testing for airborne fungal pathogens in wheat which currently cost the UK in excess of £120 million annually to control. The instrument will form the basis of a distributed detection network, providing real-time information on inoculum movement, allowing more effective timing and targeting of fungicide control. This will aid the crop science industry to further research risk prediction and development/refinement of decision support systems for fungal pathogens, benefitting the cereal industry in the first instance, but also the UK society in general by helping to secure the long term future of the food industry. The work involves integration of cyclone air sampling, automated fluidic handling and DNA analysis using Loop mediated isothermal AMPlification (LAMP) methods for direct detection and identification of fungal species. The University of Hertfordshire's (UoH) primary involvement, and thus our core objectives, are the development of the particulate capture and transport mechanisms within this unit.In particular the primary objective is the development of a cyclonic separator for spore collection (Septoria tritici, Puccinia triticina and P striiformis) with subsequent fluid handling and sample processing platform development. The cyclone separator forms the initial stage of a collection unit which will also include a particle retention chamber and mechanical/fluidic interface. The latter, comprising both milli and microfluidic systems, transfers collected analyte to the processing module to prepare the sample for the detection chamber, wherein detection will be based on sensitive real-time fluorescence detection of the target DNA. An engineering solution will be developed to integrate the air sampling, fluid handling and detection platforms.The system will sample periodically with the collected analyte analysed in batches. The approach that we propose here will offer rapid and accurate analysis of samples collected by remotely distributed in-field instrumentation. In order to achieve our objectives the work plan for UoH, is as follows:Objective 1: Development of in-field cyclonic fungal spore collector (Lead UoH)Milestone (MS) 1.1 Design & development of cyclonic collector and intake assemblyMS 1.2 Design & development of fluidic handling and processing moduleMS 1.3 Manufacture & evaluation of prototype cyclonic collector and intake assemblyMS 1.4 Cyclone aerosol collection characterisation and performance tests with dry spore simulantsMS 1.5 Manufacture & evaluation of prototype fluidic handling and processing moduleMS 1.6 Manufacture & evaluation of fluidic handling and processing moduleObjective 2: Evaluation of sample processing of fungal spores (Lead Fera)MS 2.2 Integration of sample preparation procedure with fluidic handling and processing moduleThe aim is to contribute to the core development of a precision agriculture tool to enhance efficient use of resources in the crop, maximise yield and minimise potentially negative environmental impacts associated with food production in line with the scope of the competition. The proposal brings together the knowledge and skills of a cross-disciplinary team from designers and engineers of scientific instruments (Optisense and University of Hertfordshire), representatives of the crop protection industry (Bayer), and plant pathology/detection experts (Fera). The resultant tool will therefore have input from a broad spectrum of crop science stakeholders.However, developing these new technologies is only part of the challenge. It is also necessary to make sure these new methods are fit-for-purpose and that they work in a way that meets the needs of end users including research scientists, food producers and agri-chemical specialists. To achieve this, core end users are represented in the development work within this consortium.