A Low-Power, Low-Cost Microbial Genetic Analyzer For Discovery and Monitoring of Ocean Microbes

在这个项目中，一个由工程师和生物学家组成的团队将共同开发海洋微生物测量仪(OMS)；这是一种微型、自主的遗传分析仪，可以定量分析从海洋等水环境中采集的微生物生物量的DNA和RNA。目前的技术通常是昂贵、繁琐、复杂和耗电的，限制了用户数量以及可用于科学测量的系统数量。在该项目中开发的OMS将利用生物医学研究领域的技术来实现海洋监测的新能力，使这些新技术更容易为海洋学家所用，并增加可用于科学发现的系统的数量。OMS将是廉价、低功耗、小型和自主的，以使OMS系统的大型网络得以使用，并提供新的测量能力。海洋微生物占海洋生物量的90%以上，但它们是最未被研究的生命形式之一，因为它们往往无法到达栖息地。重要的是能够在时间和空间(时空)尺度上测量其自然环境中的微生物，以了解气候变化和其他环境因素对微生物丰度、分布、功能和生产的影响。长期目标是将OMS整合到其他海洋测试平台中，并最终成为分散在全球各地的行业精细化、多目标微生物分析仪的广泛网络，掌握在不同的科学研究人员手中。该项目的更广泛影响是培养科学、技术、工程和数学(STEM)人才，为未来创新，改善社会，并让广泛的受众参与到技术和科学中来。通过在多学科研究环境中为两名博士后研究员和众多本科生提供极好的培训机会，将增加STEM人才。该项目开发的创新技术将激励不同世代的科学家和工程师探索海洋，并使人们能够从可能导致新发现的基因仪器中获得新数据。监测海洋微生物活动可能有助于社会了解关键问题，如气候变化和其他环境压力如何影响海洋微生物的初级生产。新的遗传传感器将在亚利桑那州图森市附近的生物圈2号海洋栖息地展示和操作，为学生和成人群体提供服务，使他们能够观察科学驱动的技术发展和海洋微生物监测实验。该项目将开发的OMS基于环介导的等温DNA和RNA扩增(LAMP)与微流体的集成，以产生占用空间小、低能耗的分析模块，可用于浮标、自动水下机器人(AUV)和机器人浮标等各种平台。LAMP是一种快速、选择性、灵敏的等温反应，只需一锅即可产生大量扩增产物，使简单的光学比色检测成为可能。完成的OMS原型结合了LAMP功能，将能够以用户指定的采样间隔每次部署执行50次测试。每次化验都将测量用户设计的一对DNA和RNA靶标，一式三份。将开发一种将所有硬件系统集成到单个微流控芯片中的OMS原型。该项目计划包括开发硬件子系统，包括底盘设计、电源电路、泵和阀门自动化、照明和成像系统以及热控设计。将在台式平台上开发用于微生物裂解和核酸提取的微流控芯片(芯片上提取)，然后将其集成到具有“芯片上量化”单元的单个微流控设备中，用于测量捕获的微生物中的DNA和RNA。LAMP试剂将与公司合作伙伴进行冷冻干燥，并将开发一种芯片来分配和冷冻干燥试剂。OMS单位的目标成本将不到现有仪器的十分之一，支持需要对微生物丰度和/或功能进行多节点采样的实验。

In this project, a team of engineers and biologists will work together to develop an Ocean Microbial Surveyor (OMS); a miniature, autonomous genetic analyzer that can quantitatively analyze DNA and RNA of the microbial biomass sampled from an aquatic environment such as the ocean. Current technologies are typically expensive, cumbersome, complex, and power-hungry, limiting the number of users as well as the number of systems that can be deployed for scientific measurements. The OMS developed in this project will leverage technology from the biomedical research field to enable new capabilities for ocean monitoring, to make these new technologies easily accessible to oceanographers, and to increase the number of systems that can be deployed for scientific discovery. The OMS will be inexpensive, low power, small and autonomous to enable large networks of OMS systems to be used and to provide new measurement capabilities. Marine microbes account for more than 90% of the ocean biomass, but they are among the most under-studied life forms because of their often-inaccessible habitats. It is important to be able to measure microbes in their natural environment over time and space (spatiotemporal) scales to understand the effects of climate change and other environmental factors on microbial abundance, distribution, function, and production. The long-term goal is to integrate the OMS into other ocean testing platforms and ultimately as a broad network of industry-refined, multi-target microbial analyzers dispersed throughout the globe, in the hands of diverse scientific investigators.The broader impacts of this project are to build science, technology, engineering, and mathematics (STEM) talent, innovate for the future, improve society, and engage a wide audience in the technology and science. STEM talent will be increased by providing excellent training opportunities for two postdoctoral fellows and numerous undergraduate students in a multidisciplinary research environment. The innovative technology developed in this project will inspire diverse generations of scientists and engineers to explore the oceans and enable access to new data from the genetic instruments that may lead to new discoveries. Monitoring marine microbial activities may help society understand critical issues such as how climate change and other environmental stresses impact the primary production from marine microbes. The new genetic sensors will be displayed and operated in the Biosphere 2 Ocean habitat, near Tucson, Arizona, to provide outreach to groups of school children and adults enabling them to observe science-driven technology development and ocean microbial monitoring experiments.The OMS to be developed in this project is based on the integration of loop-mediated isothermal DNA and RNA amplification (LAMP) with microfluidics to produce a small footprint, low energy consumption analytical module that can be used on various platforms such as buoys, autonomous underwater vehicles (AUVs), and robotic floats. LAMP is a fast, selective, sensitive isothermal reaction that requires only "one-pot" and produces large quantities of amplification product, enabling simple optical colorimetric detection. The completed OMS prototype, incorporating the LAMP capability, will be able to perform 50 assays per deployment with a user-specified sampling interval. Each assay will measure a user-designed pair of DNA and RNA targets in triplicate. A prototype OMS will be developed that integrates all hardware systems into a single microfluidic chip. The project plan includes development of the hardware subsystems including chassis design, power circuitry, pump and valve automation, illumination and imaging systems, and thermal control design. A microfluidic chip for microbial lysis and nucleic acids extraction (on-chip extraction) will be developed on the benchtop and then integrated into a single microfluidic device with an "on-chip quantification" unit for measurement of DNA and RNA from captured microbes. LAMP reagents will be lyophilized with a company partner, and a chip will be developed to dispense and lyophilize reagents. The target cost of the OMS unit will be less than 1/10th that of existing instruments, supporting experiments requiring multi-node sampling of microbial abundance and/or function.