Bacterial-based Biosensor Digital Twin for Microbial Community Sensing (US-Ireland-R&D Partnership)

在21世纪的世纪，微生物生态学进化的理解是一个关键的挑战，特别是当我们正在应对新出现的威胁，我们的健康以及全球环境。这个合作的美国-爱尔兰研发伙伴关系项目旨在通过开发一种系统来应对这一挑战，该系统可以感知自然环境中活细菌的分子通信，并将此信息提供给其等效的数字孪生，以便让我们能够观察和预测它们的对话，并深入了解控制其行为的内部功能。这将通过详细的计算机产生的细菌细胞内和细胞间通信模型的数字孪生模型来实现，该模型无线连接到具有电化学纳米传感器的新型集成活细胞生物传感器。该系统的最终影响是一种新的监测工具，可以了解细菌如何进化和转变其能力。该项目将开发一个跨文化的跨大西洋指导计划，来自美国和爱尔兰的本科生将由一个研究团队共同指导，目的是吸引妇女和代表性不足的少数民族进行多学科的突破性研究。该项目还将开发和提供编程活动，以初中和高中学生作为推广计划的一部分。在21世纪的世纪，微生物生态学进化的理解是一个新兴的挑战，特别是当我们正在应对新出现的威胁，我们的健康以及全球环境。这个美国-爱尔兰研发合作伙伴关系的目的是开发一种新的系统，该系统使用新型集成工程大肠杆菌生物传感器与电化学纳米传感器从活细菌细胞中感知通信分子，并将此信息馈送到数字双胞胎，从而能够预测和观察其复杂的通信模式。计算机数字双胞胎将由3D trans-omics数据模型与参数推断技术的组合构建，这些参数推断技术来自与生物物理计算模型集成的湿实验室实验数据。该系统将提供在特定环境条件下关联蜂窝内和蜂窝间通信的详细信息。固态发生器-收集器电化学传感器将被设计为消除部署到环境中的干扰，以提高传输到数字孪生的信息的准确性。该项目的研究可以为“互联网上的细菌公民”的开放平台奠定基础，研究人员可以（i）开发新形式的生态系统生物网络环境监测，（ii）为全球细菌跟踪提供合作倡议，以了解它们如何在全球范围内进化和传播，以及（iii）设计未来的生物混合植入式设备用于疾病检测。将开发一个原型演示器来展示野生型细菌与计算机之间的通信，重点是两个案例研究场景，即“慢性伤口中的细菌对话”和“土壤微生物组中的水平基因转移（HGT）对话”。“该项目由生物传感计划和刺激竞争研究的既定计划（EPSCoR）共同资助。该奖项反映了NSF的法定使命，并通过使用基金会的知识价值和更广泛的影响审查标准进行评估，被认为值得支持。

In the 21st century, the understanding of microbial ecology evolution is a critical challenge, especially as we are tackling new emerging threats to our health as well as the global environment. This collaborative US-Ireland R&D Partnership project aims to address this challenge by developing a system that can sense molecular communications from living bacteria in the natural environment, and feeding this information to its equivalent digital twin, in order to allow us to observe and predict their conversation and tap deep into their internal functionalities that control their behaviors. This will be realized through a detailed computer produced digital twin model of the bacteria’s intra and inter-cellular communication model, which is wirelessly connected to a novel integrated living cell biosensor with electrochemical nanosensors. The resulting impact of this system is a new monitoring tool to understand how bacteria evolve and transform their capabilities. This project will develop a cross-cultural Trans-Atlantic mentoring program, where undergraduates from the US and Ireland will be jointly mentored by a team of researchers with the aim of attracting women and underrepresented minorities to do multi-disciplinary breakthrough research. The project will also develop and deliver programming activities to middle-and high-school students as part of the outreach program.In the 21st century, the understanding of microbial ecology evolution is an emerging challenge, especially as we are tackling new emerging threats to our health as well as the global environment. The aim of this US-Ireland R&D Partnership is to develop a novel system that senses communication molecules from living bacterial cells using a novel integrated engineered E.Coli biosensor with an electrochemical nanosensor and feeding this information to a digital twin that will enable prediction and observation of their complex communication patterns. The in silico digital twin will be constructed from a combination of 3D trans-omics data models with parameter inferencing techniques from wet lab experimental data integrated with biophysical computational models. This system will provide detailed information that correlates the intra and inter-cellular communications under a specific environmental condition. Solid state generator-collector electrochemical sensors will be designed to eliminate interference for deployment into the environment to increase the accuracy of information that is transmitted to the digital twin. The research in this project can lay the groundwork of an open platform for “Bacterial Citizens on the Internet," where researchers can (i) develop new forms of bio-cyber environmental monitoring of ecological systems, (ii) provide collaborative initiatives for global bacterial tracking to understand how they evolve and spread globally, and (iii) design future bio-hybrid implantable devices for disease detection. A prototype demonstrator will be developed to show communication between wild-type bacteria to a computer, focusing on two case study scenarios, which are “Bacterial conversation in chronic wounds” and “Conversation enabling Horizontal Gene Transfer (HGT) in soil microbiome." This project is jointly funded by the Biosensing Program and the Established Program to Stimulate Competitive Research (EPSCoR).This award reflects NSF's statutory mission and has been deemed worthy of support through evaluation using the Foundation's intellectual merit and broader impacts review criteria.