Salcedo-Arancibia Francisco, Gutiérrez Martín, Chavoya Arturo
Universidad de Guadalajara, Centro Universitario de Ciencias Económico Administrativas, Departamento de Sistemas de Información, Periférico Norte No. 799, Núcleo Universitario Los Belenes, Zapopan, Jalisco, CP 45100, Mexico.
Universidad Diego Portales, Escuela de Informática y Telecomunicaciones, Ejército No. 441, Santiago, CP 837 0007, Chile.
Heliyon. 2024 Jul 23;10(15):e35050. doi: 10.1016/j.heliyon.2024.e35050. eCollection 2024 Aug 15.
Sensors used in precision agriculture for the detection of heavy metals in irrigation water are generally expensive and sometimes their deployment and maintenance represent a permanent investment to keep them in operation, leaving a lasting polluting footprint in the environment at the end of their lifespan. This represents an area of opportunity to design new biological devices that can replace part, or all of the sensors currently used. In this article, a novel workflow is proposed to fully carry out the complete process of design, modeling, and simulation of reprogrammable microorganisms . As a proof-of-concept, the workflow has been used to design three whole-cell biosensors for the detection of heavy metals in irrigation water, namely arsenic, mercury and lead. These biosensors are in compliance with the concentration limits established by the World Health Organization (WHO). The proposed workflow allows the design of a wide variety of completely biodevices, which aids in solving problems that cannot be easily addressed with classical computing. The workflow is based on two technologies typical of synthetic biology: the design of synthetic genetic circuits, and synthetic engineering, which allows us to address the design of reprogrammable microorganisms using software and hardware to develop theoretical models. These models enable the behavior prediction of complex biological systems. The output of the workflow is then exported in the form of complete genomes in SBOL, GenBank and FASTA formats, enabling their subsequent implementation in a laboratory. The present proposal enables professionals in the area of computer science to collaborate in biotechnological processes from a theoretical perspective previously or complementary to a design process carried out directly in the laboratory by molecular biologists. Therefore, key results pertaining to this work include the fully workflow that leads to designs that can be tested in the lab or , and a proof-of-concept of how the workflow generates synthetic circuits in the form of three whole-cell heavy metal biosensors that were designed, modeled and simulated using the workflow. The simulations carried out show realistic spatial distributions of biosensors reacting to different concentrations (zero, low and threshold level) of heavy metal presence and at different growth phases (stationary and exponential) that are backed up by the whole design and modeling phases of the workflow.
精准农业中用于检测灌溉水中重金属的传感器通常价格昂贵，有时其部署和维护需要持续投入以保持运行，在其使用寿命结束时会在环境中留下持久的污染痕迹。这为设计能够替代部分或全部现有传感器的新型生物设备提供了机会。本文提出了一种新颖的工作流程，以全面完成可重新编程微生物的设计、建模和仿真的完整过程。作为概念验证，该工作流程已用于设计三种用于检测灌溉水中重金属的全细胞生物传感器，即砷、汞和铅。这些生物传感器符合世界卫生组织（WHO）规定的浓度限值。所提出的工作流程允许设计各种各样的完全生物设备，有助于解决传统计算难以解决的问题。该工作流程基于合成生物学的两种典型技术：合成基因电路的设计和合成工程，这使我们能够使用软件和硬件来开发理论模型，从而解决可重新编程微生物的设计问题。这些模型能够预测复杂生物系统的行为。然后，工作流程的输出以SBOL、GenBank和FASTA格式的完整基因组形式导出，以便随后在实验室中实施。本提议使计算机科学领域的专业人员能够从理论角度参与生物技术过程，这在以前是与分子生物学家在实验室直接进行的设计过程互补的。因此，这项工作的关键成果包括导致可在实验室中测试的设计的完整工作流程，以及该工作流程如何以三种全细胞重金属生物传感器的形式生成合成电路的概念验证，这些生物传感器是使用该工作流程进行设计、建模和仿真的。所进行的模拟显示了生物传感器在不同生长阶段（稳定期和指数期）对不同浓度（零、低和阈值水平）重金属存在的反应的实际空间分布，这得到了工作流程的整个设计和建模阶段的支持。
