High-throughput quantification of the interactions between biomolecules and cells with engineered surfaces

生物系统复杂行为的研究往往需要大规模的实验方法，以全面描述它们对各种扰动参数的反应。在过去的几十年里，由于生物化学和（最近的）基于细胞的测试的小型化，这种大规模的实验方法已经成为可能。虽然这些技术对所研究的系统进行了一定程度的经验“蛮力”探测，但这种强大方法的最终目标是基于对潜在机制的破译来预测生物系统的行为，而不是基于经验观察的预测。通常，大规模实验已用于“组学”应用，例如基因组学，蛋白质组学，代谢组学，以获得药物发现的好处，但该方法已用于其他应用，例如新材料和生物材料的发现。为此，该计划的长期目标是推进基于理解的混合系统的行为预测，包括生物分子，特别是蛋白质；细胞，特别是微生物，与人造表面和结构相接合。这一目标将通过从(i)产生全面经验数据的大规模标准化实验的程序化进展来实现；（ii）构建生物组分（即生物分子、细胞）参数之间的半经验相关性；人工成分，即表面、微/纳米结构；（iii）对感兴趣的系统的行为进行基于模型的预测；因此，允许工程风格的设计，制造和混合生物纳米器件的操作。在短期内，该计划旨在(i)开发一个实验平台，集成微流体，微阵列，生物传感器和MEMS元件，用于生物分子和细胞与工程表面的相互作用的组合研究；通过大规模标准化实验收集有关蛋白质吸附和生物活性的数据；并发现蛋白质性质之间蛋白质吸附的统计关系；表面性能;流体性质；（iii）推导出纳米结构表面的设计规则，特别是连接单个蛋白质分子；（iv）证明生物系统运动性的量化，即细胞骨架蛋白和运动微生物，作为系统界面人工结构和表面生物活性的最终报告者。项目可交付成果与不同程度的影响相关联。首先，方法上的进步将展示集成组合检测设备的使用，这将有助于微生物学、药物发现、诊断和基础分子生物学研究领域相关研究的标准化和效率。其次，诱导特定生物行为的结构的制造，例如防污，选择性吸附，生物活性保存，将影响各种领域，如手术器械，植入物，诊断设备，消费品，食品加工，空调设备，船舶防污等。仅考虑生物材料（一个80亿美元的市场），个性化生物材料的快速“设计和测试”的可能性将大大增强解决患者而不是通用医疗状况的能力。第三，快速、全面地定量细胞骨架细丝和微生物的运动，用于癌症、神经退行性疾病等药物的发现；或新的、致命的医院传染病——这是加拿大的一个特殊问题。

The study of the complex behaviour of biological systems often asks for a large scale experimentation approach, to comprehensively describe their responses to a large variety of perturbation parameters. In the last decades, this large scale experimentation approach has been made possible due to the miniaturisation of biochemical and (more recently) cell-based tests. While these techniques present a certain degree of empirical, `brute force' probing of the systems studied, the ultimate goal of this powerful methodology is the prediction of the behavior of biological systems based on the deciphering the underlying mechanisms, rather than the prediction based on empirical observation. Usually, large scale experimentation has been used for `omics' applications, e.g., genomics, proteomics, metabolomics, for the benefits of drug discovery, but the methodology has been used for other applications, e.g., the discovery of new materials and biomaterials. To this end, the long term objective of the proposed program is to progress the understanding-based prediction of the behavior of hybrid systems comprising biomolecules, in particular proteins; and cells, in particular microorganisms, interfaced with artificial surfaces and structures. This objective will be fulfilled through a programmatic progression from (i) large scale, standardized experimentation yielding comprehensive empirical data; to (ii) construction of semi-empirical correlations between the parameters of the biological component, i.e., biomolecule, cell; and those of the artificial component, i.e., surfaces, micro/nano-structures; to (iii) model-based predictions of the behavior of the systems of interest; thus allowing for engineering-style design, fabrication and operation of hybrid bio-nano-devices.In the short term, the program aims to (i) develop an experimental platform that integrates microfluidics, microarrays, biosensors and MEMS elements for the combinatorial study of interactions of biomolecules and cells with engineered surfaces; (ii) collect data regarding protein adsorption and bioactivity from large scale, standardized experimentation; and find statistical relationships regarding protein adsorption between protein properties; surface properties; and fluid properties; (iii) derive design rules for nano-structured surfaces specifically interfacing individual protein molecules; and (iv) demonstrate the quantification of the motility of biological systems, i.e., cytoskeletal proteins and motile microorganisms, as an ultimate reporter of the bioactivity of the system interfacing artificial structures and surfaces.The program deliverables are linked to various levels of impact. Firstly, the methodological advances will demonstrate the use of the integrated combinatorial-testing device, which will help the standardization and efficiency of relevant studies in the area of microbiology, drug discovery, diagnostics and fundamental molecular biology studies. Second, the fabrication of structures that induce a specific biological behavior, e.g., antifouling, selective adsorption, bioactivity preservation, will impact on areas as diverse as surgical instruments, implants, diagnostic devices, consumer products, food processing, air conditioning equipment, antifouling of ships, etc. Considering biomaterials only (a $8bn market), the possibility of quick "design & test" of personalised biomaterials will greatly amplify the capacity of addressing the patient's, rather than a generic medical condition. Third, the quick and comprehensive quantification of the motility of cytoskeleton filaments and microorganisms, on drug discovery for e.g., cancer, neurodegenerative diseases; or new, virulent hospital-based infectious diseases - a particular problem for Canada.