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

研究生物系统的复杂行为往往需要大规模的实验方法，以全面地描述它们对各种摄动参数的响应。在过去的几十年里，由于生化测试和(最近)基于细胞的测试的微型化，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提供了一定程度的经验性的“蛮力”探测，但这种强大的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，大规模实验被用于“组学”应用，例如基因组学、蛋白质组学、代谢组学，以利于药物发现，但方法学也被用于其他应用，例如新材料和生物材料的发现。为此，拟议方案的长期目标是推进对包括生物分子，特别是蛋白质，以及细胞，特别是微生物，与人工表面和结构相互作用的杂交系统的行为的基于理解的预测。这一目标将通过以下方式实现：(1)产生全面经验数据的大规模标准化实验；(2)在生物成分(即生物分子、细胞)的参数与人造成分(即表面、微/纳米结构)的参数之间建立半经验关联；(3)对感兴趣系统的行为进行基于模型的预测；在短期内，该计划的目标是(I)开发一个集成了微流体、微阵列、生物传感器和MEMS元件的实验平台，用于组合研究生物分子和细胞与工程表面的相互作用；(Ii)从大规模标准化实验中收集关于蛋白质吸附和生物活性的数据；并找到蛋白质吸附特性、表面特性和流体特性之间的统计关系；(Iii)推导出专门与单个蛋白质分子相互作用的纳米结构表面的设计规则；以及(Iv)展示生物系统，即细胞骨架蛋白质和可移动微生物的运动性的量化，作为连接人工结构和表面的系统生物活性的最终报告。首先，方法学上的进步将展示综合组合测试装置的使用，这将有助于微生物学、药物发现、诊断学和基础分子生物学研究领域的相关研究的标准化和效率。其次，制造能够诱导特定生物行为的结构，例如防污染、选择性吸附、生物活性保存，将对各种领域产生影响，如外科器械、植入物、诊断设备、消费品、食品加工、空调设备、船舶防污等。仅就生物材料(一个80亿美元的市场)而言，快速“设计和测试”个性化生物材料的可能性将极大地增强治疗患者疾病的能力，而不是普通的医学疾病。第三，对细胞骨架细丝和微生物的运动性进行快速和全面的量化，以便发现治疗癌症、神经退行性疾病或新的、以医院为基础的致命传染病的药物--这是加拿大面临的一个特殊问题。

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.