Detecting infectious organisms: A concerted approach using genomics, molecular engineering and nano-enabled bio-MEMS technologies (AptaMEMS-ID)

人造设备和生物系统的功能集成是科学和技术的重大挑战之一，现在人们普遍认为，纳米技术和工程的结合，通过实时预测性、预防性、临时性医疗保健提供，利用基因组信息的全部潜力，将导致下一次技术革命。然而，如果没有来自用户社区的指导以及来自分子遗传学和生物信息学的跨学科投入，该领域的重大进展是不可能的。该项目位于纳米、生物、微型和基因组技术的融合的核心，建议使用纳米使能的生物传感器技术来开发用于快速检测感染性生物的护理点系统。该提案基于临床和社会对用于筛查、诊断和流行病学用途的特定医院感染进行快速检测的需求，涉及的技术组合包括：比较基因组学、新型生物信息学、验证性蛋白质组学、分子工程多肽适配子配体和微电子机械(MEMS)传感器技术，这些技术在纳米级有效利用：设计、制造、功能化和分子构型。纽卡斯尔大学研究人员使用基于e-Science网格的工作流来利用微生物基因组序列数据的能力是该提案的核心。这项技术将用于鉴定细菌细胞表面(SAP)上展示的蛋白质。一旦确定并表征了可能的汁液，就将分析表面蛋白质组的组成，以确定目标生物体群体共有的蛋白质。如果手动执行，这通常需要几周时间，而我们的方法只需要不到一天的时间来建立工作流和处理数据。一旦确定了目标蛋白，将使用蛋白质组学和转录组学相结合的方法来确定目标基因在临床样本中的表达。然后，这些发展将与分子工程相结合，生产一系列定制的工程生物分子，即多肽适体，这些生物分子将专门识别SAP蛋白。肽适配子是一种小的、健壮的肽序列，旨在用作蛋白质识别模块，将由商业合作者Aptuscan制备。然后，选定的适配子将使用我们的专利光刻三维图案化技术以纳米分辨率集成到固态MEMS微系统中，该系统将设计和开发为在单个传感器表面结合多分析物功能，使用我们的专利传感器和分子图案化技术的组合，以同时检测多种不同的有害微生物。最后，这项技术将通过与纽卡斯尔卫生保护局区域实验室主任John Magee博士和纽卡斯尔泰恩医院NHS Foundation Trust感染预防和控制主任Kate Gould教授的合作，在医疗需求驱动的应用领域进行评估。这项研究计划中包含的创新将使一套快速、定量的传感器系统得以开发，该系统在分子、纳米和微米级别设计，用于根据SAP的指纹对病原微生物进行特定检测和识别，这将提供生物体特有的唯一识别符基序。这些设备将构成对感染诊断、进展和流行病学的一线监测的宝贵帮助。这有可能通过改善患者护理和管理为NHS提供深刻的经济和人力优势。

The functional integration of man-made devices and biological systems represents one of the grand challenges of science and technology and it is now widely accepted that a combination of nanotechnology and engineering that harnesses the full potential of genomic information through real-time predictive, preventive, point-of-care healthcare provision will lead to the next technological revolution. However, major progress in the field is unlikely without guidance from the user community combined with interdisciplinary input from molecular genetics and bioinformatics.This project, which lies at the heart of the confluence of nano-, bio-, micro- and genomic technologies, proposes to use nano-enabled biological sensor technology for the development of a point-of-care system for the rapid detection of infectious organisms. The proposal is based around the clinical and societal need for rapid detection of specific nosocomal infections for screening, diagnostic and epidemiological uses and involves a combination of technologies encompassing; comparative genomics, novel bioinformatics, confirmatory proteomics, molecular engineered peptide aptamer ligands and microelectromechanical (MEMS) sensor technologies which exploit effectively at the nano-scale: design, manufacture, functionalization and molecular patterning.The ability of Newcastle University researchers to use e-Science Grid-based workflows to exploit data from microbial genome sequences is at the heart of this proposal. This technology will be used for the characterisation of proteins displayed at bacterial cell surfaces (SAPs). Once putative SAPs are identified and characterised, the composition of the surface proteome will be analysed to identify proteins that are common to target groups of organisms. If performed manually this would normally take many weeks whereas our approach takes less than a day to establish the workflows and to process the data. Once target proteins have been identified, a combination of proteomics and transcriptomics will be used to determine the expression of the target genes in clinical samples.These developments will then be combined with molecular engineering to produce a range of bespoke engineered biomolecules, peptide aptamers, which will recognize specifically the SAP proteins. Peptide aptamers, which are small, robust peptide sequences designed to act as protein recognition modules, will be prepared by the commercial collaborator Aptuscan. The selected aptamers will then be integrated with nanometre resolution, using our patented photolithographic 3-dimensional patterning technique, into solid-state MEMS microsystems which will be designed and developed to incorporate multi-analyte capabilities on a single sensor surface, using a combination of our patented sensor and molecular patterning technologies, to simultaneously detect multiple diverse harmful microorganisms. Finally, the technology will be assessed in healthcare demand-driven application areas by collaboration with Dr John Magee, Director of the Health Protection Agency regional laboratory in Newcastle and Professor Kate Gould, Director of Infection Prevention and Control at the Newcastle upon Tyne Hospitals NHS Foundation Trust.The innovations encompassed in this programme of research will allow the development of a suite of rapid, quantitative sensor systems engineered at the molecular, nano- and micro-scale levels for the specific detection and identification of pathogenic microorganisms on the basis of the fingerprint of SAPs which will provide organism-specific unique identifier motifs. These devices will constitute valuable aids to front line monitoring of infection diagnosis, progress and epidemiology. This has the potential to provide profound economic and human advantages for the NHS through improved patient care and management.