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BioEngineering from first principles.

生物工程从第一原理开始。

基本信息

批准号：
EP/I016589/1
负责人：
Steven Banwart
金额：
$ 25.71万
依托单位：
University of Sheffield
依托单位国家：
英国
项目类别：
Research Grant
财政年份：
2011
资助国家：
英国
起止时间：
2011 至无数据
项目状态：
已结题

来源：
https://gtr.ukri.org/projects?ref=EP%2FI016589%2F1
关键词：
BioEngineering first principles.

项目摘要

The research challenge is to understand the principles that control cell-surface and cell-cell interactions given the enormous variety of macromolecular structures produced by microbial cells and the complexity of their chemical and physical influences on binding interactions. We will predict attachment using computational models and gain understanding why extracellular DNA promotes or inhibits attachment under specific conditions. This is a major challenge with huge rewards if it can be met. A predictive capability of cell attachment would enable new methods of analysis and design in the fields of environmental engineering, process engineering and biomedical engineering.To tackle this challenge, we have recruited multidisciplinary expertise to combine theoretical and experimental techniques from the fields of computational chemistry, surface and polymer physics, molecular biology, polymer chemistry, engineering microbiology, analytical chemistry, X-Ray and vibrational spectroscopy and environmental engineering science.We propose to use computational chemistry techniques for simulation of cell walls, to characterise the behaviour of their individual chemical constituents, and to estimate the physical-chemical interactions that occur with specified solid surfaces. Looking 1-2 decades ahead, the aim is to develop computational methods sufficiently to allow the required interactions to be designed, identify the macromolecular structures necessary for these interactions to occur and identify the necessary gene sequences for their synthesis. This Feasibility Account study will launch theoretical chemistry into the specific challenge of tackling extracellular DNA (eDNA) binding on cells and minerals as one identified mechanism in biofilm formation. The outcome will be an evaluation of this combined approach between multidisciplinary experimentation and theoretical simulation as a case study for predicting cell attachment and growth. With the computational techniques, we shall investigate the binding of nucleic acid sequences to the surfaces using molecular dynamics simulations. Experimentally, we will first characterise eDNA produced by biofilm-forming microbes that we have isolated from environmental samples. We will then remove eDNA from biofilm-forming cells and replace it with synthetic DNA to start to quantify the relationship between the properties of eDNA and cell attachment. This 'synthetic' approach will allow us to vary systematically eDNA length, sequence and concentration and quantify cell attachment to model oxide surfaces such as negatively charged silica and positively charged alumina under defined ionic medium conditions. We will explore how eDNA is arranged on the cell surface and substratum using atomic force microscopy and fluorescence techniques, and we shall explore the use of methods that break the diffraction limit for optical resolution such as SNOM (Scanning Near Field Optical Microscopy) which, to our knowledge, has never been applied to this area. The potential for engineering applications is immense. We anticipate that virtually all fields of biotechnology would potentially profit. We propose to assess this breadth of promise by bringing a wide range of engineering experts together with the project team in a sand pit that will be held 3 months before the project end. We will hold a 2-day workshop to present our results and develop a roadmap for moving this forward as a research area and for practical application. Participants will evaluate our results, identify areas of opportunity for engineering applications, and assess the promise for generalisation across the broad field of BioEngineering through systematic application of our approach.

研究的挑战是理解控制细胞表面和细胞间相互作用的原理，因为微生物细胞产生的大分子结构种类繁多，它们对结合相互作用的化学和物理影响也很复杂。我们将使用计算模型预测附着，并了解为什么细胞外DNA在特定条件下促进或抑制附着。这是一个巨大的挑战，如果它能被满足，回报是巨大的。细胞附着的预测能力将为环境工程、过程工程和生物医学工程领域的分析和设计提供新的方法。为了应对这一挑战，我们从计算化学、表面和聚合物物理、分子生物学、聚合物化学、工程微生物学、分析化学、x射线和振动光谱学以及环境工程科学等领域招募了多学科专业知识，将理论和实验技术结合起来。我们建议使用计算化学技术来模拟细胞壁，以表征其单个化学成分的行为，并估计与特定固体表面发生的物理化学相互作用。展望未来的1-2年，目标是开发足够的计算方法来设计所需的相互作用，确定这些相互作用发生所需的大分子结构，并确定合成这些相互作用所需的基因序列。这项可行性研究将把理论化学引入到解决细胞外DNA （eDNA）与细胞和矿物质结合的具体挑战中，作为生物膜形成的一种确定机制。结果将是评估这种多学科实验和理论模拟之间的结合方法，作为预测细胞附着和生长的案例研究。利用计算技术，我们将利用分子动力学模拟来研究核酸序列与表面的结合。实验上，我们将首先表征从环境样本中分离出来的形成生物膜的微生物产生的eDNA。然后，我们将从形成生物膜的细胞中去除eDNA，并用合成DNA代替它，开始量化eDNA特性与细胞附着之间的关系。这种“合成”方法将允许我们系统地改变eDNA的长度、序列和浓度，并量化细胞在特定离子介质条件下与模型氧化物表面（如带负电荷的二氧化硅和带正电荷的氧化铝）的附着。我们将使用原子力显微镜和荧光技术探索eDNA如何排列在细胞表面和基质上，我们将探索使用打破光学分辨率衍射极限的方法，如SNOM（扫描近场光学显微镜），据我们所知，该方法从未应用于该领域。工程应用的潜力是巨大的。我们预计，几乎所有的生物技术领域都有可能获利。我们建议在项目结束前3个月召集各种工程专家与项目团队一起在沙坑中评估这一承诺的广度。我们将举行为期两天的研讨会，展示我们的成果，并制定路线图，将其作为研究领域和实际应用向前推进。参与者将评估我们的结果，确定工程应用的机会领域，并通过系统应用我们的方法评估在生物工程广泛领域推广的前景。