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.

鉴于微生物细胞产生的大分子结构的多样性及其对结合相互作用的化学和物理影响的复杂性，研究的挑战是了解控制细胞表面和细胞与细胞相互作用的原理。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。这是一项重大挑战，如果能够实现，将会带来巨大的回报。细胞附着的预测能力将使环境工程、过程工程和生物医学工程领域的新分析和设计方法成为可能。为了应对这一挑战，我们招募了多学科专业知识，将计算化学领域的理论和实验技术结合起来，表面和聚合物物理学、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。我们建议使用计算化学技术来模拟细胞壁，以表征其各个化学成分的行为，并估计物理化学与特定固体表面发生的相互作用。展望未来 1-2 年，我们的目标是开发足够的计算方法，以设计所需的相互作用，确定发生这些相互作用所需的大分子结构，并确定合成所需的基因序列。这项可行性研究将利用理论化学来解决细胞外 DNA (eDNA) 与细胞和矿物质的结合这一特定挑战，作为生物膜形成的一种已确定机制。结果将是对多学科实验和理论模拟之间的这种组合方法的评估，作为预测细胞附着和生长的案例研究。通过计算技术，我们将使用分子动力学模拟研究核酸序列与表面的结合。在实验上，我们将首先表征从环境样本中分离出的生物膜形成微生物产生的 eDNA。然后，我们将从生物膜形成细胞中去除 eDNA，并用合成 DNA 替换它，以开始量化 eDNA 特性与细胞附着之间的关系。这种“合成”方法将使我们能够系统地改变 eDNA 长度、序列和浓度，并量化细胞在特定离子介质条件下对模型氧化物表面（例如带负电的二氧化硅和带正电的氧化铝）的附着。我们将探索如何使用原子力显微镜和荧光技术将 eDNA 排列在细胞表面和基质上，并且我们将探索使用突破光学分辨率衍射极限的方法，例如 SNOM（扫描近场光学显微镜），我们的知识，从未应用到这个领域。工程应用潜力巨大。我们预计几乎所有生物技术领域都有可能获利。我们建议通过将广泛的工程专家与项目团队聚集在一个沙坑中来评估这种前景，该沙坑将于项目结束前 3 个月举行。我们将举办为期 2 天的研讨会，展示我们的成果，并制定路线图，推动这一研究领域的发展和实际应用。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来评估在生物工程广泛领域的推广前景。