BioEngineering from first principles.

Lead Research Organisation: University of Sheffield
Department Name: Kroto Research Institute

Abstract

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.

Planned Impact

The main area of impact will be economic and commercial. However, due to the broad potential for application in areas such as environmental remediation, water technology and medicine, there is strong potential for long-term social impacts through a cleaner environment, better drinking water quality and advances in healthcare, and through better scientific evidence to inform and develop government and company policy in these fields. There will be specific areas of impact achieved on much shorter time-scales; potentially within 1-3 years of the start of the Feasibility Account. Ongoing activities that we will draw on from the very beginning are current links with commercial partners. These include Maersk Oil and Gas, Accelerys (computational chemistry software), JEOL, Proctor and Gamble, and the Pfizer Institute, Cambridge U. Results on cell attachment will be of interest to these companies in the area of hydrocarbon and process water pipeline biofouling, bioprocessing, computational chemistry methods and advanced microscopy techniques. Computational methods and results will also be of immediate interest for software development and testing on cell and macromolecular chemistry. Additional activities are through a Knowledge Transfer Manager (KTM) for Water who is affiliated with the TSB Knowledge Transfer Network for Environmental Sustainability. Results on mechanisms and controls on cell attachment and biofilm formation will be of interest to water utilities and their supply chain involved in biofouling, process engineering and water quality We have recently been awarded U. Sheffield cross-faculty seed funding to translate work on biomolecule binding on surfaces to understand how cells adhere to scaffolds and skin and to develop new biological glues for tissue engineering. This Feasibility Account will be able to contribute important molecular understanding and data for this translation into medical application. Investigators also currently hold a proof-of-concept award from the Northern 8 (N8) Universities to assess with the potential for delivery of functionalised colloid particles to soil. Understanding the bio-uptake of nanomaterials by soil microbes and plant roots will draw on the concepts and data developed in the Feasibility Account on cell-surface interactions. There are number of mechanisms to achieve longer-term impact. We are already linked to the KTN for Environmental Sustainability. We will raise awareness of our expertise and its promise for commercial impact, via the KTN web portal, potentially through KTN-affiliated training activities, and via the KTN monthly newsletter to its membership. This same approach will be used via the full range of KTNs; specifically targeting those for Biosciences, Chemistry Innovation, Health Tech and Medicines and Industrial Mathematics. We have a track record in providing Continuing Professional Development training via our industry-facing MSc courses, and we will target these for impact delivery in computational methods, potentially as stand-alone training or contributing content to a broader course. The U. Sheffield KTA provides access to a Knowledge Exploitation Manager and KT mechanisms that include the Development Hot House for short-term commercial feasibility studies, Proof-of-Concept funding to take a an approach or product further towards market, the possibility to bid for KTA Industrial Fellowship funding, for outgoing/incoming secondment of from/to the university with a commercial partner. Starting with current partners, will identify commercial partners to help develop and steer future research funding applications. This is to establish strategic partnerships that design impact pathways from the very beginning. The long-term result of this approach is the establishment of a strong and highly innovative university-industry community that will help develop and join future major bids such as programme grants and EPSRC strategic partnerships.

Publications

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Li M (2012) Single cell Raman spectroscopy for cell sorting and imaging. in Current opinion in biotechnology

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Stennett M (2012) Crystal structure and non-stoichiometry of cerium brannerite: Ce0.975Ti2O5.95 in Journal of Solid State Chemistry

 
Description The outputs from this project have not yet been exploited beyond academic beneficiaries although identifying potential exploitation was completed in a project Sand Pit event in May 2012. The analysis of potential exploitation with specific industry partners will take place through an industry Knowledge Transfer event as the main KT activity of the EPSRC Programme Grant on Hard-Soft Interfaces led by PI Prof John Harding at U. Sheffield. This Feasibility Account project was directly affiliated to the programme grant as an exploratory project to develop a step-change in the biological component of the programme grant. The KT event for the EPSRC programme grant is in the planning stage with the Prof Harding and input from Prof Banwart who led this Feasibility Account project. The KT event will run during 2015.