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Background The use of high quality human biological samples with associated data and their effective life cycle management (biobanking) are increasingly critical to our understanding of the underlying mechanisms of disease and the development of diagnostics. However, despite much progress, the inadequate supply of quality samples and the excessive complexity in the organisation of biobanks is hampering biomedical research. This is partly due to a lack of unified methods and approaches being applied across samples’ life cycle: acquisition, sample processing, storage, provision and use. Organisation Strategic Tissue Repository Alliances Through Unified Methods (STRATUM) is a public-private, 18-month project to provide building blocks for a national biobanking solution that facilitates biomedical research. The project is funded by the private sector and the government, via the Technology Strategy Board. There are six partners: two UK pharmaceutical companies (AstraZeneca, GlaxoSmithKline), a clinical diagnostic SME (Lab21) and the universities of Manchester, Nottingham and Leicester. A Project Steering Committee, with overall oversight of STRATUM has representatives from each partner, the MRC, the Royal College of Pathologists, British In Vitro Diagnostics Association and Patients. Operationally a Project Lead is responsible for the co-ordination and overall delivery of the project with Work Package leads focusing on specific areas. As biobanking is so broad in its application, one of the key factors for the success of STRATUM is to engage with the wide variety of disciplines and groups across both the public and private sectors, which have an interest in or could be impacted by the deliverables. This engagement is essential for the exploitation of STRATUM, from the delivery of the building blocks for biobanking, and thence enable benefits to be delivered across R&D and healthcare in general. As such, all deliverables from STRATUM will be the result of extensive consultation with experts and the public in the relevant areas, which will be enabled by a communication specialist. Aim and Objectives The aim of STRATUM is to facilitate the co-ordination of biobanking to support innovative research, in the UK by addressing the problems defined above. It will increase the effectiveness of sample provision to ensure that UK research institutions, pharmaceutical, biotechnology and diagnostic companies have the ability to access the large numbers of well-characterised samples with data, currently being held in individual collections. It will result in operating to agreed standards and a cost model for sample life cycle management. Ultimately, this approach should enable diagnostic companies, either singly or in partnership with pharmaceutical firms and research institutes, to develop companion diagnostics that are critical to delivering the personalised healthcare agenda. Scope and Deliverables To achieve this, STRATUM aims to define a framework of policy in biobanking, which will focus on governance, access, infrastructure and ethical principles for biobanking. This framework will be based on existing best practice and consensus across the diverse range of stakeholders involved in biobanking. Overall, the project focuses on: assessing public opinion ( biobanking and the use of samples); developing standards (for tissue sample characterisation and life cycle management); creating network requirements (biobank catalogue/directory); exploring financial arrangements (cost model); defining consent templates and enabling engagement (through two-way communication). The scope for individual work packages’ is outlined below: Public Engagement • To investigate the acceptability to donate samples and towards different models of consent for the use of samples, with the general public • To explore the attitudes, including barriers and drivers, within the NHS and biobanking community in collecting tissues samples The outcome of these findings will enable and help define the policy. Policy • To deliver a biobanking policy that provides the framework for governance, infrastructure and standards for human biological sample life cycle management across the UK; thereby enabling processes to be established that amongst other things enable increased visibility of sample collections (and unidentifiable data) with rules of access to facilitate equitable sharing of samples across the value chain and to provide assurance to donors that their samples’ use will be maximised. Sample Life Cycle Management Standards • To deliver standards for the life cycle management of respiratory and generic samples, including derivatives (acquisition, processing, storage, disposal) • To publish the standards with a process for their adoption and maintenance, with metrics for measuring compliance with the standards, to be able to improve sample quality and provide feedback for continuous improvement in HBS life cycle management Register for Samples/Minimum Datasets • To deliver a user requirements document for a system that will enable collections of samples with associated metadata to be registered and viewed via a single, secure, web-based user interface • To evaluate existing and proposed platforms and their operating environments against the user requirements and provide recommendations on how the user requirements can be implemented, defined in the STRATUM Exploitation Plan • To define the minimum datasets i.e. meta data/attributes that describe and characterise collections, donors and samples (respiratory and generic samples) to support the creation of a sample collection inventory (for use as a data in the register) and a histo-library of characterised samples, enabling researchers to identify samples and select them for research, in accordance with the consent • To pilot the recommended datasets for respiratory collections to inform the development of a register Cost Model • To increase understanding of the overall costs associated with biobanking, identify hidden costs, highlight organisational models that work, and explore relationships between key variables (e.g. funding mechanisms and optimal access arrangements). • The analysis aims to make the costs and benefits of coordinating biobanking nationally more explicit, in order to develop an ‘ideal’ cost-model for a national research infrastructure that will be defined in a report that will be taken forward to the exploitation strategy and plan for STRATUM Consent • To define consent templates that are consistent with the outputs of the public engagement and policy If you would like further information about STRATUM, please do not hesitate to contact: Julie Corfield (Areteva) at juliecorfield@areteva.com

Previous data from our laboratory generated by a former BBSRC-CASE funded PhD studentship in collaboration with DRs Mark Graham and Martyn Foster at AstraZeneca has demonstrated a role for the novel globin cytoglobin in lung physiology. A detailed immunohistochemical (IHC) analysis revealed that cytoglobin expression is up-regulated in regions of the lung that have become anoxic leading us to hypothesize that cytoglobin functions by acting as a 'buffer' between normal and hypoxic tissue and that its function in these regions is either to sequester molecular oxygen to prevent normal tissue becoming hypoxic or to metabolise ROS generated during ischaemic reperfusion. In support of this hypothesis, work by our and other laboratories demonstrate that in in vitro cell culture models over expression of cytoglobin affords protection from agents that induce both oxidative stress and hypoxia. In the current proposal we wish to expand upon these observations and investigate the fundamental biological role of cytoglobin in another important organ, the liver. We will map in detail the expression of cytoglobin expression in normal liver and use an in vivo rodent model system to investigate the adaptive physiological function of cytoglobin under conditions where normal liver homeostasis is oxidatively perturbed. A study of the adaptive changes of cytoglobin expression/location will be informative regarding the normal cellular function of cytoglobin. Specific regions of the liver will be targeted using: diquat (global), CCl4 (centrilobular) and allyl alcohol (periportal) respectively. Animals will be sacrificed and analysis of liver tissue by IHC, western blotting, laser capture micro-dissection and qPCR used to investigate and map the level and profile of distribution of cytoglobin expression. Time and dose-dependency will be investigated and cytoglobin expression related to other indices of adaptive changes of liver function (e.g, fibrosis, necrosis, apoptosis, 8-oxo dG formation). We will use this data to 'map' in detail the pattern of cytoglobin expression to areas of different liver physiology to test our hypothesis that cytoglobin induction occurs at the interface between normal and hypoxic tissue. These in vivo experiments will complemented by in vitro mechanistic studies aimed at identifying the function and regulation of cytoglobin at the cellular and molecular level. We will use primary rat hepatocytes as well as the rat liver cell line MHC1 to investigate if these hepatotoxic agents induce cytoglobin expression in vitro and whether over-expression or knock down by transfection or RNAi respectively modulates sensitivity of cells to the effects of these compounds and hypoxia. Parameters related to oxidative stress will also be assessed (e.g. cellular oxidative stress by FACS analysis with DCFDA and MitoSOX, glutathione and lipid peroxidation). We will also use reporter/promoter deletion analysis and EMSA-gel shift assays to identify key regions of the cytoglobin promoter sequence and transcription factors important for regulation of induction cytoglobin gene expression. Identification of these will further our understanding of the key signaling pathways involved in cytoglobin induction and contribute to an enhanced understanding of the fundamental biology of this new globin. In addition, there is evidence that cytoglobin through interaction with protein partners may be involved directly in cell signaling but this has not been investigated in rat hepatocytes. We will use yeast two hybrid and mass spectrometry approaches to identify novel protein partners of cytoglobin in hepatocytes.

We seek Follow-on funding to support the commercial and technical development of a prototype instrument suitable for the non-contact characterization and monitoring of pharmaceutical drugs, both during their research development stage, and their subsequent manufacture. Pharmaceuticals comprise organic compounds, which can adopt a variety of distinct crystal forms (called polymorphs). Each polymorph has a set of unique physical and chemical properties, and the identification of each polymorph is critical for the successful development and manufacture of pharmaceutical drugs, since each form can exhibit profoundly different properties (changing, for example, dissolution rate, bioavailability, and manufacturability). Techniques which allow the characterisation and quantitative analysis of polymorphic forms are therefore of fundamental importance to pharmaceutical companies.Existing techniques for the analysis of polymorphs currently being employed by the pharmaceutical industry each have significant limitations. These limitations can appear in the research phase of a drug, or in its subsequent manufacture. Raman spectroscopy typically shows only very limited spectral differences between drugs having similar chemical composition. Fourier transform infrared (FTIR) spectroscopy requires expensive and difficult bolometric detection, and furthermore is subject to significant thermal background radiation. While powder X-ray analysis is currently the gold-standard for polymorph discrimination, the machines are large, expensive, and take substantial time to obtain single spectra (typically hours). The ionizing nature of the radiation and slow acquisition times also make X-ray techniques unsuitable for on-line process monitoring. Potential solutions to these problems can be found in the technique of terahertz time-domain spectroscopy (THz-TDS), which is additionally and uniquely capable of penetrating packaging material.With Follow-on funding, we will develop and exploit an on-chip analysis prototype instrument based on THz frequency vibrational spectroscopy, but distinct from free-space THz spectroscopy. Our technology is capable of identifying, analyzing, and monitoring in real-time the composition and polymorphic form of pharmaceutical drugs. The background IP for our instrument was established in 2008, during the final stages of several EPSRC grants which funded the basic scientific research; the investigators proved an on-chip THz frequency analysis technology capable of distinguishing organic compounds by their spectral signature in the THz frequency range. The distinct absorption response which different pharmaceutical polymorphs show under THz illumination allows them to be distinguished easily.Compared with the existing technique of free-space THz-TDS in use by the pharmaceutical industry, our on-chip technology offers several substantial benefits to end-users:- It can determine the composition of much smaller samples (typically one-thousandth of the volume), owing to its high (<10 micron) spatial resolution, important in the classification and imaging of drugs with excipients.- It has enhanced frequency resolution (2 GHz, compared with ~40 GHz), vital in the discrimination between polymorphs at low temperatures during drug development.- It has the potential to be an order of magnitude cheaper, since it is compatible with low power (and low-cost) laser excitation.We will use our prototype instrument to characterize the absorption spectra of a number of targeted drugs, building up proving application data with which we will attract licensees over the course of the project. Our work will also build on the underpinning technical and commercial developments we have already made, and provide the necessary work to demonstrate direct application of our technology to the pharmaceutical industry.

The organisation and function of biological systems is based on compartmentalisation, where processes occur within small volumes rather in bulk solution. A simple example of a biological compartment is a cell, which itself can contain many smaller compartments. It is becoming increasingly obvious that confining reactions in this way can dramatically affect the mechanisms and products of biological and chemical reactions by changing the way that molecules interact with each other and their environment.This project will focus on one very important category of biological processes - biomineralisation - which is the formation of mineral-based structures such as seashells, bones and teeth. There is considerable interest in understanding how Nature controls crystallisation to produce materials of this type. Although biominerals are produced under mild reaction conditions, they often exhibit properties which can not only equal but actually surpass those of engineering materials such as concrete. The research in this proposal will investigate how confinement affects crystallisation, and how Nature exploits this to produce such remarkable materials. To-date, research directed towards understanding how Nature controls the formation of minerals has concentrated on the role of organic macromolecules. Further, although biomineralisation invariably occurs within restricted volumes, experiments aiming to mimic these processes are typically carried out in bulk solution. While organic molecules are certainly important, it is very likely that confinement also has a significant affect on these crystallisation processes. Indeed, there are many biogenic crystallisation phenomena, such as the precipitation of calcium phosphate crystals in collagen fibres during bone formation, which cannot be adequately described in terms of crystallisation from bulk solution. Initial work will focus on the precipitation of calcium carbonate and calcium phosphate in small volumes. The research programme will then be extended to investigate the effect of confinement on the crystallisation of a range of other minerals. While it is clear that confinement over a wide range of length scales can strongly affect crystal nucleation and growth, with the exception of freezing phenomena, these effects are poorly understood and as yet unpredictable. The research conducted will lead to a greater understanding of crystallisation in restricted volumes, and will therefore enable us to use confinement to control crystallisation, and to profit from it in synthetic systems. Indeed, there are many technological applications which rely upon crystal growth within constrained volumes such as the fabrication of nano-materials including nanowires and nanotube arrays, general templating processes, drug delivery systems and implants. Crystallisation in confinement is also widespread in Nature, and in addition to biomineralisation processes, includes events such as weathering and frost heave - which occur with great cost to civil engineering the environment and technology. The proposed research is clearly of great relevance to both fundamental research and technology across many disciplines.