OCISBOxford Centre for Integrative Systems BiologyUniversity of OxfordNew Biochemistry Building
University of Oxford
South Parks Road
Oxford OX1 3QU

Tel: +44 (0)1865 613300
Fax: +44 (0)1865 613338
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Services & Software

Light Microscopy

  • The Systems Centre houses two state-of-the-art commercial Nikon microscopes - a TE2000 TIRF microscope and an A1 confocal/TIRF microscope - which are used for high sensitivity analysis of fluorescent proteins in bacterial cells. Access to these systems is available for collaborative projects, and in the first instance contact should be made through Dr. George Wadhams


Advanced single-molecule fluorescence imaging

  • The Systems Centre also has use of bespoke home-built microscopes which are optimised for imaging single fluorescent protein molecules in functional living cells. This includes ultra-sensitive multi-colour illumination modes such as total internal reflection fluorescence (TIRF) with high-speed fluorescence recovery after photobleaching (FRAP) capability. Real-time polarization and super-resolution imaging through photoactivated localization microscopy (PALM) are currently being developed. Interested users should investigate the Leake group web pages in the first instance. Access to these optical systems is via collaboration with Dr. Mark Leake


Dunn School Bioimaging facility

  • The Bioimaging facility in the Dunn School of Pathology has a range of light microscopes and both a TEM and an SEM.
    The light microscopes include a number of standard Zeiss instruments for conventional and fluorescence imaging of both fixed and live cells, as well as several Zeiss confocal instruments (LSMs). There are two 510 meta instruments and two Pascal microscopes. For both types of LSM there is a standard upright instrument for fixed cell work as well as an inverted microscope with a constant temperature/CO2 chamber for live cell imaging. The inverted 510 system includes the 5Live fast capture acquisition set-up.
    The EM facilities consist of an FEI Tecnai T12 120 kV TEM with the tomography acquisition software and a JOEL JSM-6390 SEM. The EM lab also has a range of preparatory equipment. There are 2 ultramicrotomes: one for cutting standard resin sections and another for cutting ultrathin frozen sections. There is also a Leica high-pressure freezer and an automatic freeze substitution system. We also have an Edwards vacuum coating unit capable of carbon coating, glow discharging or plasma etching samples as well as a rotary shadowing set-up. For SEM there is an automatic critical point dryer and a sputter coater.

    In the first instance anyone interested in using the Bioimaging facility should e-mail michael.shaw@path.ox.ac.uk.
    There is also a website that can be accessed from the Dunn School web page. On the website there are a number of standard protocols, instrument instructions and other information.


Multi-scale mathematical modelling and simulation

  • Problems in systems biology are intrinsically multi-scale, with processes occurring on many disparate spatial and temporal scales. We are developing a multi-scale framework for modelling such biological systems in which cells are modelled as discrete interacting entities, coupled to processes occurring on the tissue and sub-cellular levels.
    The multi-scale framework is implemented in an open source software library known as Chaste. This software library consists of object orientated C++, developed using an agile development approach.
    All software is tested, robust, reliable and extensible.


Proteomics facility

  • The Central Proteomics Facility at the Sir William Dunn School of Pathology can provide access to DIGE (Differential In-Gel Expression) apparatus, though DIGE is not provided as a service. This technique allows the quantitative comparison of up to three protein samples on a single 2D gel using size and charge-matched, spectrally resolvable CyDye fluors. Analyses can be extended across multiple gels by using a common control sample which allows the implementation of complex experimental designs. The DIGE system is highly sensitive (considerably more sensitive than silver staining), and will resolve several thousand proteins. 2D Gel tanks are located in the Sir William Dunn School of Pathology, while a Typhoon scanner and spot picking robot are located in the The Henry Wellcome Building for Gene Function, Department of Physiology, Anatomy and Genetics. Decyder analysis software can be accessed remotely. There are experienced users who are producing good results and can be consulted for advice.

    Please contact Neil Portman at the Dunn School in the first instance.


Biophysical Instruments

  • The Biophysical Instrument Suite, 00.073 New Building, was organised by the department and STRUBI and was initially funded by the Fell Fund. The Suite brings together equipment from various sites to one location in New Biochemistry and has an on-line booking system and charges for routine maintenance and servicing.
    Free training courses for the most popular techniques are organised for new post graduate researchers and technique specific user-groups allow informal presentation and discussion of results within the department. The instruments available include:
    • Biacore T100 surface plasmon resonance
    • Biacore 2000 surface plasmon resonance
    • Microcal VP-isothermal calorimetry
    • Perkin Elmer fluorimeter
    • Micromass LCT ESI TOF mass spectrometer
    • Beckman XL-I analytical ultracentrifuge
    • Beckman XL-A analytical ultracentrifuge
    • Viscotek dynamic light scattering
    • JPK Nanowizard atomic force microscope
    • Jasco circular dichroism spectrometer
    • Stratagene MC3005 real time PCR for thermofluor assays
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