Facilities

Facilities

The University of Manchester boasts a considerable research infrastructure, which can be accessed through collaborations with Academic and Academic-Clinical Staff. The infrastructure presented here serves as an example of what collaborations with The University of Manchester can provide clinicians wishing to expand their research into Regenerative Medicine.

BioAFM ¦ Bioimaging ¦ Bioinformatics ¦ Biomolecular Analysis ¦ DNA Sequencing ¦ Electron Microscopy ¦ Fast Reaction ¦ Flow Cytometry ¦ Genomic Technologies ¦ Histology ¦ Macromolecular Crystallography ¦ NMR Facility ¦ Protein Expression

BioAFM

High resolution AFM imagingThe BioAFM Facility offers Atomic Force Microscopy (AFM) imaging and micro/nano-mechanical characterisation capabilities to The University of Manchester and the wider scientific community. The Facility, which currently houses 3 atomic force microscopes, specializes in analysing soft, biological-related materials, although staff have experience of a wide-range of specimen types.

You can find more information about this facility on the BioAFM Facility webpages.

Enquiries: Dr Nigel Hodson ¦ Email: nigel.hodson@manchester.ac.uk ¦ Tel: +44 (0)161 275 5443 / 7054

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Highlights and achievements

The BioAFM Facility has contributed to a number of high impact publications.

Equipment

  • Bruker Multimode 8
  • Bruker Catalyst (mounted on a Nikon Eclipse Ti inverted light microscope)
  • Asylum Instruments/Oxford Instruments MFP3D

Services

The facility is primarily used for the imaging of soft (especially biological) material. However, the facility staff are happy to discuss individual requirements for all sample types. Please contact us for details.

  • A comprehensive service including advice on sample preparation, experimental design and assistance with data analysis
  • Full training and support provided by experienced staff

Bioimaging

A mitotic HeLa cell following deconvolution on the delta vision microscope with its chromasomes labeled in blue, spindle microtubules in green and its kinetochores in red. Image supplied by Mailys Vergnolle (FLS)

The Bioimaging Facility offers state-of-the-art imaging equipment to all members of the Faculty, the University and beyond. There are over 16 different microscope systems, so if you have a project that requires imaging we should have a system to meet your specifications.

Enquiries: Dr Peter March ¦ Email: peter.march@manchester.ac.uk ¦ Tel: +44 (0)161 275 1571

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Highlights and achievements

The Bioimaging Facility has contributed to a number of high impact publications including Genes and Development and Nature. We have also a number of collaborations with other imaging facilities around the country and have close working relationships with many of the microscope and imaging companies. We run regular imaging workshops for Life Sciences’ members and also host workshops, in collaboration with the microscope companies, for external users.

Equipment

  • Leica SP5 inverted
  • Leica SP5 upright
  • Leica SP2 inverted
  • Nikon C1 upright
  • Nicon C1 inverted
  • API Delta Visions
  • Leica AS MDW
  • PALM laser
  • BD Pathway
  • Roper widefield
  • Widefields
  • Bioluminescence
  • Off-line image analysis

Services

The Bioimaging facility has three full time members of staff that are able to assist you in all areas of your imaging project from design through to image processing and analysis. Before you begin your project we encourage you to discuss your requirements with us and we can advise you on your protocols and which system to use. We then provide full training on all of the systems and offer continued support right through the project.

Bioinformatics

Desktop PCThe Bioinformatics Facility provides bioinformatics expertise to the Faculty of Biology, Medicine and Health. It brings together experts in genomics analysis, as well as providing data management support. The facility also supports analytical software for genomics analysis.

Enquiries: Dr Leo Zeef ¦ Email: leo.zeef@manchester.ac.uk ¦ Tel: +44 (0)161 275 1482

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Highlights and achievements

Since its inception in 2006 the facility has contributed to a number of publications in a broad range of journals. In 2012 a local Galaxy server was created, part of the facility’s efforts to provide services and training enabling University Biologists to analyse their own data.

Services

The Bioinformatics facility comprises five full-time members of staff. Users are encouraged to discuss their requirements in advance, which allows us to assist in the design of experiments so as to provide the most effective data analysis at the end of the project. While our primary role is to work with the Genomic Technologies Core Facility, we also work directly with researchers throughout the University to help with the integrative analysis of their genomic datasets. Data management support is also offered in the form of optimising and automating routine tasks.

Biomolecular Analysis

biomolThe Biomolecular Analysis Facility is a state-of-the-art resource for the identification of proteins and the subsequent investigation of their size, shape and interactions.

Enquiries:

Dr Tom Jowitt (Biomolecular Analysis) ¦ Email: t.jowitt@manchester.ac.uk ¦ Tel: +44 (0)161 275 1561

Dr David Knight (Mass Spectrometry) ¦ Email: david.knight@manchester.ac.uk ¦ Tel: +44 (0)161 275 1561

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Highlights and achievements

The Biomolecular Analysis Core Facility is one of the largest of its kind in the country. It contains 16 complimentary analysis systems (9 biophysical and 7 mass spectrometric) supported by high resolution electrophoretic and chromatographic micro separation systems. The five dedicated facility staff provide service support for the most popular applications as well as developing and establishing new methodologies using the equipment. Recent publications using data created within the facility include ones in Nature and Journal of Cell Science.

Equipment

  • Analytical ultracentrifugation
  • Calorimetry
  • Circular dichroism (CD)
  • Fluorescence spectroscopy
  • HPLC
  • Mass spectrometry
  • Multi-angle light scattering
  • Surface plasmon resonance

Services

The facility has been set up to promote and facilitate the use of biomolecular analysis techniques in the Faculty. There are a number of different modes of interaction with the facility including tailored project advice, full service provision, project work involving facility staff and supported instrument access.

DNA Sequencing

dnaThe DNA Sequencing facility provides high quality, high throughput sequence data to the entire campus of the University of Manchester and beyond. The facility operates two primary platforms: a 48 capillary ABI 3730 Genetic analyser for Sanger sequencing, and a Roche 454 GS Junior+ for metagenomic analyses and related next-generation sequencing projects. The facility additionally offers human cell line authentication and mycoplasma testing of cell lines.

Enquiries: Paul Fullwood, Graeme Fox, Fraser Combe ¦ Email: dnasequencing@manchester.ac.uk ¦ Tel: +44 (0)161 275 4867

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Highlights and achievements

The Sequencing facility processes thousands of samples per week, contributing data to hundreds of projects from the Faculty of Life Sciences, the Faculty of Medical and Human Sciences and further afield. Both Sanger sequencing and Roche 454 pyrosequencing can provide read lengths of >1000bp. Sequencing facility staff are on hand to provide troubleshooting, sequencing advice, and assistance with sequence data analysis.

Equipment

  • ABI 3730 DNA analyser
  • Roche 454 GS Junior+
  • Agilent 2100 Bioanalyzer
  • Beckman Coulter Biomek 3000
  • Eppendorf Epmotion 5075
  • NanoDrop ND-1000
  • Qubit 2.0 Fluorometer
  • ABI Genemapper software

Services

The Sequencing facility offers two levels of Sanger sequencing: pre-mixed samples and load-only samples. Pre-mixes are a mix of primer and template to be sequenced and processed at the facility, whilst load-only samples have been pre-sequenced, precipitated to a dry pellet and delivered to the facility to be loaded onto the sequencer. The facility also offers genotyping services (eg. microsatellite, TRFLP analysis), human cell line authentication (STR analysis) and PCR-based mycoplasma testing.

Long-read next-generation sequencing can typically provide >150 000 reads in a single run. Read lengths of up to 1100bp in a single read (not paired-end) are readily achievable. The Roche 454 GS Junior has proven to be ideal for metagenomics projects, which benefit from this long read length providing enhanced coverage of the gene of interest.

Please contact the sequencing facility directly for information on sample preparation and delivery.

Electron Microscopy

TEMThe facility houses five electron microscopes, a comprehensive preparation
laboratory which includes a range of specialised sample preparation equipment, a
photographic dark room, digital imaging facilities and a suite of computer
workstations for image processing. The facility is staffed by a manager, an
experimental officer and two experienced microscopists.

Enquiries: Dr. Aleksandr Mironov ¦ Email: aleksandr.mironov@manchester.ac.uk ¦ Tel: +44 (0)161 275 5645

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Highlights and achievements

The facility is actively involved in a wide range of research topics across the faculty and in the past few years has contributed to over 50 scientific publications in high profile biological journals including 22 publications where EM staff members were authors. EM staff are available to train and assist both staff and students in all aspects of electron microscopy and is regularly involved in the promotion of electron microscopy to schools and colleges through talks and hands on demonstrations.

Equipment

  • FEI Polara 300kV FEG transmission electron microscope with postcolumn energy filter
  • FEI Tecnai12 BioTwin transmission electron microscope
  • FEI Tecnai12 Twin transmission electron microscope
  • Leica EMpact high pressure freezing equipment
  • Reichert Jung Ultramicrotomes and Leica Cryo Ultramicrotomes
  • Miscellaneous TEM, cryo TEM and SEM sample preparation equipment
  • High resolution large format digital film scanner
  • Baltec high pressure freezing equipment

Techniques

Techniques routinely available in the facility include embedding, sectioning and staining, negative staining and immuno-labelling. Additionally, the facility has expertise in the specialist techniques of cryo-sectioning, quantitative STEM mass mapping, single particle image analysis, 3D reconstruction using electron tomography or serial sections.

Fast Reaction

Laser flash photolysis apparatusThe Fast Reaction facility consists of a suite of fast reaction kinetic
instrumentation for the measurement of chemical reactions on the nanosecond to
millisecond timescale. The kinetics equipment is located in state-of-the-art
laboratories within the MIB,
adjacent to the wet laboratories of the Molecular Enzymology Group on floor 3.
To support the fast reaction kinetic measurements we have a number of peripheral
instruments including spectrophotometers, CD machine, fluorimeters, and
potentiometry apparatus. A number of our instruments are maintained in anaerobic
glove box environments.

Enquiries: Dr Derren Heyes ¦ Email: derren.heyes@manchester.ac.uk ¦ Tel: +44 (0)161 306 5159

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Highlights and achievements

The facility offers state-of-the art equipment, which can be used to study many different types of reactions from the nanosecond through to minute timescales. The facility is actively involved in a wide range of research topics and has contributed to a number of publications in a broad range of journals. We are available to train and assist both staff and students in all aspects of fast reaction work.

Equipment

  • Several conventional stopped-flow rapid mixing instruments with absorption, fluorescence, polarisation and diode array detection systems.
  • Laser flash photolysis apparatus, comprising a ‘tunable’ Nd YAG laser system, with absorption, fluorescence and diode array detection.
  • T-jump equilibrium perturbation instrument.
  • High Pressure stopped-flow instrument with absorption, fluorescence and diode array detection.
  • Cryogenic stopped-flow instrument with absorption, fluorescence and diode array detection.
  • Magnetic field effect stopped-flow instrument with absorption, fluorescence and diode array detection.
  • FTIR stopped-flow machine

Services

The facility has been set up to promote and facilitate the use of fast reaction techniques, mainly for the study of enzyme-catalysed reactions. All users are encouraged to discuss their requirements in advance to allow us to advise on the type of experiments that are most suitable for a particular project. We provide full training for new users to ensure safe and proper use of all instrumentation and can provide further support and instruction, depending on the level of user competence.

Flow Cytometry

Forward versus side scatter.As the original high content analysis technique, flow cytometry is an essential tool for cellular analysis. A flow cytometer has the ability to make multiple measurements on individual cells and to do that on thousands of cells per second, which can reveal the heterogeneity in cell populations hidden by other techniques.

On flow cytometers with the “sorting” capability, it is possible to go beyond analysis of the sample and physically separate out particular cell populations for further analysis by other techniques, or to put them in to culture.

Enquiries: Mr Mike Jackson ¦ Email: m.c.jackson@manchester.ac.uk ¦ Tel: +44 (0)161 275 5468

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Equipment

  • Beckman Coulter Cyan ADP
  • BD Bioscience FACSAria

Services

  • Beckman Coulter ADP Analysis: 488, 633 & 405nm lasers for excitation, 8 fluorescence detectors
  • FACSAria Analysis: 488, 633 & 592nm excitation, 9 fluorescence detectors
  • Sorting: In to tubes (1.5ml, 5ml, 15ml), multiwell plates and on to slides

Genomic Technologies

genomeThe Genomic Technologies Core Facility (GTCF) is housed in purpose built laboratory space in the Michael Smith Building. Funded largely from grants from the Wellcome Trust, the Facility was established to provide access to cutting-edge post-genomic technologies.

The Facility supports five main technology categories, namely:

  • Digital nucleic acid analyses (NanoString nCounter Analysis System)
  • Next-generation sequencing
  • Affymetrix GeneChip Microarrays
  • Real-time PCR instruments
  • RNAi library screening

Also, we have extensive liquid handling and automation capacity, together with instrumentation for quantification and sample QC. The facility operates in close association with the bioinformatics core facility to facilitate a complete service from experimental design through to bioinformatic analyses.

Enquiries: Dr Andy Hayes ¦ Email: andy.hayes@manchester.ac.uk ¦ Tel: +44 (0)161 275 1589

Histology

CellThe Histology Facility provides the equipment and technical support for
producing high quality tissue sections for microscopy. Handling of tissue prior
to histology is a key step in obtaining good data. We provide advice and
protocols on the best methods for tissue preparation, preservation and
processing in order to achieve the best from your samples.

Enquiries: Mr Peter Walker ¦ Email: peter.walker@manchester.ac.uk ¦ Tel: +44 (0)161 275 1476

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Highlights and achievements

Histology supports a wide range of research projects within the Faculty across most research groups. Our state-of-the-art facility is housed within the AV Hill Building and provides advice, training and support for all histological procedures from tissue/cell acquisition through processing, sectioning, staining (including standard histological, immuno and in situ protocols) and imaging. For high end imaging and analysis we refer you to the Bioimaging facility.

Equipment

  • Automated tissue processor: Shandon Citadel 2000
  • Wax embedding station: ThermoShandon Histocentre2
  • Automated microtome: Leica RM 2155
  • Manual microtome: Microm HM 330
  • Vibratome: GS series 1000 classic
  • Manual cryostat: Shandon AS260
  • Automated staining: ThermoShandon Varistain 24-4
  • A Microm HM560 automated cryostat
  • A Microm automated tissue processor
  • A Microm wax-embedding station
  • 2 Microm HM355s automated microtomes
  • A Thermo Shandon Linistain GLX stainer (for H&E staining)

Services

The facilities cover the preparation and processing of tissues, their cutting/sectioning and staining. The labs house modern equipment, much of which is fully or partially automated. Our equipment supports both paraffin-embedded and frozen cryo sectioning, making both these processes as easy as possible within a friendly and helpful environment.

Macromolecular Crystallography

xrayThe high level of detailed insight and understanding of macromolecule structure and function offered by crystallography is undoubtedly unparalleled and underpins much of our present understanding of life at the cellular level.
Located in the Manchester Interdisciplinary Biocentre (MIB), the Macromolecular Crystallography Facility contains state-of-the art instrumentation that supports the structural biology groups within the Faculty and offers a dedicated crystallisation and crystal characterisation service. Inquiries from other Faculties and external organisations are encouraged.

The Facility acts as a focal point for diverse crystallographic structural studies throughout the Faculty. User interaction is encouraged and hence knowledge sharing is at a premium. A formal ‘structuring’ service is available. Support and instruction is continually provided depending on level of user competence.

Enquiries: Dr Colin Levy ¦ colin.levy@manchester.ac.uk ¦ Tel: +44 (0)161 275 5190

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“…crystal structures are crucial to our interdisciplinary programs focusing on enzyme mechanism and catalysis. The MPSF has, and continues to play a major role in structure determination in our programmes on enzyme catalysed H-transfer, cofactor chemistry and in developing physical models for catalysis.”

Professor Nigel S. Scrutton

Professor of Molecular Enzymology

X-Ray crystallography utilises X-ray diffraction by single protein crystals to elucidate three dimensional structures at atomic resolution. The technique plays a pivotal role in understanding how individual amino acids interact with small molecule ligands and cofactors.

The MPSF (Manchester Protein Structure Facility) provides a complete service pipeline, taking you from purified protein to crystal structure. The MPSF is serviced by two full time senior experimental officers. Expert users can gain access to the facility equipment, whilst non experts are offered a complete service pipeline for structure elucidation.

Meeting the often rate limiting challenge of crystallogenesis are two complimentary high throughput nanolitre dispensing robots (Mosquito & Phoenix) allowing rapid screening and optimisation. The facility also houses two rotating anode X-ray generators and associated data collection equipment. These in-house facilities are further supplemented with regular synchrotron access.

All services and equipment are available to both University of Manchester researchers and external users (academic & commercial).

Enquiries

Dr Colin Levy ¦ colin.levy@manchester.ac.uk ¦ Tel: +44 (0)161 306 5185

Highlights

The facility is actively involved in a wide range of research topics across several faculties and has contributed to a number of publications in a broad range of journals.

Services

The standard access point to the MPSF is purified protein, however technical support can be provided to help you achieve this goal. If you are thinking of determining a crystal structure then the time to talk to the MPSF is now.

The MPSF provides an efficient and streamlined approach to protein crystallography. Complete crystal growth, characterisation, data collection and subsequent structure determination services are available.

For assistance with Protein Production

Dr Edward McKenzie | edward.a.mckenzie@manchester.ac.uk | +44 (0)161 257 5617

For assistance with Biomolecular Analysis including MALS analysis

Dr Thomas A. Jowitt | thomas.a.jowitt@manchester.ac.uk | +44 (0)161 306 5176, Email:

Equipment

Crystallogenesis

To meet the challenge of this rate limiting step two complimentary robotic systems (Mosquito & Phoenix) enable the rapid and reproducible creation of crystal trials. Both capable of nanolitre dispensing, broad screening and optimisation experiments are rapidly carried out consuming minimal quantities of protein.

Experimental crystallisation plates may be incubated at a variety of temperatures in either a dedicated cold room housed within the facility or using one of two incubators. More sophisticated temperature screening is available through the use of two TG-40 temperature control units.

A Belle Technology glove box provides an anaerobic environment for all aspects of crystallogenesis and sample preparation. Samples grown under anaerobic conditions can be cryocooled within the box prior to transfer for diffraction data collection either in-house or at a synchrotron facility.

Plates are inspected using one of three Nikon SMZ 1000 microscopes (2 with camera facilities) or with an Art Robbins CrysCam visualisation system. An aditional Nikon SMZ 1000 microscope is located within the cold room for inspecting temperature sensitive samples.

Microspectrophotometry

A microspectrophotometer from 4DX Systems AB is available to acquire absorption spectra measurements from single crystals in the UV-VIS-NIR spectral range. A dedicated Oxford cryosystems cold head allows exquisite temperature control at the sample. The cold head is fitted with an in-house designed cryo shutter allowing flash freezing for cryo trapping experiments.

X-Ray Diffraction

The facility houses both a Bruker Microstar microfocus X-ray source and a Rigaku Micromax 007. In addition to the exceptional flexibility this dual setup affords us, we are able to exploit the Rigaku vertical Phi arrangement to couple the 4DX microspec system directly into the X-Ray setup allowing X-ray and spectroscopic data collection from a single crystal.

NMR Facility

nmrWe can help with advice on the type of NMR experiments that will be most suitable, appropriate and informative for a particular project, and provide help with setting up experiments and training for regular NMR users.

Enquiries: Dr Matthew Cliff ¦ Email: matthew.cliff@manchester.ac.uk ¦ Tel: +44 (0)161 306 5179

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Equipment

Housed at the MIB, the Faculty has both state-of-the-art very high magnetic field strength instruments, and more economical lower field instruments. All are designed for solution measurements.

  • 800 MHz Bruker four-channel liquid-state spectrometerThis new instrument represents an important step change in the applicability of new NMR experimentation developments providing high-resolution, three-dimensional structures and dynamical properties of membrane proteins, complex carbohydrates, nucleic acids and protein-protein complexes, and maps their macromolecular interactions. The probe on this machine has cryo-cooled carbon and proton coils, providing very high sensitivity measurements, which in turn allows measurements of more complex systems with higher molecular weights.
  • 600 MHz Bruker DRX four-channel liquid-state spectrometerEquipped with a high sensitivity TXI cryoprobe with cooled proton channel.
  • 500 MHz liquid-state 5-channel NMR spectrometerEquipped with a high sensitivity proton/fluorine cryoprobe. Fluorine NMR provides additional information to the standard nuclei set of 1H, 13C and 15N.
  • 400 MHz NMR spectrometerCarbon and proton detection for small molecule work. This is a walk-up service spectrometer for determining the results of chemical syntheses.

Protein Expression

proteinexpThis core facility provides a comprehensive resource for the production of
recombinant proteins. Currently we offer a choice of three expression systems:
bacteria, insect and mammalian cells. Depending on particular needs we are able
to provide either small scale production facilities for biochemical analysis and
antibody production or larger scale production for structural studies.

Enquiries: Dr Edward McKenzie ¦ Email: edward.a.mckenzie@manchester.ac.uk ¦ Tel: +44 (0)161 275 5106

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Highlights and achievements

The Protein Expression facility has been developed following the success of a one
year pilot project within the Faculty. One of these pilot projects has already
contributed to a Biochemical J. publication on the phosphoregulation of human
Mps1 kinase.

Services

  • High level expression and scale-up production of recombinant proteins
  • Protein purification
  • Cloning service
  • Troubleshooting service
  • In-house R&D vector design
  • Vector DNA and E.coli strain bank
  • Training courses

GMP Compliant Manufacturing Capability

The University of Manchester Cleanroom Facility provides researchers with the ability to translate their Regenerative Medicine research from bench to bedside, offering GMP expertise and training, technology transfer, scale up and validation for projects.