Discovery Science

 

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Purification, production and quantification of small molecules, macromolecules, proteins, peptides & recombinant proteins

University of Leeds:

University of Liverpool, GeneMill:

University of York:

Laser Capture Microdissection

Isolation of cells from tissue sections

Durham University:

University of Manchester:

University of York:

 

Flow Cytometry

Rapid measurement of fluorescently labelled cells. Common applications include immunophenotyping, cell cycle analysis, proliferation, apoptosis, live/dead assays and expression analysis. This technology can also be used to separate out individual cells of interest to give pure populations for further analysis.

Durham University

University of York

University of Leeds

 

Microinjection

Direct manipulation of single cells

Durham University

 

Live Cell Imaging

The study of live cells in real time in a controlled environment

Durham University

University of York

University of Liverpool

University of Manchester

Bioinformatics, full systems biology, big data research, Multi-omics data integration, Statistical analysis and modelling, Machine learning, Pathway analysis and biomarker discovery, Protein structure modelling, Functional inference and redesign, custom bioinformatics pipelines, study design and power analysis

Liverpool:

Phytotrons/Growth Cabinets

Durham University:

  • Contact: Marc Knight (m.r.knight@durham.ac.uk)
  • Facilities: Arctic and tropical temperatures to be set with variable CO2 levels and light intensities and wavelengths.

University of Leeds:

University of Sheffield:

  • Website: https://www.sheffield.ac.uk/sustainable-food/about/facilities 
  • Facilities: 43 individual units are independently able to simulate the majority of terrestrial environments from Tropical to Polar regions as well as past and future global atmospheric environments including elevated and sub-ambient CO2 equipped with the very latest technologies and the ability to track worldwide weather stations. Recent adoption of cutting edge LED lighting allows researchers to simulate a wide-range of lighting conditions. By controlling the Red:FR ratio of the light, researchers are able to accurately mimic natural sunrise and sunset conditions, and promote shading responses. The LED bars allow high light intensities up to 1000umol m-2 s-1 to be achieved

University of York:

University of Manchester:

  • Contact: Prof David Johnson; david.johnson-2@manchester.ac.uk
  • Facilities: Numerous controlled cabinets providing CO2 manipulation and 13CO2 pulse labelling of whole plants

Lancaster University:

  • Contact: Growth Facility Manager Maureen Harrison; m.harrison@lancaster.ac.uk; +44 (0)1524 593199
  • Website: https://www.lancaster.ac.uk/lec/research/research-facilities/
  • Facilities: 10 walk-in growth rooms and six high-specification growth chambers (Snijder Scientific Microclima 1750) provide a range of controlled environments. Detailed investigation of plants and many other organisms require that experiments are performed in precisely controlled environmental conditions, for example, temperature, day length, light intensity, humidity etc.

 

Glasshouses

Durham University:

  • Contact: Marc Knight (m.r.knight@durham.ac.uk)
  • Facilities: Transgenic glasshouses with individually controlled compartments and cabinets and a wide variety of growth rooms that can be customised for plant pathogen studies.

University of Manchester:

  • Contact: Prof Giles Johnson; giles.johnson@manchester.ac.uk
  • Facilities: New £2M state-of-the-art glasshouses comprising modular growth spaces and high-tech environmental control at the Firs Experimental Gardens

University of Leeds:

University of Sheffield:

  • Website: https://www.sheffield.ac.uk/sustainable-food/about/facilities 
  • Facilities: The Arthur Willis Environment Centre: The facility provides a state of the art ‘Grodome’ in which 16 discrete units can be used to simulate plant growth conditions for different regions around the globe, as well as future climate scenarios. It contains dedicated laboratory, office and meeting room space to enable researchers to investigate the wide variety of environmental challenges facing the planet. The cooling/heating system allows the creation and maintenance of specific environmental conditions, allowing researchers to investigate the impact of present and future climate change.

University of York:

Lancaster University:

  • Contact: Growth Facility Manager Maureen Harrison; m.harrison@lancaster.ac.uk; +44 (0)1524 593199
  • Website: https://www.lancaster.ac.uk/lec/research/research-facilities/
  • Facilities: 10 walk-in growth rooms and six high-specification growth chambers (Snijder Scientific Microclima 1750) provide a range of controlled environments. Detailed investigation of plants and many other organisms require that experiments are performed in precisely controlled environmental conditions, for example, temperature, day length, light intensity, humidity etc.

Crystallography

Durham University:

  • Contact: Ehmke Pohl (ehmke.pohl@durham.ac.uk)
  • Facilities: High-throughput nanoliter crystallization experiments are offered, as little as 50 µl of sample are needed to setup 192 crystallization experiments. Crystals as small as 50 µm can be tested and may be suitable for structure determination. Crystallization and structure determination of novel biological macromolecules as well as the structure and solutions of known proteins with novel ligands and/or inhibitors.

University of Leeds:

 

NMR

Nuclear magnetic resonance

University of Leeds:

University of Liverpool:

Genome Editing

Crop transformation and genome editing using CRISPR/Cas9 system/ TALENs

Durham University:

  • Cunjin Zhang; cunjin.zhang@durham.ac.uk
  • Crops: rice, wheat & tomato
  • Facilities: Rice transformation: Full service: Provide R0 plants or R1 seeds, PCR to confirm the existence of marker gene and gene of interest, Realtime PCR to detect gene copy number for R0 plantlet. Basic service: Provide R0 transgenic plants, PCR to confirm the existence of marker gene and gene of interest. Protocols: Modified from Nature Protocol (YukohHiei, 2008) Plasmids: pIPKb002 for overexpression and pIPKb027 for RNAi (From Prof JochenKumlehn, Leibniz Institute of Plant Genetics and Crop Plant Research, Germany). Rice variety: Nipponbareor Kitaake. Duration: 5-7months. Wheat Transformation: Full service: Provide R0 plants or R1 seeds, PCR to confirm the existence of marker gene and gene of interest, Realtime PCR to detect gene copy number for R0 plant. Basic service: Provide R0 transgenic plants, PCR to confirm the existence of marker gene and gene of interest. Protocols:Modified from Weeks J. (Plant Physiology 1993) Plasmids: pUbiGUSand pAB1 from X. Ye (ETHZurich, Switzerland) Variety: Bobwhite and other Spring varieties Duration: 10-12 months.

University of Liverpool:

 

Synthetic Biology

Construct design, DNA synthesis (sequence verified) from plasmid libraries to artificial chromosomes. Synthetic biology experiments that can be applied to structure/function analysis, directed evolution, de novo design, synthetic pathway creation and biosensors, biological re-engineering.

University of Liverpool:

Next Generation Sequencing

State-of-the-art next generation sequencing and high throughput technologies

Durham University:

University of Leeds:

University of Liverpool:

University of Manchester:

University of York:

 

Bioinformatics Analysis

Expertise in analysis from guidance on experimental design through to performing complete analyses

University of Manchester:

University of Liverpool:

University of York:

Soil Moisture and Soil Respiration Chambers

Lancaster University:

Newcastle University:

  • Contact: James Standen; James.standen@ncl.ac.uk; +44(0) 191 2082288 or +44 (0) 1661 830222
  • Contact: Teresa Jordon; nu.farms@newcastle.ac.uk; +44 (0) 191 2084689 or +44 (0) 7749 434121
  • Facilities: TDR soil moisture probe – topsoil moisture (0-20cm) measurement; COSMOS-UK site on-farm – stationary wide area soil moisture sensor

 

Gamma Radiometer

Gamma radiometer (SoilOptix from Practical Precision Inc.) (Only known instrument in the UK to measure emissions of naturally occurring gamma radiation which is linked to soil type/genesis)

Newcastle University:

 

Electrical Conductivity of the Soil

DualEM-2s electromagnetic induction sensor – high resolution maps of the electrical conductivity of the soil at 4 different depths which relates to soil texture

Newcastle University:

GasLab

Mobile greenhouse gas laboratory (GasLab): a bespoke 4 x 4 vehicle with capacity to measure greenhouse gas (N2O, CH4, CO2) and trace gas (NH3) fluxes in situ, and analyse the isotopic composition of these gases

University of Manchester:

Lancaster University:

  • Contact: Ian Dodd; i.dodd@lancaster.ac.uk; +44 (0)1524 593809
  • Facilities: Four Scholander-type pressure chambers to measure root (when plants are grown in specialised pots that fit the chamber dimensions – two sizes available) and shoot water potentials, with addition of defined overpressures to collect xylem sap, to determine root hydraulic conductivity and measure xylem sap (nutrient / hormonal) composition. Twenty thermocouple psychrometers to measure soil, root and leaf water potentials. Whole plant pressure chambers to collect xylem sap from transpiring leaves of intact plants at any canopy position (Netting et al. 2012 Plant Methods 8, 11). High throughout radioimmunoassay to measure tissue and xylem ABA concentration. High throughput benchtop photoacoustic laser spectroscopy for headspace ethylene analysis.

Photosynthesis and phenotyping facilities

Lancaster University:

  • Contact: Ian Dodd; i.dodd@lancaster.ac.uk; +44 (0)1524 593809
  • Facilities: Eight Infrared Gas Analysers are used for medium and low throughput photosynthesis measurements in various experimental settings, including glasshouses, controlled CO2 cabinets, field and in parallel with online mass spectroscopy-linked growth facilities aimed at understanding plant-atmospheric chemistry interactions. One system is allocated to a whole plant gas exchange chamber that can regulate the evaporative demand the plants are exposed to (Jauregui et al. 2018; Plant Methods 14, 97). The photosynthesis systems are used to measure CO2 assimilation, transpiration, respiration, chlorophyll fluorescence, and provide a sampling platform for plant emitted VOCs.

Microphenotron Service

Automated micro-phenotyping platform allowing both root and shoot development to be monitored under a variety of abiotic and chemical stimulants or interventions with focus on novel chemicals and chemical library screening. The system is based on a 96 well plate format utilising bespoke strips of 8 wells ‘phytostrips’ which can be presented and imaged by an automated robotic arm delivered through a  bespoke  software package. Handling area has the potential to screen over 5000 individual treatments from 54-96 well plates

Lancaster University:

Advanced Light Microscopy

Advanced light microscopy technologies can address many scientific questions including localisation, nanoscopy, subcellular architecture, phenotyping, tracking, gene expression, changes in chemical environment, protein:protein interactions & membrane dynamics

Durham University:

University of Manchester:

University of York:

University of Liverpool:

University of Leeds:

 

Electron Microscopy

For sub-micron and even sub-nanometre resolution of various sample types, the transmission electron microscope (TEM) is extensively used for both biological and chemical studies of cell sections and novel compounds. The scanning electron microscope (SEM) is used for morphological studies of even more varied sample types. These vary from single cells to light bulb elements.

Durham University

University of York

University of Leeds

 

Atomic Force Microscopy

Application: Imaging down to 1 nm lateral and 0.05 nm vertical resolution of any surface in any environment. Specialising in the dynamics of soft-matter/biological samples in an aqueous environment.

University of Leeds

University of Liverpool

University of Manchester

Services including: Metabarcoding (e.g. for studies of eDNA, species diversity, diet analysis, parasite screening), SNP marker development and typing, Microsatellite marker development and typing, High-throughput DNA extraction, Quantitative PCR (including telomere length analysis) and Genotyping by sequencing

University of Sheffield:

Analysis of the biophysical properties of molecules as well as protein-protein and protein-nucleic acid interactions

University of York:

University of Leeds:

Plant Cell Wall Monoclonal Antibodies

Leeds Centre for Plant Sciences is home to one of the world’s largest collections of monoclonal antibodies directed to plant cell walls

University of Leeds:

Wolfson P3 Phenomics Platform

A state-of-the-art facility for selecting crop varieties that express durable resistance to pests and diseases. The facility is at the forefront of the advancement and application of phenotyping (characterization) of disease-resistant crops. With this phenotyping platform, we can accelerate genetic selection schemes for disease-resistant crop varieties and develop new treatments that can prime the immune system in existing crop varieties. The facility has the technological capacity to identify specific biochemical, physical and genetic markers of disease susceptibility and/or resistance in crops using robotics linked to quantitative chlorophyll fluorescence imaging, hyper spectral imaging, advanced microscopy, next generation sequencing (PacBio Sequel 2) and mass spectrometry

Sheffield University:

Bioanalytics

Facilities for the study of proteomis, metabolomics, bioanalytics, structural molecular biology, glycomics, carbohydrates, post-translational modifications, small molecule identification and quantification

Durham University:

  • Contact: Facility Manager Adrian Brown (a.p.brown@durham.ac.uk)
  • Facilities: Chromatographic and mass spectrometric analysis of a wide range of compounds from biological systems comprising small molecule primary and secondary metabolites to proteins, as well as drugs and pesticides. Using state-of-the art chromatographic and mass spectrometry equipment, both qualitative and quantitative analyses can be performed. The Proteomics Facility specialises in protein identification, the detection of post-translational modifications and the identification of contaminates in purified samples. Relative protein quantification between samples is available using either fluorescent labelling on gel-based systems (2D-DIGE) or by shotgun LC-MS methods using isobaric peptide tags (iTRAQ). In both cases proteins are digested and the resultant peptides analysed by MALDI and ESI tandem mass spectrometry. In-house search engines match MS and MS-MS fragment ion data against sequence databases to identify the constituent proteins. The Facility is equipped with two mass spectrometers which use different ionisation methods: A Sciex 6600 TripleTOF mass spectrometer with electrospray ionisation(ESI) and a 4800 Plus MALDI TOF-TOF mass spectrometer that is used for high throughput protein identification and molecular weight determination from gel spots or bands.

University of Sheffield:

University of Leeds:

University of York:

University of Liverpool:

Soil Physical Properties Analysis

Determination of physical properties of soil samples. Including particle size classification & distribution, saturated permeability of samples, grain size in aqueous suspension, raw fibre analysis & X-ray CT scanning

University of Leeds:

University of Manchester:

Lancaster University:

  • Website: https://www.lancaster.ac.uk/lec/research/research-facilities/
  • Contact: Prof Andrew Binley; a.binley@lancaster.ac.uk; +44 (0)1524 593927
  • Facility: X-ray CT (Computerised Tomography) creates 3D or 2D images of an object through X-ray attenuation. The non-invasive technique, widely used in medicine, is now commonly used for investigating and characterising materials in other fields. Our system is a Xtek CT 160Xi scanner, which is capable of up to 5-micron resolution and can image objects (with a lower resolution) up to 75 mm diameter and 150 mm in length. Mainly used for the characterisation of soil and rock samples to help understand the physical structures that control fluid and gas transport processes in these porous media.

University of Sheffield:

  • Facility: Sheffield Universities teams have a long history in assessing effects of crop and other land managements on soil function and soil health.  They deploy a wide range of techniques including traditional analyses for nutrients, metal contaminants, soil structure and biological activity measures allied to stable isotope and other soil functional assays and assessments of links to soil communities.
  • Contact: Duncan Cameron; d.cameron@sheffield.ac.uk
  • Contact: Jonathan Leake; j.r.leake@sheffield.ac.uk
  • Contact: Tim Daniell; t.j.daniell@sheffield.ac.uk
  • Contact: Gareth Phoenix; g.phoenix@sheffield.ac.uk

 

Soil & Water Chemical Properties Analysis

Determination of chemical properties of soil & water samples. Including analysis of nutrients, carbon, stable isotopes, anions & elemental analysis in liquid & solid samples

University of Leeds:

University of Manchester:

Lancaster University:

 

Soil Microbial Community Composition and Diversity Analysis

University of Manchester:

University of Sheffield:

  • Facility: Sheffield has a dedicated suite of labs for the assessment of microbial community dynamics linking with their associated soil functions and soil health.  This includes access to high throughput sample and sequence analyses and their associated bioinformatic demands and other low cost alternatives including real time PCR.
  • Contact: Duncan Cameron; d.cameron@sheffield.ac.uk
  • Contact: Tim Daniell; t.j.daniell@sheffield.ac.uk
  • Contact: Helen Hipperson; h.hipperson@sheffield.ac.uk

A greenhouse-based, purpose-built facility comprising 100-200 balances (different loads / greenhouse configurations are possible) across 2 independent greenhouses (with separate environmental regulation) that are continuously logging water consumption (Ryan et al. 2016; Plant Science 251, 101-109)

Lancaster University:

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