School of Biological Sciences

Our facilities

Cutting-edge environments

As one of our students, you will be taught in modern laboratories during your practical sessions. These are large and well-equipped, containing up-to-date equipment which gives you valuable experience of using a professional facility.

Final-year and postgraduate research projects are carried out using our academic research laboratories. These were renovated as part of the ongoing expansion of our School and its facilities. Our aim is to provide you with state-of-the-art equipment and ensure your studies are as relevant and productive as possible.

Examples of our Facilities

Bioimaging Facility

We have high-end and routine microscopes in darkrooms, workstations for image processing and analysis, and a lab for sample preparation. Using mainly fluorescence microscopy, we are well-equipped to carry out fluorescent protein localisation, morphology and quantified phenotype analysis from single cells to tissues. Areas of expertise are live cell imaging, large-sample macroscopy, and fluorescent-protein-based biosensors. We also develop our own instruments, algorithms for computational image analysis, and sample preparation techniques. We have a FACS BD Accuri C6 flow cytometer equipped with a blue and red laser, two light scatter detectors, and four fluorescence detectors with optical filters optimised for the detection of fluorochromes, including FITC, PE, PerCP, and APC, and can also detect many variants of fluorescent proteins, such as GFP, YFP, and mCherry. The School is also in the process of purchasing a new FACS-sorter for separation and isolation of primary human cells and genetically modified cells. The sorter will support applications from all research groups in the School of Biological Sciences such as CRISPR/Cas9, purification of pure cancer cell populations for further analysis, advance immunology and isolation of plant cell organelles.

 

Bioinformatics and Computational Biology

The department now has two 'dry laboratories' and a high-performance computing cluster accessible on and off campus (via VPN), and is configured for both interactive and batch use.  The cluster currently has 128 processor cores and a total of 2 Tb of memory, plus 100 Tb of storage, and a separate webserver. Expansion of this system is ongoing. A broad range of bioinformatics software is installed including all commonly used DNA sequence analysis software and numerous R packages. There is a Galaxy instance on the webserver for teaching purposes. The cluster is in use by numerous PG students, staff and some UG students and actively supported by a dedicated staff member and the genomics group.

Biophysical and Biochemical Facilities

The School is fully equipped to perform cutting-edge biophysical and biochemical research using a combination of conventional and custom designed apparatus including: circular dichroism to monitor secondary structures including chemical and thermal denaturation; stopped flow optical/fluorescence and laser flash photolysis set-ups for kinetic analysis of enzyme reactions and ligand binding; extensive facilities for UV/visible/near infra-red and fluorescence spectroscopy from isolated samples and for proteins within cells (Olis instrument); a microcal isothermal titration calorimetry instrument for deriving the thermodynamics of protein ligand binding; surface plasmon resonance (SPR) facilities to permit the study of a range of biomolecular interactions; extensive protein production and purification facilities; specialist facilities for X-band Electron Paramagnetic Resonance (EPR) spectroscopy – including a liquid helium cryostat and apparatus for preparation of rapid-freeze quench samples; potentiometry set-up for measurement of redox potentials by cyclic voltammetry and redox titration. Structural bioinformatics /computational chemistry facilities for modelling protein structures include specialist drug design software (from Schrödinger) and high performance GPU-based computing designed specifically for molecular dynamics simulations.

A crystallisation laboratory is equipped with a state of the art ‘Gryphon’ crystallisation robot, Leica M125 microscopes (with digital camera) for crystal viewing, variable-temperature vibration-free crystal incubators, full facilities for ‘manual’ crystallisation, and apparatus for manipulating, cryo-cooling and transporting protein crystals to synchrotron facilities. A single crystal microspectrophotometer is also in place.

Ecology and Environmental Microbiology Facilities

Field-to-mesocosms sampling: Fieldwork sites are accessed by two fieldwork vehicles with full off-road 4x4 capability; two (7m & 3m) Rigid Inflatable Boats (RIBS). Field sampling is facilitated by Van Veen grab samplers; diving PAMs; underwater video cameras; full face diving masks with communications equipment; GPS units; multiple remote sensing drones (e.g. Phantoms); field portable spectrophotometers; fish surveying equipment including fyke nets, passive traps, pelagic trawls, and backpack electrofishing gear (E-fish 500W); and a FluoroProbe profiler for the analysis of chlorophyll with algae class determination. Experimental work is support through a range of aquatic and terrestrial mesocosms, including: 62 large (>100L) temperature-controlled aquaria for simulating tropical or temperate and fresh or marine systems; replicated environmental outdoor mesocosms simulating tidal and terrestrial systems; a state-of-the-art tropical coral-reef research facility devoted to fully climate-controllable experiments; and multiple pH-stating systems to control CO2 concentration for ocean acidification experiments. Microbial culturing facilities support our experimental work and comprise dozens of constant-temperature (and light) growth rooms, and walk-in incubators, across a -12°C to +40°C gradient, used for culturing both Prokaryotes and Eukaryotes. 

Analytical equipment: All field sampling and experimental work is underpinned by high-accuracy analytical measurements provided by: four gas chromotographs (GCs) with diverse detectors (MS, FID, FPD, ECD) for trace gases; hydrocarbon and polysaccharide analyses; purpose-built purge-and-trap systems for the cryogenic enrichment of trace gases (one for sulfur gases, one for non-methane hydrocarbons); a Fast Isoprene Sensor; Pfeiffer model QMG 422 mass spectrometer with membrane inlet for measuring dissolved gases; a uPLC; a new Nutrient Autoanalysis suite as well as sediment oxygen/nutrient flux systems; dionex anion and cation exchange chromatography; an HPLC; atomic absorption spectrophotometer; 2 X CTG FastTracka II Fast Repetition Rate Fluorometers with Fast Act Laboratory Systems; PAM fluorometers; bench top spectrofluorometers; LED Flash-Yield systems; Leica DMI600B inverted light Limnology microscope – auto XYZ image capture (inc, Dark Phase); Gilson liquid-handling robot for high-throughput microbial culturing in microtiter plates; and a multi-mode (fluorescence, optical density, luminescence) microtiter plate reader.

Molecular ecology: In the post-genomics era, we have invested heavily in high-throughput molecular ecology facilities, based around advances in 2nd and 3rd generation sequencing technologies, which we apply across taxonomic domains and level of biological organisation, these include: Hamilton Robotics liquid handling robot; DNA, RNA and protein extraction equipment; banks (dozens) of PCR thermal cyclers; a range of 96 and 384 well qPCR machines; Blue Pippin DNA size-selection system; Stable Isotope Probing equipment and a designated radio isotope laboratory; Agilent Bioanalyser; NanoDrop 3300 fluorospectrometer and a NanoDrop 1000 spectrometer; FLUOstar Omega Microplate Reader; and an Illumina MiSeq Benchtop Sequencing System. 

Molecular Cell Biology and Cell Culture

The School has excellent facilities for cellular molecular biology research, with dedicated molecular biology and cell/tissue culture rooms facilitating the use of recombinant DNA, the study of protein function, siRNA library screens, various cellular assays and the generation and use of recombinant viruses. Facilities include: level I and II cell/tissue culture facilities with multiple laminar flow cabinets; CO2 incubators; FACS and cell sorter facility; microscopes; centrifuges and ultracentrifuges; Bioruptor Sonicator; immunohistochemistry suite; equipment for mammalian cell manipulation including electroporators and viral transfection technology; PCR thermocyclers including quantitative PCR using Taqman and SYBR Green-based methods; bioanalyzer; Optical/fluorescence/luminescence/ELISA plate readers; chemiluminescent, UV and LI-COR imaging systems; Illumina MiSeq sequencing machine; Metrocubo GPU workstations for compute-intensive molecular dynamics simulations; recently refurbished radioisotope suite.

Plant Physiology and Phentoyping

The Plant Productivity Group employs a range of non-invasive techniques including state-of-the-art imaging for plant phenotyping and have developed and built in-house instrumentation and software to extend our considerable plant physiology suite. We are fully equipped to perform cutting edge plant physiology and phenotyping research using a combination of conventional and custom designed apparatus including: Chlorophyll fluorescence imaging of whole plants (low res ) and cells (high res); High resolutions imaging of wavelength specific bands (e.g. for imaging ROS); Thermal imaging of stomatal conductance; Imaging plant Water Use Efficiency; Infra-red gas exchange analysis – including whole plant chambers for Arabidopsis; Phenotyping plant form with watering control capabilities and dynamic light regimes; Dynamic lighting platforms; Spectral reflectance; Water regimes including hydraulic conductance. These state-of-the-art facilities are underpinned by our plant growth capability using computer controlled glasshouse and controlled environment facilities.

Proteomics

The School is well equipped with mass spectrometers including a state-of-the-art hybrid high-resolution LTQ/Orbitrap Velos instrument interfaced with a splitless nano-scale liquid chromatography system for fully automatic genome-scale analysis of protein abundance and post-translational modifications. Academic and technical staff have extensive experience in quantitative proteomics utilising stable isotope labelling and label-free approaches, mass spectrometry-based analysis of protein phosphorylation and protein-protein interactions.

Biological Sciences Intranet

We maintain and update bsintra as a visual resource for all Biological Sciences staff, students and visitors for the daily running of our department.

It serves as an invaluable source for knowledge without the need to download any source material to your computer.  It is only available on campus but if accessed off-site an essex username and password are required.

http://bsintra.essex.ac.uk/