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Facilities
Our group has two main laboratory facilities: the UCC Palaeobiology Laboratory and the UCC Mary Ward Microbeam Laboratory. These are key facilities for our experimental work, and analytical work, respectively.
Palaeobiology Laboratory
The Palaeobiology Laboratory is located in the Butler Building (BB_1.03) and is a dedicated experimental taphonomy lab that allows controlled investigation of processes relating to decay, transport, and thermal maturation of fossil tissues and other materials.
Click on images of the equipment below to find out more.
Three 260 L Memmert incubators are effectively our “decay chambers” – they are used for experiments requiring decay of organic matter (or mineralisation or other processes) at surface temperatures and pressures. Temperature can be set (or cycled) between 20°C and 45°C. The large capacity of the incubators facilitates the use of many replicates, and three incubators allow separate experiments to run concurrently at different temperatures.
The microwelder is used to make and seal Au capsules from Au tubing. The sealed capsules are then placed in the high pressure rig for thermal maturation.
The rig is a cold-seal water-pressurized system that allows samples (housed in Au capsules) to be experimentally matured at elevated temperatures (up to 600°C) and pressures (up to 500 bar). Sample size is constrained by the diameter of the reactor inner chamber, which is ca. 8 mm wide. The reactor can accommodate many samples at the same time. Initial experimental pressures in the reactor are generated in a two-step process involving use of a pump to generate initial pressures of ca. 50 bar and using thermal expansion (i.e. elevated temperatures) to achieve the desired experimental pressure. Intelligent temperature sensors ensure that the system learns from each experiment and gets better at achieving set temperatures with successive experimental runs.
This 100 L vacuum oven is an understated but well-used piece of equipment in the lab that allows rock samples and fossil tissues to be impregnated with resin under vacuum. Temperature and pressure can be set (or cycled) between 20°C and 200°C, and between 10 mb to 1013 mb.
Our Lulzbot Mini v2.0 3D printer is a plug-and-play machine that allows rapid printing of items up to 4608cm³ with a layer resolution of 0.05mm-0.90mm.
Our shakers include a Balco Rotabarrel rotary tumbling barrel 6L, a WiseShake® SHO-21D digital reciprocal shaker, and a Sci-Quip Incu-Shake Mini incubating orbital shaker. These shakers have diverse applications where agitation is required, e.g. in mixing, melanin extraction, and transport experiments.
The Leica EZ4W microscope allows easy and rapid imaging with incident and transmitted light and can live-stream images to devices using its internal wifi signal.
Mary Ward Microbeam Laboratory
The UCC Mary Ward Microbeam Laboratory is a new high-spec analytical facility located in the Cooperage building (Coop_G12A) that offers cross-platform options for surface analyses, including imaging surface structure at the micro- to nano-scale, bulk analysis of sample chemistry, plus chemical imaging.
The lab also provides a service to all academic departments within UCC and also to the broader community of scientists working in the earth-, environmental, materials, chemical and bio-sciences and to industry. For access to the instrumentation in the Mary Ward Laboratory, and to learn more about applications, please contact the laboratory Experimental Officer Peter Chung (peter.chung@ucc.ie).
Click on the images of the equipment below to find out more.
The JEOL IT-100 variable pressure (VP)-SEM is equipped with a backscatter detector, dedicated VP-secondary electron detector and a 30 mm2 EDS detector. This equipment allows quick, routine imaging and analysis of sample structure and chemistry at a sub-mm to nanometer scale.
The secondary electron detector (SED) is used for imaging of sample structure at the micrometre- to nanometre scale, with an ultimate resolution of < 20 nm at 20 kV on gold-coated samples.
The backscatter electron (BSE) detector allows chemical imaging of specimens with a mean atomic mass variation of ca. 0.1.
The equipment can run in VP mode (> 30 Pa) in conjunction with the environmental SE and BSE detectors, which allows (fully non-destructive) analysis of non-coated samples. TEM sections can be checked and analysed using a dedicated STEM holder.
The EDS detector provides standardless quantification and advanced X-ray mapping of elements heavier than (and including) carbon. Chemical mapping allows sample chemistry to be correlated with sample microstructure.
Sputter-coating of samples can be performed at the bench using our in-house sputter coater fitted with an Au/Pd target.
The Perkin Elmer Spotlight 400i near- and mid-IR FTIR microscope is coupled to a Frontier FTIR instrument and is equipped with a diamond compression cell and extra large sample stage. The equipment offers quick and routine analysis of bulk sample chemistry and chemical imaging of molecular composition at a micron-scale; especially useful for polar materials (e.g. with O-, N-, S-bonds).
Spatial resolution for chemical maps is ca. 5 µm in standard micro-ATR/transmission/reflectance mode.
The dedicated ATR imaging accessory provides enhanced spatial resolution of 1.56 µm pixel size for maps up to 1 mm x 1 mm.
The diamond compression cell allows routine analysis of samples with unusual shapes, e.g. crystals or fibres.
The extra large sample stage allows movement in X, Y and Z planes and can accommodate irregularly-shaped samples up to A4 in size and up to ca. 25 mm thick.
This Raman microscope is a flexible research-grade instrument that includes unique real-time focus tracking capabilities. It is equipped with two diode-pumped solid-state lasers (DPSS) with wavelengths of 532 nm and 785 nm coupled to a high-performance Raman spectrometer.
The laser spot size is continuously variable from 1 to 300 µm (objective and excitation wavelength dependent) with fully optimised beam path achieving high levels of confocality (up to 2.5 µm depth resolution).
High spectral performance is assisted by an automated, kinematically mounted, magnetically attached, Rayleigh line rejection filter set for 532 nm excitation, using paired filters, allowing ripple-free measurement of the Raman spectrum to 100 cm-1 from the laser line. It can resolve spectral features narrower than 0.5 cm-1, and can detect minute shifts in Raman band position (as low as 0.02 cm-1).
For accuracy and sensitivity, the CCD array is a near infrared enhanced, deep depletion detector (1024 x 256 pixels), Peltier cooled to minus 70°C (-70°C).
LiveTrack™ focus-tracking technology allows the production of chemical images (maps) from samples with uneven surfaces with the function to view in 3D.
Additional software allows ultra-fast mapping with speeds up to 1000 spectra per second with StreamHR™ Rapide and the Particle Analysis module can derive detailed statistical information from chemical images.
The Leica Ultracut UC7 Ultramicrotome is used to prepare consistently high-quality freestanding semi- and ultrathin sections of soft materials for electron microscopy or to generate perfectly smooth, polished block face surfaces for light microscopy, AFM or chemical characterization via e.g. FTIR or Raman spectroscopy.
The fully motorized knife stage minimizes user-related vibration and allows delivery of consistent sample thickness of 1 nm – 15 µm.
The control unit allows quick adjustment of feed, cutting window, cutting speed and illumination parameters during sectioning. The vibration-decoupled gravity-stroke cutting arm allows chatter-free sectioning.
Semi-thin sections can be stained at the bench with Alcian blue, dried on a hotplate and checked for sample structure.
The Leica DM 2700 compound microscope is coupled to an Ocean Optics 2000+ spectrophotometer aligned with the microscope C-axis to provide easy measurement of spectral reflectance of macroscopic and microscopic materials.
A beam splitter allows the microscope to be operated with all light directed to the eyepieces or split between the eyepieces and C-mount.
The microscope is fitted with 5x, 10x, 20x, and 100x objective lenses.
An inbuilt diaphragm allows reduction of the size of the area from which reflected light is collected and analysed to approx. 15 µm wide.
The spectrophotometer can be easily swapped with a Leica digital camera for photography of analysed regions.
Spectra can be calibrated against white and mirror standards for hue and reflectance, respectively. Left- and right-circularly polarized filters allow materials to checked for circular polarization.
A versatile, modular, digital microscope with a large range of magnifications to 2500x with 1600 x 1200 pixel resolution, and the ability to generate scalable 3D images and real-time stitched images.
This equipment allows quick and easy sputter coating of samples with a thin film (< 5 nm thick) of Au or Au/Pd to reduce sample charging during high-vacuum SEM analysis.
This microscope has a wide base and extra long working distance to accommodate thick samples. A ring light plus fully adjustable fibre optic lights provide a high level of control over lighting, including the production of extremely low angle light for surface features with low relief.
The Perkin Elmer TurboMatrix HS-40 Headspace Trap Sampler allows the solvent-free extraction of volatile compounds using precision thermostatting and pressure-balanced technology. The headspace trap increases analytical sensitivity by 100 times compared to a standard standalone GC-MS. This equipment allows monitoring of high-temperature stability reactions for specific biomolecules in solid or liquid samples up to 15 ml. The Clarus 590 GC-MS features a flame ionisation detector (FID) for separation and identification of molecular fragments.
These dedicated palaeo lab facilities are supported a dedicated histology lab including:
- Tissue-Tek TEC 5 Tissue Embedding Console System inc. cryostat
- Leica RM2235 microtome + microbath
- Leica ST5010 Autostainer XL
This equipment allows easy preparation of wax-embedded blocks and control of sample orientation relative to the blockface.
Standard equipment for easy preparation of histological sections 10 -30 microns thick.
This equipment provides fully automated staining of histological thin sections using standard stains such as Ailcian blue.
The palaeo lab facilities are also supported by the collections of the Cork Geological Museum which are housed within the School of BEES. The Museum includes a dedicated and growing collection linked to the UCC Palaeontology Group that includes diverse vertebrate fossils preserving soft tissues.
Contact
For user access, bookings and enquiries relating to the equipment in the Mary Ward lab, please contact:
Prof. Maria McNamara (Lab Manager)
Email: maria.mcnamara@ucc.ie
Tel: +353 21 490 4570
(general enquiries and specific queries relating to the FTIR, ultramicrotome and microspectrophotometer)
Peter Chung (Experimental Officer)
Email: peter.chung@ucc.ie
Tel.: +353 21 490 4527
(general enquiries relating to the FTIR and SEM)
Dr Richard Unitt
Email: r.unitt@ucc.ie
Tel: +353 21 490 4549
(specific queries relating to the Raman microscope and high-resolution light microscope)
Funding
The Mary Ward laboratory is funded by three SFI Infrastructure Development Programme grants, by European Research Council Starting Grant H2020-2014-StG-637691-ANICOLEVO and by European Research Council Consolidator Grant H2020-ERC-COG-101003293.
Other UCC facilities
Other facilities within UCC that are available to the research group include: