In the second of our case studies about equipment sharing we focus on an interdisciplinary project based at Swansea University.
The context
Sarah Aldridge is PhD student in the College of Engineering at Swansea University. Her research combines the fields of engineering, sports science, osteology and genetics. Working with the remains from Henry VIII’s warship the Mary Rose, the eventual aim is to attempt to identify a team of archers believed to be aboard at the time of sinking. In preparation for this she is attempting to non-destructively examine the internal structure of arm bones. It is critical that this investigation is non-destructive on the DNA samples so there was a need to test the effects of micro-CT on DNA.
What equipment was required?
Micro-CT (micro computed tomography) uses the same method as CT (CAT) scans in hospitals, which is 3D x-ray imaging, but with much higher resolution on a small scale. A series of x-rays is used to build up volumetric data that includes structural details. Working on microscopic level, the equipment uses higher energy x-rays and longer exposures to reveal a large amount of detail.
The samples in Sarah’s research are very precious and it was important that high energy x-rays didn’t damage them. No DNA investigation has yet been performed on the Mary Rose artifacts, so it was critical to preserve this for any future research. It was decided to test the technique on other samples, irradiating them with x-ray CT then using analytical chemistry techniques to look for evidence of the damage. A liquid chromatography (LC) process was needed – typically an LC unit is coupled to a mass spectrometer.
Whilst mass spectrometers are commonly available at many institutions, Sarah needed to perform a more specialist technique preparing and extracting DNA from a liquid sample. For this she needed specialist expertise that Swansea University didn’t have.
Finding the equipment
Having spoken to colleagues at Swansea University, Sarah got in touch with the Central Biotechnology Services (CBS) at nearby Cardiff University who recommended other facilities. After several conversations Sarah opted for the Chemical Characterisation and Analysis Facility (CCAF) at Bath University based on their previous and current experience of similar research and the involvement of specialist support. The equipment used is a Bruker MAXIS ultra-high resolution ESI-QTOF-MS mass spectrometer, coupled to an Ultimate 3000 UPLC (Ultra-Performance Liquid Chromatography), used to separate the different components found in mixtures.
Bath and Cardiff universities are part of the GW4 Alliance. The alliance provide an equipment database service that is powered by Jisc’s national equipment.data database (which each GW4 institute provides data to individually).
Although Sarah was unaware of the search facility, searching for ‘liquid chromatography’ in the GW4 database returns CCAF at Bath University and the Bruker MAXIS mass spectrometer is found in the Jisc equipment.data database.
How did she access the equipment?
For her test samples, Sarah prepares and packages the samples and sends them to Bath for processing. If the results are successful (i.e. the DNA is not damaged), she will travel with her main samples to Bath. Being present during the processing and analysis is important to her for sharing knowledge, and she sees this as a collaborative relationship rather than outsourcing. She has spoken to the technicians in advance who have provided valuable advice on the best way to prepare the samples, which she will do in advance. She has also spoken to other researchers who have experience doing similar work.
What were the barriers?
Had she been aware of the equipment database for searching, Sarah feels she might have found the right equipment more easily and greater awareness of this service with researchers could be very useful.
However, what was critical to her was the availability of expert support of specialists who had performed similar analysis. Good preparation is essential for obtaining pure DNA, which involves a series of extracting, digesting and cleaning processes. The expertise available to advise on preparation of the sample is therefore an important part of using the equipment. If this information was available in the information in the equipment databases it would be of great value to her.
Benefits and the future
Sarah sees huge benefits to her research in sharing equipment. It promotes collaboration between universities and the sharing of knowledge. Although there is a charge to use the facilities, this includes local expertise and is considerably less than running their own equipment. It is something Sarah will definitely do again as she feels it is a very efficient way of achieving results with her research. It makes sense to concentrate specialist knowledge at facilities. She suggests that good communication with the staff supporting the equipment is important to good research outcomes.