Tag Archives for sampling

Stepping Into The Genomics Age: A DNA Bank at World Museum, National Museums Liverpool.

By John-James Wilson, Curator of Vertebrate Zoology, World Museum, National Museums Liverpool.

From World Museum’s founding collection of study skins and taxidermy mounts bequeathed by the 13th Earl of Derby to the spirit-preserved amphibians collected by curator Malcolm Largen in the 1980s, World Museum’s Vertebrate Zoology collection has continued to expand and reflect the state-of-the-art in specimen preparation and storage.

As ethics around the sacrifice of animals for science have modernised, ‘traditional’ specimen types are no longer being prepared at the same rates, and growth of the collection has slowed abruptly. At the same time usage of the collection has diversified, including increases in requests for destructive sampling. In particular, the removal of small tissue samples, usually bird toe pad scrapes, is regularly requested for use in DNA extraction which produces a ‘pure’ DNA extract that can be used in a number of genomic investigations.

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CryoArks Biobank and COVID-19

Written by Andrew Kitchener, Principal Curator of Vertebrates, National Museums Scotland.

Biobanks may sound a bit dull when compared to shelves teeming with boxes filled with fascinating skeletons, or cabinets stuffed with colourful skins, beautiful eggs or pinned insects. Serried ranks of anonymous freezers, enhanced with the odd fridge magnet, could make your heart sink, but peep inside the biobanks’ databases and you will see an amazing array of biodiversity. 

CryoArks Biobank at National Museums Scotland ©National Museums Scotland

At National Museums Scotland we host one of the main hubs of the CryoArks Biobank initiative alongside our partners at the Royal Zoological Society of Scotland, who also host a hub of the European Association of Zoos and Aquaria Biobank, and the Natural History Museum in London. CryoArks is a project led by Professor Mike Bruford of Cardiff University and funded by the Biotechnology and Biological Sciences Research Council to establish zoological biobanking in the UK. As well as the -80o freezer infrastructure to store the tissue samples long term, CryoArks is developing an online database that will allow researchers to find out what genetic resources are available in the CryoArks Biobank hubs and in member institutions. With the advent of the Nagoya Protocol on Access and Benefits Sharing in 2014, access to genetic samples from species from range countries is more challenging. Therefore, it is vital that we make the best use of the samples already available in the UK and make these freely available to support research, much of which may benefit the conservation of endangered species worldwide. 

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CryoArks – Discover The UK’s First Zoological Biobank

Written by Andrew Kitchener, Principal Curator of Vertebrates, National Museums Scotland.

Many of us have probably been approached by eager PhD students and other researchers who want to snip a bit off those specimens or drill a few holes in others. As curators we start to feel somewhat uncomfortable about seeing our precious collections sliced and diced, and yet we are also keen to discover more about the genetic content of our specimens for their own sake. This is partly because collectively we can contribute to studies that benefit wild populations of species, including the conservation biology of many endangered species and the possibility of rewilding extirpated species. You may also have a chest freezer bursting with grip-seal bags or plastic tubes filled with tissue samples collected from specimens you have acquired, but you’ve no idea what to do with them, but you know they will be useful one day. Or maybe you have a freezer full of specimens you want to get rid of. CryoArks is a new initiative that just might help you to solve all these problems.

Sorting through lemur muscle samples at National Museums Scotland © National Museums Scotland

CryoArks is a BBSRC-funded project led by Professor Mike Bruford at Cardiff University, which has established the UK’s first comprehensive zoological biobank for research and conservation. CryoArks is a consortium of museums, zoos, academic institutions and biobanks, which is working together to establish common standards and working practices to store tissue and DNA samples and make them available on a common web portal, so that researchers and conservation biologists will be able to find out what is available for their research. This will help cut down on the sampling of our permanent collections by giving researchers something else to sink their scalpels into. CryoArks has two main sample storage hubs – at the Natural History Museum in London and at National Museums Scotland in Edinburgh – that currently house more than 65,000 samples, but we have room for almost a quarter of a million. The Royal Zoological Society of Scotland is also a joint CryoArks and European Association of Zoos and Aquaria biobank storage hub, bringing the zoo and non-zoo biobank communities together.

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Meet the NatSCA Committee – Kirsty Lloyd

Written by Kirsty Lloyd, BBSRC CryoArks Technician at the Natural History Museum, London.

What is your role on the NatSCA Committee?

I have recently become a member of the NatSCA committee after attending their conferences and events for several years.

Thus far I have taken on the role of tracking and supporting collections at risk. A natural sciences collection provides a perpetual physical snapshot of the natural world and holds important information which can help us better understand our planet today. However, this valuable resource is often the first to experience the strain of funding cuts, staff shortages and redundancies. Collections in long-term storage, especially those that exist outside of the public eye, are frequently underutilized and therefore undervalued.

NatSCA is trying to keep track of threats to collections and offer our support to those in need; with the intention of increasing awareness and acknowledgement of the value of natural sciences collection and the people with the skills to care for them. If you know of any collections that are at risk from staff loss or collection disposal, please get in touch at advocacy@natsca.org.

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Bill Pettit Memorial Fund: Discovery Collections Project

The Bill Pettit Memorial Award was set up a few years ago by NatSCA to support projects including the conservation, access, and use of natural science collections. One of the recent projects we have been able to help with was the curation of some amazing specimens from the voyage of the Discovery. Hear more about the project from Tammy below.

David Gelsthorpe

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In early 2013 we set about organising the task to begin with the curation of the largest, most recent and least organised of the three collections – that of the ECOMAR collection. The start of the ECOMAR project coincided with commissioning of the new UK Royal Research Ship James Cook officially named by the Princess Royal on 6 February 2007. The first ECOMAR cruise departed from Southampton on 13 July 2007. The ECOMAR project was designed to investigate the Charlie Gibbs Fracture Zone area which lies approximately mid-way between Iceland and the Azores. Four super stations were defined (two north of the Charlie Gibbs Fracture Zone and two to the south), all had the same bottom depth (2500m) and were revisited during voyages by the R.R.S. James Cook and the R.R.S. Discovery during the years 2007–2010 to replicate sampling, time-series investigations and flux studies.

The Discovery Collections have no full-time curatorial post and we rely on the goodwill and interest of students and other volunteers (including scientific visitors and work experience volunteers) to help with cataloguing, labelling, respiriting, and general curatorial jobs. The samples, though incredibly valuable should be considered at risk. I look after the collections in as much that I manage the visitors to the collections, host students, and manage public enquiries, visits and displays of the specimens. I am also a taxonomist employed to conduct research, describing new species and studying the ecology of the deep-sea benthic fauna. I was employed for four years to work on the ECOMAR program to describe the ecology of the scavenging fauna of the area. I therefore had a particular interest in the curation of this collection.

We employed Amanda Serpell-Stevens, to work on this project, but we had funds for only 8 weeks of her time. Thus the project was reduced from cataloguing the three large collections to just one. When Amanda’s contract ended there was still much reshelving and reordering of the material to be carried out which was carried out on an ad hoc basis by myself, a retired member of staff, Mike Thurston, and Amanda who returned on a voluntary basis to continue work on the project.

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The project began by working shelf by shelf to curate and to catalogue (in paper record) what was held including location and size of each jar, and to change containers for those specimens that were in plastic containers or inappropriate sized jars. The preservative was also replaced in most of the jars and a new label produced for each specimen, as many were poorly labelled. This curation and cataloguing process took the majority of the 8 weeks, with just enough time remaining to enter the data into Excel.

With the availability of a digital catalogue the task of reorganising the lots into taxonomic order was greatly eased. This meant adjustment of shelf heights to incorporate the various sizes of tubs and jars (some of the lots are 20 litre tubs full of holothurian specimens of a single species), and removing all the specimens in turn, which were then replaced first by taxonomic order then by station order using Excel to sort the data. The spreadsheet was updated with the new locations of the specimens as we progressed. The final part of the process involved cross referencing the specimens with the newly published papers and updating the names where they had changed (on both the specimen labels and in the spreadsheet).

There were numerous new species described during the ECOMAR project, which meant further problems in allocating the correct new name to specimens in the collections variously named as e.g. Peniagone sp. nov ‘pink’. While holotypes have been registered in the NHM, London, the rest of the material needs updating to current knowledge, a process which is often neglected, despite it being referenced in the many new publications resulting from the project.

It is very satisfying to have the ECOMAR collection properly curated and to know that I can locate any specimen needed easily. In total we curated, relabelled and catalogued a total of 1300 lots comprised of 1148 smaller jars, 88 tubs (between 5 and 20 litres) and 64 loan specimens. We plan to publish a detailed analysis of this work for the NatSCA journal, including a list of available species, and will make the catalogue available online when time and funding allow. In the meantime interested parties can contact Tammy Horton (tammy.horton@noc.ac.uk) for a copy.

Dr Tammy Horton
Ocean Biogeochemistry and Ecosystems
National Oceanography Centre,
Waterfront Campus,
European Way, Southampton SO14 3ZH
UK