D2.8 - Protocols for DNA extraction


The SYNTHESYS Networking Activities (NAs) are an integrated package that support and develop the natural history infrastructure in Europe. The more integrated the actions resulting from these activities, the better the experience of SYNTHESYS Access users, the exchange between institution, and the general public access will be.

The NAs aim to raise awareness of good practices in handling and sampling collections by offering guidelines for the care, storage and conservation of collections, ensuring usability of collections. This practice is reinforced by the increased adoption of common standards and protocols. As a result, an integrated European resource will arise bringing together the biological and geological collections held by major Natural History (NH) museums and other institutions.

This report refers to the sub-task 2.3 (“Develop protocols for collecting data from sequencing activities on NH collections and feedback on the success of different methodologies”) within objective 2 named “Developing Strategic Priorities for molecular NH collections” linked to the WP2 “Improving collections management and Enhancing accessibility”.

All Natural History collections in SYNTHESYS project pursue the same common aims: preservation, uses and accessibility. Thereby, the main objective of Tissues and DNA Collections, also known as biobanks, in these institutions are to preserve and make accessible the molecular genomic biodiversity (both physical
samples/specimens, either extinct or extant and information data) to the maximum number of beneficiaries on short, medium and long-term.

In the 1980s, nucleic acid-based research reached all disciplines, including the non-molecular such as taxonomy and phylogeny, housed in museums and other institutions with traditional NH collections. As a result, a new type of collections was created and the possibility of giving new uses to classic collections was opened (Dessauer & Hafner, 1984; Dessauer et al., 1990; Sherwin, 1991; Thomas, 1994, Rey, 2013, 2014). These new collections specifically designed as source of DNA, which mainly kept samples dry or frozen, were consolidated as an important scientific infrastructure for genomic and genetic studies in the current century (Prendini et al., 2002; Savolainen et al., 2006). Furthermore, these collections became vital to preserve orphaned molecular samples remaining after the finalization of many research projects. From a quantitative perspective, the number of samples (tissues and DNA) managed by specific laboratories or research teams should normally be less than in biobanks. However, as common also to most SYNTHESYS institutions, in reality the set of samples from the different projects is usually much larger than the samples kept in the biobanks and the lack of professional management of these will cause problems in future and. Here, we
consider a biobank as defined by ISBER -International Society for Biological and Environmental Repositories-(Hewitt & Watson, 2013). In order to be considered as such, the data and samples must be associated with a database backup with defined standards and the curatorial work within the collection must be carried on by a specialist and professional staff.

From our perspective the protocols, processes and goals from the two types of facilities are different. If we take the definition given above into account, in a molecular laboratory, samples are processed only to obtain specifics results from partial or complete genomes that are normally linked to research goals usually to
produce a scientific paper or report. The external use of those samples is not always granted once the project ends. This is common practice also in SYNTHESYS institutions (Biobanks Collection managers and curators, pers. comm.). Due to different temporal frames (long-term vs. short-term), the databases associated with each of these facilities have very different contents. In the case of long-term preservation of collections the main aim in databasing is to retain the information related to preservations, extraction methods and access for futures uses, while the techniques applied (e.g., amplification or genotyping) might not be as relevant (although they could be considered as supplemental data). In contrast, in molecular laboratories, due to their objective-driven nature - e.g., species or gender identification -, the preservation of the molecular extracts may not be a priority and related information (e.g. localities, geo-referencing, preservation history, etc.) may even not be included in the databases, while this information is of vital importance for NH collections. Experiences have shown that field sampling, the type of death induction (particularly interesting for insects), historical information of specimens or samples (old or modern), preservation and molecular extraction
methods, as well as environmental parameters, are crucial for obtaining good quality DNA.

To accomplish this task we aimed to quantify the tissues and molecular collections as well as NH biobanks that exist in the different SYNTHESYS institutions involved, and to investigate what kind of information associated with them is retained. For this reason, a simple survey to determine the state of the art was
designed and conducted. DNA collections and preservation of data from DNA extraction were assessed through the answers of an online survey, and by contacting the person in charge of this task at each institution, working in NH molecular collections. The “Survey Synthesys 3 WP2 Task 2.3” collected information
on conservation and care of NH molecular collections, available in SYNTHESYS institutions. The survey was made available online via Survey Monkey (https://www.surveymonkey.com/s/DQLLJNG) from 5 February 2015 to 4 March 2015.

The detailed questionnaire is presented in the Annex I and partners invited to participate are listed in the Annex II.

Scratchpads developed and conceived by (alphabetical): Ed Baker, Katherine Bouton Alice Heaton Dimitris Koureas, Laurence Livermore, Dave Roberts, Simon Rycroft, Ben Scott, Vince Smith