JRA 2: SCREENING - New Screening protocol for non-or minimal destructive analyses

To complement the PrediCtoR software being developed in JRA1, JRA2 will develop a new protocol that will enable users to estimate the ancient DNA preservation status of rare and unique bone specimens far more accurately than is possible with current protocols. PCR of extracted DNA is by far the best current method to test for the survival of ancient DNA, but its main drawback is that is always destructive. JRA2 aims to devise a new protocol/tool that correlates with PCR’s levels of success with only minimal and hardly visible destruction of specimens. By comparing PCR success of selected bone samples with data gathered from various state-of-the-art screening techniques JRA2 will identify a low-cost technique that best predicts the presence of usable DNA. .

Aims and objectives

  • Statistical evaluation of DNA preservation/degradation factors
  • Developing non-destructive or minimally-destructive techniques (tests to include: UV- or IR-spectroscopy, immunohistochemistry, immunochemistry of decalcified bone, protein gel electrophoresis, surface antibody staining, laser microscopy).
  • Based on the known PCR success from specimens (resulting from JRA3), define an optimal non-destructive technique with results that correlate with increased preservation of DNA (without destroying precious museum specimens). Such a refined tool for predicting good DNA recovery will greatly enhance PCR success and lead to the relaxing of protection policies and liberate more fossil/bone specimens for DNA studies
  • If the optimal tool developed is portable, it will be rolled-out to Users and collections managers to evaluate correctly the DNA preservation of new finds on location

The new system will enable Users to estimate the DNA preservation status of rare collections specimens more accurately. PCR of extracted DNA is the best current method to test for the survival of ancient DNA; its main drawback is that is always destructive. JRA2 aims to devise a new method that correlates with the PCR levels of success without the destruction of specimens. By comparing PCR success of selected bone samples with data gathered from various state-of-the-art screening techniques JRA2 will identify the technique that best predicts DNA preservation. This will become an essential tool for curators and bone collection Users as it will both facilitate more efficient specimen selection and the avoidance of specimens with poor preservation profiles.

JRA2 will combine the taphonomic knowledge obtained for all techniques in order to find a simple and easily applicable screening technique that can potentially be adopted by Beneficiaries and beyond without the need for highly specialist laboratories. The final aim of JRA2 is to develop a DNA screening device that will allow the collection manager to predict the utility of freshly excavated bones to yield usable DNA on–site with a non-destructive tool.

Description of work

Evaluating DNA preservation/degradation factors

Generate and deliver statistically-validated analysis that reveals the key and easily measurable factors that predict good preservation of DNA in archived bone specimens. Based on this, JRA2 will include these factors in PrediCtoR. This will improve the Web-based retrieval of the individual history of a find and thus the ancient DNA survival prediction. The results will also yield a theoretical basis for developing the most appropriate pre-dissemination screening technique.

Identifying the optimal screening technique and development of a screening device/protocol

Empirically determine a screening technique which highly correlates with successful ancient DNA preservation in bones. Depending on predictive results JRA2 will develop a low-cost, pilot screening device. There is a risk of that the favourable correlations will only result with high cost technology (isotope analysis). JRA2 will address this by focusing the tests on easy to apply techniques, such as UV- or IR spectroscopy that, in combination with PrediCtoR, could potentially provide the results that correlate with DNA yield.

Testing the screening device/protocol

In 2013, the established procedures/protocols will be tested. Therefore, with a limited number of bone samples will be acquired from museums. Within the framework of a blind test, DNA results will be compared to the predictions made by museum curators using PrediCtoR and the selected screening method/device.

Progress reports

Work started in Sept 2009. Nothing to report yet.

Outcomes and deliverables

Work started in Sept 2009. Nothing to report yet.

Events

There are no planned events at this stage.

How can I get involved

This wide-ranging testing and first phase pilot development work will conclude in September 2012. The resultant prototypes will be provided to museums by October 2012 for testing.

For more information contact synthesys@nhm.ac.uk.