Final Activity Report Summary - RE-PAIR (Restoration of the past genetic heritage)
The original purpose of this project was to enhance the recovery and quality of DNA from ancient samples improving extraction techniques, developing a better comprehension of the typology of chemical damage present on this kind of samples and finally to apply a specific enzymatic approach to repair these alterations. However it was not possible for me to conduct the project as planned, due to changes occurred in the research group structure (my supervisor moved to Canada). I therefore worked under the direct supervision of Prof. Matthew Collins. With his expertise in degradation of proteinaceous residues and amino acids in ancient samples and my experience in protein investigation we decided to reconfigure the project to pursue the same target with a different approach, using protein sequence as a proxy for DNA. We had the opportunity to use the most advanced technology and were able to explore the survival rate of each protein and each peptide, both from a qualitative and quantitative point of view. Development of a dedicated bioinformatics approach allowed more efficient data mining from these unconventional data sets allowing detection, on specific amino acids, of chemical modifications due to the action of time. To validate our approach, we also compared our results with those obtained using already established techniques. In particular the evaluation of amino acid racemisation extent was used to assess the preservation of biomolecules from an exceptional context: soil residues from the bottom of the Dye 3 ice core from Greenland.
Our results proved that the level of preservation of the biomolecules present in the sample was compatible with sequencing of ancient DNA. Our forecasts were confirmed by experiments performed by an international team lead by Prof. Eske Willerslev. The results obtained from probably the most ancient DNA ever sequenced allow environmental reconstruction of the past flora and fauna present in southern Greenland around 450 million years ago, revealing a northern boreal forest ecosystem rather than today's Arctic environment. The highlight of the work was represented by the publication on the prestigious magazine Science (v. 316, 7 July 2007): Ancient Biomolecules from Deep Ice Cores Reveal a Forested Southern Greenland. The implications of this discovery will help to improve the modelling for the reconstruction of climate variation in the past and future climate change.
The proteomic approach on ancient samples is pioneered in only a few laboratories in the world. Full exploitation of this new source of molecular information from the past requires development of specific methodologies. The data obtained with this approach perfectly complement ancient DNA information enriching our knowledge of many different biological and cultural aspects of the past.
Among the many different typologies of tested samples it appeared that archaeobotanical remains, namely seeds, appeared to be particularly suitable as a source of ancient proteins. We sequenced a wide number of proteins and, comparing these results with the equivalent ones from modern samples, it was possible to evaluate the state of preservation for many different proteins and peptides, both from a qualitative and quantitative point of view. Combined analysis of DNA and proteins is still in progress and we expect to integrate information relative to ancient biomolecular preservation with data useful to better understand the domestication and selection process experience by the crops we are studying.
We immediately realised that the investigation of degraded proteinaceous residues can have a practical application which exceeds the archaeological field. Specifically we are now involved in collaboration with Government agencies to develop an application of our analytical techniques to support decision making in food safety legislation at European level.
My career and my scientific training had a strong benefit from this fellowship. I had the opportunity to learn and use cutting-edge methodologies and to apply them on relevant topics. At the moment I continue to work at York as coordinator of the Ancient Protein Mass Spectrometry group.
Our results proved that the level of preservation of the biomolecules present in the sample was compatible with sequencing of ancient DNA. Our forecasts were confirmed by experiments performed by an international team lead by Prof. Eske Willerslev. The results obtained from probably the most ancient DNA ever sequenced allow environmental reconstruction of the past flora and fauna present in southern Greenland around 450 million years ago, revealing a northern boreal forest ecosystem rather than today's Arctic environment. The highlight of the work was represented by the publication on the prestigious magazine Science (v. 316, 7 July 2007): Ancient Biomolecules from Deep Ice Cores Reveal a Forested Southern Greenland. The implications of this discovery will help to improve the modelling for the reconstruction of climate variation in the past and future climate change.
The proteomic approach on ancient samples is pioneered in only a few laboratories in the world. Full exploitation of this new source of molecular information from the past requires development of specific methodologies. The data obtained with this approach perfectly complement ancient DNA information enriching our knowledge of many different biological and cultural aspects of the past.
Among the many different typologies of tested samples it appeared that archaeobotanical remains, namely seeds, appeared to be particularly suitable as a source of ancient proteins. We sequenced a wide number of proteins and, comparing these results with the equivalent ones from modern samples, it was possible to evaluate the state of preservation for many different proteins and peptides, both from a qualitative and quantitative point of view. Combined analysis of DNA and proteins is still in progress and we expect to integrate information relative to ancient biomolecular preservation with data useful to better understand the domestication and selection process experience by the crops we are studying.
We immediately realised that the investigation of degraded proteinaceous residues can have a practical application which exceeds the archaeological field. Specifically we are now involved in collaboration with Government agencies to develop an application of our analytical techniques to support decision making in food safety legislation at European level.
My career and my scientific training had a strong benefit from this fellowship. I had the opportunity to learn and use cutting-edge methodologies and to apply them on relevant topics. At the moment I continue to work at York as coordinator of the Ancient Protein Mass Spectrometry group.