A Methodological Approach Related to the Decontamination Process from Ancient Skeletal Samples in Different Conditions

Year 2017, Issue: 34, 31 - 47, 30.12.2017

Apak Merve İyras Yeşim Doğan

https://doi.org/10.1501/antro_0000000346

Abstract

Understanding that DNA can be obtained from ancient remains has made valuable contribution to the work of anthropologists. Despite this important contribution, ancient DNA analysis brings many challenges due to the nature of the studied specimens. The most important problem in these studies is to select well-preserved samples and to obtain the best quality DNA possible from these samples. Ancient samples should be purified from external contaminants that they are exposed to at different stages prior to DNA extraction. The success of the purification process is of great importance in terms of the reliability of the results. Results obtained at the end of the process should be defended by researcher showing that they did not take place due to contamination. The methodological approach used in ancient DNA studies is therefore of great importance. In the study, the femur and talus bones were compared in terms of their suitability for this methodology. Samples with different levels of preservation required different applications in the pre-DNA preparation stage. As a result, no significant difference was found between the amount of DNA obtained from the two sample types and it was observed that the samples were successfully purified from modern human DNA contamination

Keywords

Ancient DNA, decontamination, DNA extraction, talus, femur

Farklı Koşullarda Bulunan Antik İskelet Örneklerinden Dekontaminasyon Süreci ile İlgili Metodolojik Yaklaşım

Abstract

Antik kalıntılardan DNA elde edilebileceğinin anlaşılması antropologların çalışmalarına yeni bir boyut kazandırmıştır. Bu önemli katkıya rağmen antik DNA analizleri, üzerinde çalışılan örneklerin doğası gereği birçok güçlüğü de beraberinde getirir. Bu çalışmalarda en önemli sorun yeterince korunmuş örnekleri seçmek ve bu örneklerden mümkün olan en kaliteli DNA’yı elde etmektir. Antik örnekler DNA eldesinden önce farklı aşamalarda maruz kaldıkları dış kontaminantlardan arındırılmalıdır. Arındırma sürecinin başarısı, alınacak sonuçların güvenirliliği açısından büyük önem taşır. Süreç sonunda alınan her sonuç araştırmacı tarafından kontaminasyon nedeni ile gerçekleşmediği gösterilerek savunulmalıdır. Antik DNA çalışmalarında kullanılan metodolojik yaklaşım bu nedenle büyük önem taşır. Çalışmada Femur ve Talus kemikleri bu metodolojiye uygunlukları açısından kıyaslanmıştır. Korunma düzeyleri farklı olan örnekler DNA eldesi öncesi hazırlık sürecinde farklı uygulamalar gerektirmiştir. Sonuç olarak iki örnek tipinden elde edilen DNA miktarı arasında belirgin bir fark bulunamamış ve örneklerin modern insan DNA’sı kontaminasyonundan arındırılabildiği gözlenmiştir

Keywords

Antik DNA, dekontaminasyon, DNA ekstraksiyonu, Talus, Femur

References

• Alakoc, Y. D. ve Aka, P. S. (2009). “Orthograde entrance technique to recover DNA from ancient teeth preserving the physical structure”, Forensic Sci Int, 188(1- 3): 96-8.
• Boberova K., Drozdova E. ve Pizova K. (2012). “Application of Molecular Genetic Methods in Antropological and Paleodemographic Studies of Fragmentary and Damaged Skeletal Material from Resque Excavations”, Journal of Life Science, 6, 961-969
• Gilbert, M. T., Bandelt H. J., Hofreiter M. ve Bernas I. (2005). "Assessing ancient DNA studies", Trends Ecol Evol, 20(10), 541-4
• Brothwell DR. (1981) Digging up Bones. Cornell University Press, ss. 18-21.
• Burger J., Hummel S., Herrmann B. ve Henke W. (1999). “DNA preservation: A microsatellite-DNA study on ancient skeletal remains”, Electrophoresis, 20, 1722–1728.
• Cipollaro M., Bernardo G., Galano G., Galderisi U., Guarino F., Angelini F. ve Cascino A. (1998). “Ancient DNA in human bone remains from Pompeii Archeological Site”, Biochemical and Biophysical Research Communications, 247, 901–904.
• Rizzi, E., Lari, M., Gigli, E., de Bellis, G. ve Caramelli, D. (2012). “Ancient DNA studies: new perspectives on old samples”, Genetics Selection Evolution, 44(1), 21.
• Hagelberg E., Clegg J. B. (1991). “Isolation and characterization of DNA from archaeological bone”, Proc Biol Sci., 244(1309), 45-50.
• Handt, O., Hoss M. ve Pääbo S. (1994). "Ancient DNA: methodological challenges”, Experientia, 50(6), 524-529
• Hanna, J., Bouwman, A.S., Brown, K.A., Parker Pearson, M. ve Brown, T. A. (2012). “Ancient DNA typing shows that a Bronze Age mummy is a composite of different skeletons”, Journal of Archaeological Science, 39(8), 2774-2779
• Hoff-Olsen P., Mevag B., Staalstrom E., Hovde B., Egeland T. ve Olaisen B. (1999). “Extraction of DNA from decomposed human tissue: An evaluation of five extraction methods for short tandem repeat typing”, Forensic Science International, 105, 171-183.
• Hummel S. (2003). Ancient DNA typing; methods, strategies and applications. Springer-Verlag, Berlin.
• Gamba, C., Jones, E. R., Teasdale, M. D., McLaughlin, R. L., Gonzalez-Fortes, G., Mattiangeli, V., ... , Pinhasi, R. (2014). “Genome flux and stasis in a five millennium transect of European prehistory”, Nature Communications, 5(5257), 1-9.
• Gamba, C, Fernández, E., Tirado, M., Deguilloux, M. F., Pemonge, M. H., Utrilla, P., ... , Arroyo-Pardo, E. (2012). “Ancient DNA from an Early Neolithic Iberian population supports a pioneer colonization by first farmers”, Molecular Ecology, 21(1), 45-56.
• Garcia A. A., Munoz, I., Pestoni, C., Lareu, M. V., Rodriguez Calvo, M. S., Carracedo, A. (1996). “Effect of environmental factors on PCR-DNA analysis from dental pulp”, International Journal of Legal Medicine, 109(3), 125–159.
• Gilbert, M. T., Bandelt H. J., Hofreiter M. ve Bernas I. (2005). "Assessing ancient DNA studies", Trends Ecol Evol, 20(10), 541-544.
• Kemp B. M. ve Smith D. G. (2005). “Use of bleach to eliminate contaminating DNA from the surface of bones and teeth”, Forensic Science International, 154, 53-61.
• Kuhn, S. L. (2002). "Paleolithic Archeology in Turkey" Evolutionary Anthropology, 11, 198-210.
• Lindahl, T. (1993). "Recovery of antediluvian DNA”, Nature, 365(6448), 700.
• Malaver, P. C. ve Yunis J. J. (2003). “Different dental tissues as source of DNA for human identification in forensic cases”, Croat Med J., 44(3), 306-309.
• Martinez S. M. (2015). Ancient DNA: A multifunctional Tool for Resolving Anthropological Questions, Doktora Tezi, Universitat Autonoma de Barcolena, ss. 33-42.
• Meyer, E., Wiese, M., Bruchhaus, H., Claussen, M. ve Klein, A. (2000). “Extraction and amplification of authentic DNA from ancient human remains”, Forensic Science International, 113, 87-90.
• Damgaard, P. B., Margaryan, A., Schroeder, H., Orlando, L., Willerslev, E. ve Allentoft, M. E. (2015). “Improving access to endogenous DNA in ancient bones and teeth”, Scientific Reports, 5(11184), 1-12.
• Rohland, N., ve Hofreiter, M. (2007). “Ancient DNA extraction from bones and teeth”, Nat Protoc., 2(7), 1756-1762.
• Prado, V. F., Castro, A. K. F., Oliveria, C. L., Souza, K. T. ve Pena S. D. J. (1997). “Extraction of DNA from human skeletal remains: practical applications in forensic sciences”, Genetic Analysis: Biomolecular engineering, 14, 41-44.
• Prinz, M., Carracedo, A., Mayr, W. R., Morling, N., Parsons, T. J, Sajantila, A., Scheithauer, R., Schmitter, H. ve Schneider, P. M. (2007). “DNA Commission of the International Society for Forensic Genetics (ISFG): Recommendations regarding the role of forensic genetics for disaster victim identification (DVI)”, Forensic Science International: Genetics, 1, 3–12.
• Simon, M. (1998). Archeology of Human Bones. Routledge UK, London, ss. 42-206.
• Paabo, S., Poinar, H., Serre, D., Jaenicke-Despres, V., Hebler, J., Rohland, N., ... , Hofreiter, M. (2004). “Genetic Analyses from Ancient DNA”, Annu. Rev. Genet., 38, 645-679.
• Von Wurmb-Schwark, N., Harbeck, M., Wiesbrock, U., Schroeder, I., Ritz-Timme, S. ve Oehmichen, M. (2003). "Extraction and amplification of nuclear and mitochondrial DNA from ancient and artificially aged bones", Leg Med (Tokyo), 5(Suppl 1), S169-72.
• Watt, K. E. (2005). Decontamination techniques in ancient DNA analysis. Yüksek Lisans Tezi, Simon Fraser University, ss. 12-25.
• White, T. D., Black, M. T. ve Folkens, P. A. (2012). Human Osteology, Third Edition. Elsevier Academic Press, ss. 241-252.
• Yang, D. Y ve Watt, K. (2005). "Contamination controls when preparing archaeological remains for ancient DNA analysis", Journal of Archaeological Sceince, 32, 331-336.