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van der Sluis LG, McGrath K, Thil F, Cersoy S, Pétillon JM, Zazzo A. Identification and tentative removal of collagen glue in Palaeolithic worked bone objects: implications for ZooMS and radiocarbon dating. Sci Rep 2023; 13:22119. [PMID: 38092830 PMCID: PMC10719399 DOI: 10.1038/s41598-023-49242-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/05/2023] [Accepted: 12/06/2023] [Indexed: 12/17/2023] Open
Abstract
Collagen glue has been used for nearly two centuries to consolidate bone material, although its prevalence in museum collections is only now becoming visible. Identifying and removing collagen glue is crucial before the execution of any geochemical or molecular analyses. Palaeolithic bone objects from old excavations intended for radiocarbon dating were first analysed using ZooMS (Zooarchaeology by Mass Spectrometry) to identify the animal species, however peaks characteristic of both cattle and whale were discovered. Two extraction methods for ZooMS were tested to identify the authentic animal species of these objects, which revealed that these were originally whale bone objects that had been consolidated with cattle collagen glue. This is the first time animal collagen glue has been identified in archaeological remains with ZooMS, illustrating again the incredible versatility of this technique. Another technique, Fourier Transform Infrared Spectroscopy in Attenuated Total Reflectance mode (FTIR-ATR), was also tested if it could rapidly identify the presence of collagen glue in archaeological bone material, which was not the case. Two other cleaning methods were tested to remove bone glue contamination prior to radiocarbon dating, along with two modified collagen extraction methods for ZooMS. These methods were applied to bone blank samples (FmC = 0.0031 ± 0.0002, (n = 219), 47 336 ± 277 yr BP) that were experimentally consolidated with collagen glue and to the Palaeolithic bone material (ca. 15 000 and 12 000 yr BP). The experimental bone blanks produced excellent 14C ages, suggesting the cleaning methods were successful, however the 14C ages for some of the Palaeolithic material remained too young considering their contextual age, suggesting that the collagen glue contamination had most likely cross-linked to the authentic collagen molecule. More research is needed in order to gain a deeper understanding of the occurrence and elimination of cross-linked collagen-based glues in material from museum collections.
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Affiliation(s)
- L G van der Sluis
- UMR 7209, Archéozoologie, Archéobotanique: Sociétés, Pratiques et Environnements (AASPE), CNRS, Muséum national d'Histoire naturelle, Paris, France.
- Department of Evolutionary Anthropology, University of Vienna, Djerassiplatz 1, 1030, Vienna, Austria.
- Human Evolution and Archaeological Sciences (HEAS), University of Vienna, 1030, Vienna, Austria.
| | - K McGrath
- Department of Prehistory and Institute of Environmental Science and Technology (ICTA-UAB), Universitat Autònoma de Barcelona, 08193, Cerdanyola del Vallès, Barcelona, Spain
| | - F Thil
- Laboratoire des Sciences du Climat et de l'Environnement, LSCE/IPSL UMR 8212, CEA-CNRS-UVSQ, Université Paris Saclay, 91198, Gif-sur-Yvette, France
| | - S Cersoy
- Centre de Recherche sur la Conservation (CRC), UAR 3224, CNRS, Muséum national d'Histoire naturelle, Paris, France
| | - J-M Pétillon
- Travaux et Recherches Archéologiques sur les Cultures, les Espaces et les Sociétés (TRACES) UMR 5608, CNRS, Université Toulouse Jean Jaurès, Toulouse, France
| | - A Zazzo
- UMR 7209, Archéozoologie, Archéobotanique: Sociétés, Pratiques et Environnements (AASPE), CNRS, Muséum national d'Histoire naturelle, Paris, France
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Edson SM. The effect of chemical compromise on the recovery of DNA from skeletonized human remains: A study of three World War II era incidents recovered from tropical locations. Forensic Sci Med Pathol 2019; 15:10.1007/s12024-019-00179-2. [PMID: 31712986 DOI: 10.1007/s12024-019-00179-2] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 08/19/2019] [Indexed: 12/21/2022]
Abstract
The use of DNA extracted from skeletonized human remains is a common challenge for those working in human identification. Thermal age and chemical compromise should be considered prior to performing DNA testing on skeletonized remains. Both heat and chemical contamination may cause damage to the DNA present in the osseous materials and a subsequent increase in both the difficulty and expense of DNA testing. For this study, three World War II era mass fatality events involving the US military, the USS Oklahoma, the Battle of Tarawa, and the Cabanatuan Prison Camps, were examined for the overall success of DNA testing using five DNA modalities: Sanger sequencing of mitochondrial DNA, AmpFlSTR® MiniFiler™; PowerPlex® Fusion; a modified AmpFlSTR® Yfiler™; and a Next Generation Sequencing (NGS) protocol. Decedents from the three chosen incidents were buried in tropical environments and have the same approximate post mortem interval of 75 years, however, the chemical conditions that decedents were exposed to at each of the incidents vary. Remains from the USS Oklahoma were soaked in fuel oil and salt water immediately post-mortem; Cabanatuan Prison Camp remains were treated with a 'hardening' compound; and those from the Battle of Tarawa were not treated. Skeletal elements from each incident were compared across the 5 tested DNA modalities for success. Chemical insult to skeletal materials appears to have the greatest impact on every modality of DNA testing examined.
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Affiliation(s)
- Suni M Edson
- Armed Forces DNA Identification Laboratory, Armed Forces Medical Examiner System, Dover AFB, Dover, DE, USA.
- College of Science and Engineering, Flinders University, Adelaide, South Australia.
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Müller R, Roberts CA, Brown TA. Biomolecular identification of ancientMycobacterium tuberculosiscomplex DNA in human remains from Britain and continental Europe. AMERICAN JOURNAL OF PHYSICAL ANTHROPOLOGY 2013; 153:178-89. [DOI: 10.1002/ajpa.22417] [Citation(s) in RCA: 31] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/13/2013] [Accepted: 10/21/2013] [Indexed: 11/07/2022]
Affiliation(s)
- Romy Müller
- Manchester Institute of Biotechnology; Faculty of Life Sciences, University of Manchester; Manchester M1 7DN UK
| | | | - Terence A. Brown
- Manchester Institute of Biotechnology; Faculty of Life Sciences, University of Manchester; Manchester M1 7DN UK
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Fattorini P, Marrubini G, Ricci U, Gerin F, Grignani P, Sorçaburu Cigliero S, Xamin A, Edalucci E, La Marca G, Previderé C. Estimating the integrity of aged DNA samples by CE. Electrophoresis 2009; 30:3986-95. [DOI: 10.1002/elps.200900283] [Citation(s) in RCA: 13] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
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López-Polín L, Ollé A, Cáceres I, Carbonell E, Bermúdez de Castro JM. Pleistocene human remains and conservation treatments: the case of a mandible from Atapuerca (Spain). J Hum Evol 2008; 54:539-45. [PMID: 18400257 DOI: 10.1016/j.jhevol.2007.07.011] [Citation(s) in RCA: 13] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/04/2006] [Revised: 07/24/2007] [Accepted: 07/30/2007] [Indexed: 11/18/2022]
Abstract
Research on human evolution depends in many cases on the study of fossil remains that have been treated by conservators. Conservation is a discipline with its own principles and methods. Its goal is not only long-term preservation, but also information recovery and the facilitation of research. Therefore, specialists in conservation propose and carry out the interventions, while research requirements must act as a guide in many steps of the process. In this article, we present an example of a strict conservation methodology applied to a human mandible from the Pleistocene site of Gran Dolina (Sierra de Atapuerca, Spain). An extensive diagnostic examination before the intervention included a computer tomography (CT) scan and stereoscopic light microscopy. This paper describes both the intervention and the mechanical preparation in detail. Finally, the intervention is discussed, as well as general conservation techniques. The compiled details show how this interdisciplinary work allowed retention of both the integrity of the specimen and its information. In conclusion, the development of a suitable method of conservation requires collaboration among all the specialists involved in the study of fossil remains.
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Affiliation(s)
- Lucía López-Polín
- Area de Prehistòria, Universitat Rovira i Virgili, Institut Català de Paleoecologia Humana i Evolució Social, Pl. Imperial Tarraco, 1, 43005 Tarragona, Spain.
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Mitchell D, McAllister P, Stick K, Hauser L. Sperm contamination in archived and contemporary herring samples. Mol Ecol Resour 2008; 8:50-5. [PMID: 21585717 DOI: 10.1111/j.1471-8286.2007.01840.x] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
Studies using archived scales and otoliths to examine ancient fish populations have become increasingly common, despite many methodological challenges in ancient DNA research. Here, we describe a case of DNA contamination in both modern and historical samples of Pacific herring (Clupea pallasii), where the source of the contamination is likely from milt spillage during collection. We describe a series of experiments to remove contamination using pre-extraction wash treatments. Though contamination was easily removed from contemporary fin clippings, no method was successful at removing contamination from historical scales. We discuss the implications of our findings to the genetic analysis of archived samples.
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Affiliation(s)
- Danielle Mitchell
- School of Aquatic and Fishery Sciences, University of Washington, Box 355020, Seattle, WA 98195, USA, Fish Management Division, Washington Department of Fish and Wildlife, PO Box 1100, La Conner, WA 98257, USA
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Pusch CM, Broghammer M, Nicholson GJ, Nerlich AG, Zink A, Kennerknecht I, Bachmann L, Blin N. PCR-Induced Sequence Alterations Hamper the Typing of Prehistoric Bone Samples for Diagnostic Achondroplasia Mutations. Mol Biol Evol 2004; 21:2005-11. [PMID: 15254256 DOI: 10.1093/molbev/msh208] [Citation(s) in RCA: 13] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Abstract
Achondroplasia (ACH) is a skeletal disorder (MIM100800) with an autosomal dominant Mendelian inheritance and complete penetrance. Here we report the screening of ancient bone samples for diagnostic ACH mutations. The diagnostic G-->A transition in the FGFR3 gene at cDNA position 1138 was detected in cloned polymerase chain reaction (PCR) products obtained from the dry mummy of the Semerchet tomb, Egypt (first dynasty, approximately 4,890-5,050 BP [before present]), and from an individual from Kirchheim, Germany (Merovingian period, approximately 1,300-1,500 BP), both of which had short stature. However, these mutations were also reproducibly observed in four ancient control samples from phenotypically healthy individuals (false-positives), rendering the reliable molecular typing of ancient bones for ACH impossible. The treatment of a false-positive DNA extract with uracil N-glycosylase (UNG) to minimize type 2 transitions (G-->A/C-->T) did not reduce the frequency of the false-positive diagnostic ACH mutations. Recently, it was suggested that ancient DNA extracts may induce mutations under PCR. Contemporary human template DNA from a phenotypically healthy individual was therefore spiked with an ancient DNA extract from a cave bear. Again, sequences with the diagnostic G-->A transition in the FGFR3 gene were observed, and it is likely that the false-positive G-->A transitions result from errors introduced during the PCR reaction. Amplifications in the presence of MnCl(2) indicate that position 1138 of the FGFR3 gene is particularly sensitive for mutations. Our data are in line with previously published results on the occurrence of nonrandom mutations in PCR products of contemporary human mitochondrial HVRI template DNA spiked with ancient DNA extracts.
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Affiliation(s)
- C M Pusch
- Institute of Anthropology and Human Genetics, Division of Molecular Genetics, University of Tübingen, Tübingen, Germany
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Kaestle FA, Horsburgh KA. Ancient DNA in anthropology: methods, applications, and ethics. AMERICAN JOURNAL OF PHYSICAL ANTHROPOLOGY 2003; Suppl 35:92-130. [PMID: 12653310 DOI: 10.1002/ajpa.10179] [Citation(s) in RCA: 106] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]
Abstract
Anthropologists were quick to recognize the potential of new techniques in molecular biology to provide additional lines of evidence on questions long investigated in anthropology, as well as those questions that, while always of interest, could not have been addressed by more traditional techniques. The earliest ancient DNA studies, both within anthropology and in other fields, lacked rigorous hypothesis testing. However, more recently the true value of ancient DNA studies is being realized, and methods are being applied to a wide variety of anthropological questions. We review the most common methods and applications to date, and describe promising avenues of future research. We find that ancient DNA analyses have a valuable place in the array of anthropological techniques, but argue that such studies must not be undertaken merely to demonstrate that surviving DNA is present in organic remains, and that no such work should be performed before a careful consideration of the possible ethical ramifications of the research is undertaken.
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Affiliation(s)
- Frederika A Kaestle
- Department of Anthropology, Indiana University, Bloomington, Indiana 47405-7100, USA.
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