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Végh EI, Douka K. SpecieScan: semi-automated taxonomic identification of bone collagen peptides from MALDI-ToF-MS. Bioinformatics 2024; 40:btae054. [PMID: 38337062 PMCID: PMC10918634 DOI: 10.1093/bioinformatics/btae054] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/19/2023] [Revised: 01/08/2024] [Accepted: 02/07/2024] [Indexed: 02/12/2024] Open
Abstract
MOTIVATION Zooarchaeology by Mass Spectrometry (ZooMS) is a palaeoproteomics method for the taxonomic determination of collagen, which traditionally involves challenging manual spectra analysis with limitations in quantitative results. As the ZooMS reference database expands, a faster and reproducible identification tool is necessary. Here we present SpecieScan, an open-access algorithm for automating taxa identification from raw MALDI-ToF mass spectrometry (MS) data. RESULTS SpecieScan was developed using R (pre-processing) and Python (automation). The algorithm's output includes identified peptide markers, closest matching taxonomic group (taxon, family, order), correlation scores with the reference databases, and contaminant peaks present in the spectra. Testing on original MS data from bones discovered at Palaeothic archaeological sites, including Denisova Cave in Russia, as well as using publicly-available, externally produced data, we achieved >90% accuracy at the genus-level and ∼92% accuracy at the family-level for mammalian bone collagen previously analysed manually. AVAILABILITY AND IMPLEMENTATION The SpecieScan algorithm, along with the raw data used in testing, results, reference database, and common contaminants lists are freely available on Github (https://github.com/mesve/SpecieScan).
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Affiliation(s)
- Emese I Végh
- Department of Evolutionary Anthropology, University of Vienna, University Biology Building, A-1030 Vienna, Austria
- Human Evolution and Archaeological Sciences (HEAS), University of Vienna, Vienna, Austria
- Archaeology, Environmental Changes, and Geochemistry, Vrije Universiteit Brussel, 1050 Brussels, Belgium
| | - Katerina Douka
- Department of Evolutionary Anthropology, University of Vienna, University Biology Building, A-1030 Vienna, Austria
- Human Evolution and Archaeological Sciences (HEAS), University of Vienna, Vienna, Austria
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2
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Surovell TA, Litynski ML, Allaun SA, Buckley M, Schoborg TA, Govaerts JA, O'Brien MJ, Pelton SR, Sanders PH, Mackie ME, Kelly RL. Use of hare bone for the manufacture of a Clovis bead. Sci Rep 2024; 14:2937. [PMID: 38316967 PMCID: PMC10844228 DOI: 10.1038/s41598-024-53390-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/23/2023] [Accepted: 01/31/2024] [Indexed: 02/07/2024] Open
Abstract
A tubular bone bead dating to ~ 12,940 BP was recovered from a hearth-centered activity area at the La Prele Mammoth site in Converse County, Wyoming, USA. This is the oldest known bead from the Western Hemisphere. To determine the taxonomic origin of the bead, we extracted collagen for zooarchaeology by mass spectrometry (ZooMS). We also used micro-CT scanning for morphological analysis to determine likely skeletal elements used for its production. We conclude that the bead was made from a metapodial or proximal phalanx of a hare (Lepus sp.). This find represents the first secure evidence for the use of hares during the Clovis period. While the use of hare bone for the manufacture of beads was a common practice in western North America during the Holocene, its origins can now be traced back to at least the terminal Pleistocene.
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Affiliation(s)
- Todd A Surovell
- Department of Anthropology, University of Wyoming, Laramie, WY, USA.
| | | | - Sarah A Allaun
- Office of Archaeology and Historic Preservation, History Colorado, Denver, CO, USA
| | - Michael Buckley
- Manchester Institute of Biotechnology, The University of Manchester, Manchester, UK
| | - Todd A Schoborg
- Department of Molecular Biology, University of Wyoming, Laramie, WY, USA
| | - Jack A Govaerts
- Department of Molecular Biology, University of Wyoming, Laramie, WY, USA
| | | | - Spencer R Pelton
- Office of the Wyoming State Archaeologist, Department of Anthropology, University of Wyoming, Laramie, WY, USA
| | - Paul H Sanders
- Office of the Wyoming State Archaeologist, Department of Anthropology, University of Wyoming, Laramie, WY, USA
| | - Madeline E Mackie
- Department of Sociology and Anthropology, Weber State University, Ogden, UT, USA
| | - Robert L Kelly
- Department of Anthropology, University of Wyoming, Laramie, WY, USA
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3
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Taniguchi K, Miyaguchi H. COL1A2 Barcoding: Bone Species Identification via Shotgun Proteomics. J Proteome Res 2024; 23:377-385. [PMID: 38091499 DOI: 10.1021/acs.jproteome.3c00615] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/06/2024]
Abstract
Species identification of fragmentary bones remains a challenging task in archeology and forensics. A species identification method for such fragmentary bones that has recently attracted interest is the use of bone collagen proteins. Here, we describe a method similar to DNA barcoding that reads collagen protein sequences in bone and automatically determines the species by performing sequence database searches. The method is almost identical to conventional shotgun proteomics analysis of bone samples, except that the database used by the SEQUEST search engine consisted only of entries for collagen type 1 alpha 2 (COL1A2) proteins from various vertebrates. Accordingly, the COL1A2 peptides that differ in sequence among species act as species marker peptides. In SEQUEST-based shotgun proteomics, the protein entries that contain more marker peptide sequences are assigned higher scores; therefore, the highest-scoring protein entry will be the COL1A2 entry for the species from which the analyzed bone was derived. We tested our method using bone samples from 30 vertebrate species and found that all species were correctly identified. In conclusion, COL1A2 can be used as a bone protein barcode and can be read through shotgun proteomics, allowing for automatic bone species identification. Data are available via ProteomeXchange with the identifier PXD045402.
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Affiliation(s)
- Kei Taniguchi
- National Research Institute of Police Science, 6-3-1, Kashiwanoha, Kashiwa 277-0882, Chiba, Japan
| | - Hajime Miyaguchi
- National Research Institute of Police Science, 6-3-1, Kashiwanoha, Kashiwa 277-0882, Chiba, Japan
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4
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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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Rayfield KM, Mychajliw AM, Singleton RR, Sholts SB, Hofman CA. Uncovering the Holocene roots of contemporary disease-scapes: bringing archaeology into One Health. Proc Biol Sci 2023; 290:20230525. [PMID: 38052246 DOI: 10.1098/rspb.2023.0525] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/03/2023] [Accepted: 11/06/2023] [Indexed: 12/07/2023] Open
Abstract
The accelerating pace of emerging zoonotic diseases in the twenty-first century has motivated cross-disciplinary collaboration on One Health approaches, combining microbiology, veterinary and environmental sciences, and epidemiology for outbreak prevention and mitigation. Such outbreaks are often caused by spillovers attributed to human activities that encroach on wildlife habitats and ecosystems, such as land use change, industrialized food production, urbanization and animal trade. While the origin of anthropogenic effects on animal ecology and biogeography can be traced to the Late Pleistocene, the archaeological record-a long-term archive of human-animal-environmental interactions-has largely been untapped in these One Health approaches, thus limiting our understanding of these dynamics over time. In this review, we examine how humans, as niche constructors, have facilitated new host species and 'disease-scapes' from the Late Pleistocene to the Anthropocene, by viewing zooarchaeological, bioarchaeological and palaeoecological data with a One Health perspective. We also highlight how new biomolecular tools and advances in the '-omics' can be holistically coupled with archaeological and palaeoecological reconstructions in the service of studying zoonotic disease emergence and re-emergence.
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Affiliation(s)
- Kristen M Rayfield
- Department of Ecology and Evolution, Stony Brook University, Stony Brook, NY, USA
- Laboratories of Molecular Anthropology & Microbiome Research, University of Oklahoma, Norman, OK, USA
- Department of Anthropology, University of Oklahoma, Norman, OK 73019-0390, USA
- Department of Anthropology, National Museum of Natural History, Smithsonian Institution, Washington, DC, USA
| | - Alexis M Mychajliw
- Laboratories of Molecular Anthropology & Microbiome Research, University of Oklahoma, Norman, OK, USA
- Department of Anthropology, University of Oklahoma, Norman, OK 73019-0390, USA
- Department of Anthropology, National Museum of Natural History, Smithsonian Institution, Washington, DC, USA
- Department of Biology & Program in Environmental Studies, Middlebury College, Middlebury, VT 05753-6203, USA
| | - Robin R Singleton
- Laboratories of Molecular Anthropology & Microbiome Research, University of Oklahoma, Norman, OK, USA
- Department of Anthropology, University of Oklahoma, Norman, OK 73019-0390, USA
| | - Sabrina B Sholts
- Department of Anthropology, National Museum of Natural History, Smithsonian Institution, Washington, DC, USA
| | - Courtney A Hofman
- Laboratories of Molecular Anthropology & Microbiome Research, University of Oklahoma, Norman, OK, USA
- Department of Anthropology, University of Oklahoma, Norman, OK 73019-0390, USA
- Department of Anthropology, National Museum of Natural History, Smithsonian Institution, Washington, DC, USA
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6
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Wang N, Xu Y, Tang Z, He C, Hu X, Cui Y, Douka K. Large-scale application of palaeoproteomics (Zooarchaeology by Mass Spectrometry; ZooMS) in two Palaeolithic faunal assemblages from China. Proc Biol Sci 2023; 290:20231129. [PMID: 37876197 PMCID: PMC10598447 DOI: 10.1098/rspb.2023.1129] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/23/2023] [Accepted: 09/22/2023] [Indexed: 10/26/2023] Open
Abstract
The application of Zooarchaeology by Mass Spectrometry (ZooMS) on Pleistocene sites in Europe and northern Asia has resulted in the discovery of important new hominin fossils and has expanded the range of identified fauna. However, no systematic, large-scale application of ZooMS on Palaeolithic sites in East Asia has been attempted thus far. Here, we analyse 866 morphologically non-diagnostic bones from Jinsitai Cave in northeast China and Yumidong Cave in South China, from archaeological horizons dating to 150-10 ka BP. Bones from both sites revealed a high degree of collagen preservation and potentially time-related deamidation patterns, despite being located in very distinct environmental settings. At Jinsitai, we identified 31 camel bones, five of which were radiocarbon dated to 37-20 ka BP. All dated specimens correspond to colder periods of Marine Isotope Stages 3 and 2. We regard the presence of camels at Jinsitai as evidence of wild camels being a megafauna taxon targeted, most likely by early modern humans, during their expansion across northeast Asia. This large-scale application of ZooMS in China highlights the potential of the method for furthering our knowledge of the palaeoanthropological and zooarchaeological records of East Asia.
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Affiliation(s)
- Naihui Wang
- School of Life Sciences, Jilin University, 130012 Changchun, People's Republic of China
- Max Planck Institute of Geoanthropology, 07745, Jena, Germany
- Department of Early Prehistory and Quaternary Ecology, University of Tübingen, Schloss Hohentübingen, 72070 Tübingen, Germany
| | - Yang Xu
- School of Life Sciences, Jilin University, 130012 Changchun, People's Republic of China
| | - Zhuowei Tang
- School of Archaeology, Jilin University, 130012 Changchun, People's Republic of China
| | - Cunding He
- China-Central Asia ‘the Belt and Road’ Joint Laboratory on Human and Environment Research, 710127 Xi'an, People's Republic of China
- School of Cultural Heritage, Northwest University, 710127 Xi'an, People's Republic of China
| | - Xin Hu
- Chongqing China Three Gorges Museum, 400013 Chongqing, People's Republic of China
| | - Yinqiu Cui
- School of Life Sciences, Jilin University, 130012 Changchun, People's Republic of China
| | - Katerina Douka
- Max Planck Institute of Geoanthropology, 07745, Jena, Germany
- Department of Evolutionary Anthropology, Faculty of Life Sciences, University of Vienna, 1030 Vienna, Austria
- Human Evolution and Archaeological Sciences (HEAS), University of Vienna, 1030 Vienna, Austria
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7
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Jeanjean M, McGrath K, Valenzuela-Lamas S, Nieto-Espinet A, Schafberg R, Parés-Casanova PM, Jiménez-Manchón S, Guintard C, Tekkouk F, Ridouh R, Mureau C, Evin A. ZooMS confirms geometric morphometrics species identification of ancient sheep and goat. ROYAL SOCIETY OPEN SCIENCE 2023; 10:230672. [PMID: 37771960 PMCID: PMC10523075 DOI: 10.1098/rsos.230672] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 05/17/2023] [Accepted: 08/25/2023] [Indexed: 09/30/2023]
Abstract
Geometric morphometrics can effectively distinguish isolated third lower molars of present-day sheep and goat, but its applicability to archaeological specimens has yet to be established. Using a modern reference collection of 743 sheep and goats and a two-dimensional landmark-based geometric morphometric (GMM) protocol, this study aimed to morphometrically identify 109 archaeological specimens, used as case studies, dating from the Late Neolithic to the modern period/era. These morphometric identifications were then compared to molecular identifications via collagen peptide mass fingerprinting, known as Zooarcheology by Mass Spectrometry (ZooMS). ZooMS confirmed the morphometric identifications for 104 specimens, with the five misidentified specimens all morphometrically identified as goat. Modern sheep and goats have larger teeth and distinct shapes compared to their archaeological counterparts, suggesting strong differences between archaeological and modern specimens potentially linked with recent breed improvement or geographical origin of the specimens. In addition, for both species, some of the archaeological dental morphologies do not match with any of our modern references. This study validates the applicability of geometric morphometrics for identifying isolated archaeological sheep and goat teeth. It represents a stepping stone for future, non-destructive, bioarchaeological studies of the two species.
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Affiliation(s)
- Marine Jeanjean
- Institute of Evolutionary Science-Montpellier (ISEM), University of Montpellier, CNRS, EPHE, IRD, Montpellier, France
| | - Krista McGrath
- Department of Prehistory & Institute of Environmental Science and Technology (ICTA), Universitat Autònoma de Barcelona, 08193, Barcelona, Spain
| | - Silvia Valenzuela-Lamas
- Archaeology of Social Dynamics (ASD), Institució Milà i Fontanals de Recerca en Humanitats, Consejo Superior de Investigaciones Científicas (IMF-CSIC), C/ Egipcíaques 15, 08001 Barcelona, Spain
| | - Ariadna Nieto-Espinet
- Grup d'Investigació Prehistòrica (GIP), Departament d'Història, Universidad de Lleida, 25005 Lleida, Spain
| | - Renate Schafberg
- Central Natural Science Collections, Martin Luther University Halle-Wittenberg, Domplatz 4, 06108 Halle (Saale), Germany
| | | | - Sergio Jiménez-Manchón
- Archaeology of Social Dynamics (ASD), Institució Milà i Fontanals de Recerca en Humanitats, Consejo Superior de Investigaciones Científicas (IMF-CSIC), C/ Egipcíaques 15, 08001 Barcelona, Spain
| | - Claude Guintard
- Laboratoire d'Anatomie comparée, Ecole Nationale Vétérinaire, de l'Agroalimentaire et de l'Alimentation, Nantes Atlantique – ONIRIS, Nantes Cedex 03, France
- GEROM, UPRES EA 4658, LABCOM ANR NEXTBONE, Faculté de santé de l'Université d'Angers, Angers, France
| | - Faiza Tekkouk
- Institut des Sciences Vétérinaires, Laboratoire « Gestion de la santé et productions animales », Université des frères Mentouri, El Khroub, Algérie
| | - Rania Ridouh
- Institut des Sciences Vétérinaires, Laboratoire « Gestion de la santé et productions animales », Université des frères Mentouri, El Khroub, Algérie
| | - Cyprien Mureau
- Institute of Evolutionary Science-Montpellier (ISEM), University of Montpellier, CNRS, EPHE, IRD, Montpellier, France
| | - Allowen Evin
- Institute of Evolutionary Science-Montpellier (ISEM), University of Montpellier, CNRS, EPHE, IRD, Montpellier, France
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Bray F, Fabrizi I, Flament S, Locht JL, Antoine P, Auguste P, Rolando C. Robust High-Throughput Proteomics Identification and Deamidation Quantitation of Extinct Species up to Pleistocene with Ultrahigh-Resolution MALDI-FTICR Mass Spectrometry. Anal Chem 2023; 95:7422-7432. [PMID: 37130053 DOI: 10.1021/acs.analchem.2c03301] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/03/2023]
Abstract
Peptide mass fingerprinting (PMF) using MALDI-TOF mass spectrometry allows the identification of bone species based on their type I collagen sequence. In the archaeological or paleontological field, PMF is known as zooarchaeology mass spectrometry (ZooMS) and is widely implemented to find markers for most species, including the extinct ones. In addition to the identification of bone species, ZooMS enables dating estimation by measuring the deamidation value of specific peptides. Herein, we report several enhancements to the classical ZooMS technique, which reduces to 10-fold the required bone sample amount (down to the milligram scale) and achieves robust deamidation value calculation in a high-throughput manner. These improvements rely on a 96-well plate samples preparation, a careful optimization of collagen extraction and digestion to avoid spurious post-translational modification production, and PMF at high resolution using matrix-assisted laser desorption ionization Fourier transform ion cyclotron resonance (MALDI-FTICR) analysis. This method was applied to the identification of a hundred bones of herbivores from the Middle Paleolithic site of Caours (Somme, France) well dated from the Eemian Last Interglacial climatic optimum. The method gave reliable species identification to bones already identified by their osteomorphology, as well as to more challenging samples consisting of small or burned bone fragments. Deamidation values of bones originating from the same geological layers have a low standard deviation. The method can be applied to archaeological bone remains and offers a robust capacity to identify traditionally unidentifiable bone fragments, thus increasing the number of identified specimens and providing invaluable information in specific contexts.
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Affiliation(s)
- Fabrice Bray
- Univ. Lille, CNRS, UAR 3290─MSAP - Miniaturisation pour La Synthèse, L'Analyse et La Protéomique, Lille F-59000, France
| | - Isabelle Fabrizi
- Univ. Lille, CNRS, UAR 3290─MSAP - Miniaturisation pour La Synthèse, L'Analyse et La Protéomique, Lille F-59000, France
| | - Stéphanie Flament
- Univ. Lille, CNRS, UAR 3290─MSAP - Miniaturisation pour La Synthèse, L'Analyse et La Protéomique, Lille F-59000, France
| | - Jean-Luc Locht
- Inrap Hauts-de-France, 32, avenue de l'Étoile-du-Sud, Glisy 80440, France
- Univ. Paris I & UPEC, CNRS, UMR 8591, Laboratoire de Géographie Physique, Environnements quaternaires et actuels, Thiais F-94230, France
| | - Pierre Antoine
- Univ. Paris I & UPEC, CNRS, UMR 8591, Laboratoire de Géographie Physique, Environnements quaternaires et actuels, Thiais F-94230, France
| | - Patrick Auguste
- Univ. Lille, CNRS, UMR 8198 - Evo-Eco-Paléo, Lille F-59000, France
| | - Christian Rolando
- Univ. Lille, CNRS, UAR 3290─MSAP - Miniaturisation pour La Synthèse, L'Analyse et La Protéomique, Lille F-59000, France
- Shrieking Sixties, 1-3 Allée Lavoisier, Villeneuve-d'Ascq F-59650, France
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9
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Xu Y, Wang N, Gao S, Li C, Ma P, Yang S, Jiang H, Shi S, Wu Y, Zhang Q, Cui Y. Solving the two-decades-old murder case through joint application of ZooMS and ancient DNA approaches. Int J Legal Med 2023; 137:319-327. [PMID: 36625884 PMCID: PMC9902420 DOI: 10.1007/s00414-022-02944-5] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/20/2022] [Accepted: 12/29/2022] [Indexed: 01/11/2023]
Abstract
Bones are one of the most common biological types of evidence in forensic cases. Discriminating human bones from irrelevant species is important for the identification of victims; however, the highly degraded bones could be undiagnostic morphologically and difficult to analyze with standard DNA profiling approaches. The same challenge also exists in archaeological studies. Here, we present an initial study of an analytical strategy that involves zooarchaeology by mass spectrometry (ZooMS) and ancient DNA methods. Through the combined strategy, we managed to identify the only biological evidence of a two-decades-old murder case - a small piece of human bone out of 19 bone fragments - and confirmed the kinship between the victim and the putative parents through joint application of next-generation sequencing (NGS) and Sanger sequencing methods. ZooMS effectively screened out the target human bone while ancient DNA methods improve the DNA yields. The combined strategy in this case outperforms the standard DNA profiling approach with shorter time, less cost, as well as higher reliability for the genetic identification results. HIGHLIGHTS: • The first application of zooarchaeology by mass spectrometry technique in the forensic case for screening out human bones from bone fragment mixtures. • Application of ancient DNA technique to recover the highly degraded DNA sequence from the challenging sample that failed standard DNA profiling approaches. • A fast, sensitive, and low-cost strategy that combines the strengths of protein analysis and DNA analysis for kinship identification in forensic research.
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Affiliation(s)
- Yang Xu
- School of Life Sciences, Jilin University, Changchun, 130012 China
| | - Naihui Wang
- Max Planck Institute for the Science of Human History, 07745 Jena, Germany
| | - Shizhu Gao
- School of Pharmaceutical Sciences, Jilin University, Changchun, 130021 China
| | - Chunxiang Li
- School of Life Sciences, Jilin University, Changchun, 130012 China
| | - Pengcheng Ma
- School of Life Sciences, Jilin University, Changchun, 130012 China
| | - Shasha Yang
- School of Life Sciences, Jilin University, Changchun, 130012 China
| | - Hai Jiang
- Criminal Police Detachment, Qingdao Municipal Public Security Bureau, Qingdao, 266034 China
| | - Shoujin Shi
- Criminal Investigation Team, Jimo Branch, Qingdao Municipal Public Security Bureau, Qingdao, 266205 China
| | - Yanhua Wu
- Division of Clinical Research, First Hospital of Jilin University, Changchun, 130021 China
| | - Quanchao Zhang
- Bioarchaeology Laboratory, Jilin University, Changchun, 130012 China ,School of Archaeology, Jilin University, Changchun, 130012 China
| | - Yinqiu Cui
- School of Life Sciences, Jilin University, Changchun, 130012, China. .,Bioarchaeology Laboratory, Jilin University, Changchun, 130012, China.
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10
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Bonicelli A, Mickleburgh HL, Chighine A, Locci E, Wescott DJ, Procopio N. The 'ForensOMICS' approach for postmortem interval estimation from human bone by integrating metabolomics, lipidomics, and proteomics. eLife 2022; 11:e83658. [PMID: 36583441 PMCID: PMC9803353 DOI: 10.7554/elife.83658] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/22/2022] [Accepted: 12/09/2022] [Indexed: 12/31/2022] Open
Abstract
The combined use of multiple omics allows to study complex interrelated biological processes in their entirety. We applied a combination of metabolomics, lipidomics and proteomics to human bones to investigate their combined potential to estimate time elapsed since death (i.e., the postmortem interval [PMI]). This 'ForensOMICS' approach has the potential to improve accuracy and precision of PMI estimation of skeletonized human remains, thereby helping forensic investigators to establish the timeline of events surrounding death. Anterior midshaft tibial bone was collected from four female body donors before their placement at the Forensic Anthropology Research Facility owned by the Forensic Anthropological Center at Texas State (FACTS). Bone samples were again collected at selected PMIs (219-790-834-872days). Liquid chromatography mass spectrometry (LC-MS) was used to obtain untargeted metabolomic, lipidomic, and proteomic profiles from the pre- and post-placement bone samples. The three omics blocks were investigated independently by univariate and multivariate analyses, followed by Data Integration Analysis for Biomarker discovery using Latent variable approaches for Omics studies (DIABLO), to identify the reduced number of markers describing postmortem changes and discriminating the individuals based on their PMI. The resulting model showed that pre-placement metabolome, lipidome and proteome profiles were clearly distinguishable from post-placement ones. Metabolites in the pre-placement samples suggested an extinction of the energetic metabolism and a switch towards another source of fuelling (e.g., structural proteins). We were able to identify certain biomolecules with an excellent potential for PMI estimation, predominantly the biomolecules from the metabolomics block. Our findings suggest that, by targeting a combination of compounds with different postmortem stability, in the future we could be able to estimate both short PMIs, by using metabolites and lipids, and longer PMIs, by using proteins.
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Affiliation(s)
- Andrea Bonicelli
- The Forensic Science Unit, Faculty of Health and Life Sciences, Northumbria UniversityNewcastle upon TyneUnited Kingdom
| | - Hayley L Mickleburgh
- Amsterdam Centre for Ancient Studies and Archaeology (ACASA) – Department of Archaeology, Faculty of Humanities, University of AmsterdamAmsterdamNetherlands
- Forensic Anthropology Center, Texas State UniversitySan MarcosUnited States
| | - Alberto Chighine
- Department of Medical Science and Public Health, Section of Legal Medicine, University of CagliariMonserratoItaly
| | - Emanuela Locci
- Department of Medical Science and Public Health, Section of Legal Medicine, University of CagliariMonserratoItaly
| | - Daniel J Wescott
- Forensic Anthropology Center, Texas State UniversitySan MarcosUnited States
| | - Noemi Procopio
- The Forensic Science Unit, Faculty of Health and Life Sciences, Northumbria UniversityNewcastle upon TyneUnited Kingdom
- Forensic Anthropology Center, Texas State UniversitySan MarcosUnited States
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Pilaar Birch SE, Szpak P. Current developments and future directions in archaeological science. Proc Natl Acad Sci U S A 2022; 119:e2212490119. [PMID: 36252010 PMCID: PMC9618125 DOI: 10.1073/pnas.2212490119] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 08/03/2023] Open
Affiliation(s)
- Suzanne E. Pilaar Birch
- Department of Anthropology, Department of Geography, University of Georgia, Athens, GA 30602
| | - Paul Szpak
- Department of Anthropology, Trent University, Peterborough, K9L 0G2 ON, Canada
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12
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Abstract
Paleoproteomics, the study of ancient proteins, is a rapidly growing field at the intersection of molecular biology, paleontology, archaeology, paleoecology, and history. Paleoproteomics research leverages the longevity and diversity of proteins to explore fundamental questions about the past. While its origins predate the characterization of DNA, it was only with the advent of soft ionization mass spectrometry that the study of ancient proteins became truly feasible. Technological gains over the past 20 years have allowed increasing opportunities to better understand preservation, degradation, and recovery of the rich bioarchive of ancient proteins found in the archaeological and paleontological records. Growing from a handful of studies in the 1990s on individual highly abundant ancient proteins, paleoproteomics today is an expanding field with diverse applications ranging from the taxonomic identification of highly fragmented bones and shells and the phylogenetic resolution of extinct species to the exploration of past cuisines from dental calculus and pottery food crusts and the characterization of past diseases. More broadly, these studies have opened new doors in understanding past human-animal interactions, the reconstruction of past environments and environmental changes, the expansion of the hominin fossil record through large scale screening of nondiagnostic bone fragments, and the phylogenetic resolution of the vertebrate fossil record. Even with these advances, much of the ancient proteomic record still remains unexplored. Here we provide an overview of the history of the field, a summary of the major methods and applications currently in use, and a critical evaluation of current challenges. We conclude by looking to the future, for which innovative solutions and emerging technology will play an important role in enabling us to access the still unexplored "dark" proteome, allowing for a fuller understanding of the role ancient proteins can play in the interpretation of the past.
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Affiliation(s)
- Christina Warinner
- Department
of Anthropology, Harvard University, Cambridge, Massachusetts 02138, United States
- Department of Archaeogenetics, Max Planck Institute for Evolutionary Anthropology, Leipzig 04103, Germany
| | - Kristine Korzow Richter
- Department
of Anthropology, Harvard University, Cambridge, Massachusetts 02138, United States
| | - Matthew J. Collins
- Department
of Archaeology, Cambridge University, Cambridge CB2 3DZ, United Kingdom
- Section
for Evolutionary Genomics, Globe Institute,
University of Copenhagen, Copenhagen 1350, Denmark
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