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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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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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Bradfield J, Kitchener AC, Buckley M. Selection preferences for animal species used in bone-tool-manufacturing strategies in KwaZulu-Natal, South Africa. PLoS One 2021; 16:e0249296. [PMID: 33793614 PMCID: PMC8016335 DOI: 10.1371/journal.pone.0249296] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/27/2020] [Accepted: 03/15/2021] [Indexed: 11/18/2022] Open
Abstract
Animal symbolism is a prominent feature of many human societies globally. In some cases, these symbolic attributes manifest in the technological domain, influencing the decision to use the bones of certain animals and not others for tool manufacture. In southern Africa, animals feature prominently in the cosmogenic narratives of both hunter-gatherer and Bantu-speaking farmer groups. Whenever these two culturally distinct groups came into contact with each other there would be an assimilation of cosmogenic concepts of power and the adoption of certain symbolically important animals. In this paper, we report on which animals were selected to make bone tools during the first millennium AD contact period in KwaZulu-Natal Province, South Africa, and explore the extent to which this selection may have been influenced by the symbolic associations of specific animals. Our results show selective targeting of specific animals for tool manufacture at some sites, with a narrowing of the range of selected species during the first millennium AD contact period. Certain antelope tribes, such as Aepycerotini, Cephalophini and Antilopini, appear to have been deliberately avoided, thus arguing against opportunistic selection. Nor does the range of selected animals appear to show any obvious mechanical considerations, as has been noted in similar studies. We highlight the potential of ZooMS for understanding the dynamics of animal symbolism in the past.
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Affiliation(s)
- Justin Bradfield
- Palaeo-Research Institute, University of Johannesburg, Johannesburg, South Africa
- * E-mail:
| | - Andrew C. Kitchener
- Department of Natural Sciences, National Museums Scotland, Edinburgh, United Kingdom
- School of Geosciences, University of Edinburgh, Edinburgh, United Kingdom
| | - Michael Buckley
- School of Natural Sciences, Manchester Institute of Biotechnology, The University of Manchester, Manchester, United Kingdom
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Herrando-Pérez S. Bone need not remain an elephant in the room for radiocarbon dating. ROYAL SOCIETY OPEN SCIENCE 2021; 8:201351. [PMID: 33614076 PMCID: PMC7890471 DOI: 10.1098/rsos.201351] [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: 07/30/2020] [Accepted: 12/08/2020] [Indexed: 06/12/2023]
Abstract
Radiocarbon (14C) analysis of skeletal remains by accelerator mass spectrometry is an essential tool in multiple branches of science. However, bone 14C dating results can be inconsistent and not comparable due to disparate laboratory pretreatment protocols that remove contamination. And, pretreatments are rarely discussed or reported by end-users, making it an 'elephant in the room' for Quaternary scientists. Through a questionnaire survey, I quantified consensus on the reliability of collagen pretreatments for 14C dating across 132 experts (25 countries). I discovered that while more than 95% of the audience was wary of contamination and would avoid gelatinization alone (minimum pretreatment used by most 14C facilities), 52% asked laboratories to choose the pretreatment method for them, and 58% could not rank the reliability of at least one pretreatment. Ultrafiltration was highly popular, and purification by XAD resins seemed restricted to American researchers. Isolating and dating the amino acid hydroxyproline was perceived as the most reliable pretreatment, but is expensive, time-consuming and not widely available. Solid evidence supports that only molecular-level dating accommodates all known bone contaminants and guarantees complete removal of humic and fulvic acids and conservation substances, with three key areas of progress: (i) innovation and more funded research is required to develop affordable analytical chemistry that can handle low-mass samples of collagen amino acids, (ii) a certification agency overseeing dating-quality control is needed to enhance methodological reproducibility and dating accuracy among laboratories, and (iii) more cross-disciplinary work with better 14C reporting etiquette will promote the integration of 14C dating across disciplines. Those developments could conclude long-standing debates based on low-accuracy data used to build chronologies for animal domestications, human/megafauna extirpations and migrations, archaeology, palaeoecology, palaeontology and palaeoclimate models.
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Naihui W, Samantha B, Peter D, Sandra H, Maxim K, Sindy L, Oshan W, Stefano G, Michael C, Liora HK, Matthew S, Glenn S, Michael S, Kristine RK, Katerina D. Testing the efficacy and comparability of ZooMS protocols on archaeological bone. J Proteomics 2020; 233:104078. [PMID: 33338688 DOI: 10.1016/j.jprot.2020.104078] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/08/2020] [Revised: 12/03/2020] [Accepted: 12/12/2020] [Indexed: 12/27/2022]
Abstract
Collagen peptide mass fingerprinting, best known as Zooarchaeology by Mass Spectrometry (or ZooMS) when applied to archaeology, has become invaluable for the taxonomic identification of archaeological collagenous materials, in particular fragmentary and modified bone remains. Prior to MALDI-based spectrometric analysis, collagen needs to be extracted from the bone's inorganic matrix, isolated and purified. Several protocols are currently employed for ZooMS analysis, however their efficacy and comparability has not been directly tested. Here, we use four different ZooMS protocols to analyze 400 bone samples from seven archaeological sites, dating to between ~500,000-2000 years ago. One of them, single-pot solid-phase-enhance sample preparation (SP3), is used for the first time as a ZooMS protocol. Our results indicate that the least-destructive ZooMS protocol which uses an ammonium bicarbonate buffer as a means of extracting collagen is most suitable for bones with good collagen preservation, whereas the acid-based methodologies can improve success rates for bones with low-to-medium collagen preservation. Since preservation of biomolecules in archaeological bones is highly variable due to age and environmental conditions, we use the percent nitrogen by weight (%N) value as an independent semi-quantitative proxy for assessing collagen content and for predicting which bones will likely result in a successful ZooMS-based identification. We find that 0.26%N as a threshold for screening material could optimize the number of spectra which produce identifications using ZooMS. SIGNIFICANCE STATEMENT: We present a direct comparison of three previously published ZooMS protocols for the analyses of archaeological bones, and the first use of an SP3-based approach to ZooMS analysis. Our results show that the acid-based ZooMS protocols increase the success rate for bones with low-medium collagen preservation. We identify 0.26%N as a threshold for optimizing the number of samples with enough collagen for successful peptide mass fingerprinting.
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Affiliation(s)
- Wang Naihui
- Department of Archaeology, Max Planck Institute for the Science of Human History (MPI-SHH), Kahlaische Straße 10, 07745 Jena, Germany.
| | - Brown Samantha
- Department of Archaeology, Max Planck Institute for the Science of Human History (MPI-SHH), Kahlaische Straße 10, 07745 Jena, Germany.
| | - Ditchfield Peter
- School of Archaeology, University of Oxford, 1 South Parks Road, Oxford, UK.
| | - Hebestreit Sandra
- Department of Archaeology, Max Planck Institute for the Science of Human History (MPI-SHH), Kahlaische Straße 10, 07745 Jena, Germany.
| | - Kozilikin Maxim
- Institute of Archaeology and Ethnography, Siberian Branch, Russian Academy of Sciences, Pr. Akademika Lavrentieva, 17, Novosibirsk 630090, Russia
| | - Luu Sindy
- Department of Anatomy, University of Otago, PO Box 56, Dunedin 9054, New Zealand.
| | - Wedage Oshan
- Department of Archaeology, Max Planck Institute for the Science of Human History (MPI-SHH), Kahlaische Straße 10, 07745 Jena, Germany; Department of History and Archaeology, University of Sri Jayewardenepura, Gangodawila, Nugegoda, Sri Lanka.
| | - Grimaldi Stefano
- LaBAAF -Laboratorio Bagolini Archeologia, Archeometria, Fotografia, CeASUm - Centro di Alti Studi Umanistici, Dipartimento di Lettere e Filosofia, Università di Trento, via T.Gar14, I-38122 Trento, Italy; IsIPU - Istituto Italiano di Paleontologia Umana, Anagni, Italy.
| | - Chazan Michael
- Department of Anthropology, Canada Institute of Evolutionary Studies, University of Toronto, 19 Russell Street, Toronto, Canada; University of the Witwatersrand, Johannesburg, South Africa.
| | - Horwitz Kolska Liora
- National Natural History Collections, The Hebrew University, Berman Building, E. Safra-Givat Ram Campus, 91904 Jerusalem, Israel
| | - Spriggs Matthew
- School of Archaeology and Anthropology, Sir Roland Wilson Bldg 120, The Australian National University, Canberra, ACT 2600, Australia.
| | | | - Shunkov Michael
- Institute of Archaeology and Ethnography, Siberian Branch, Russian Academy of Sciences, Pr. Akademika Lavrentieva, 17, Novosibirsk 630090, Russia
| | - Richter Korzow Kristine
- Department of Archaeology, Max Planck Institute for the Science of Human History (MPI-SHH), Kahlaische Straße 10, 07745 Jena, Germany.
| | - Douka Katerina
- Department of Archaeology, Max Planck Institute for the Science of Human History (MPI-SHH), Kahlaische Straße 10, 07745 Jena, Germany.
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Smrhova T, Junkova P, Kuckova S, Suchy T, Supova M. Peptide mass mapping in bioapatites isolated from animal bones. JOURNAL OF MATERIALS SCIENCE. MATERIALS IN MEDICINE 2020; 31:32. [PMID: 32152749 DOI: 10.1007/s10856-020-06371-z] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/08/2019] [Accepted: 02/26/2020] [Indexed: 06/10/2023]
Abstract
Bioapatite ceramics produced from biogenic sources provide highly attractive materials for the preparation of artificial replacements since such materials are not only more easily accepted by living organisms, but bioapatite isolated from biowaste such as xenogeneous bones also provides a low-cost material. Nevertheless, the presence of organic compounds in the bioapatite may lead to a deterioration in its quality and may trigger an undesirable immune response. Therefore, procedures which ensure the elimination of organic compounds through bioapatite isolation are being subjected to intense investigation and the presence of remaining organic impurities is being determined through the application of various methods. Since current conclusions concerning the conditions suitable for the elimination of organic compounds remain ambiguous, we used the mass spectrometry-based proteomic approach in order to determine the presence of proteins or peptides in bioapatite samples treated under the most frequently employed conditions, i.e., the alkaline hydrothermal process and calcination at 500 °C. Since we also investigated the presence of proteins or peptides in treated bioapatite particles of differing sizes, we discovered that both calcination and the size of the bioapatite particles constitute the main factors influencing the presence of proteins or peptides in bioapatite. In fact, while intact proteins were detected even in calcinated bioapatite consisting of particles >250 µm, no proteins were detected in the same material consisting of particles <40 µm. Therefore, we recommend the use of powdered bioapatite for the preparation of artificial replacements since it is more effectively purified than apatite in the form of blocks. In addition, we observed that while alkaline hydrothermal treatment leads to the non-specific cleavage of proteins, it does not ensure the full degradation thereof.
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Affiliation(s)
- Tereza Smrhova
- Department of Biochemistry and Microbiology, University of Chemistry and Technology, Prague, Technická 3, 166 28, Prague 6, Czech Republic
| | - Petra Junkova
- Department of Biochemistry and Microbiology, University of Chemistry and Technology, Prague, Technická 3, 166 28, Prague 6, Czech Republic
| | - Stepanka Kuckova
- Department of Biochemistry and Microbiology, University of Chemistry and Technology, Prague, Technická 3, 166 28, Prague 6, Czech Republic
| | - Tomas Suchy
- Department of Composite and Carbon Materials, Institute of Rock Structure and Mechanics, The Czech Academy of Sciences, V Holešovičkách 41, 182 09, Prague, Czech Republic
| | - Monika Supova
- Department of Composite and Carbon Materials, Institute of Rock Structure and Mechanics, The Czech Academy of Sciences, V Holešovičkách 41, 182 09, Prague, Czech Republic.
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7
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Wasinger VC, Curnoe D, Bustamante S, Mendoza R, Shoocongdej R, Adler L, Baker A, Chintakanon K, Boel C, Tacon PS. Analysis of the Preserved Amino Acid Bias in Peptide Profiles of Iron Age Teeth from a Tropical Environment Enable Sexing of Individuals Using Amelogenin MRM. Proteomics 2019; 19:e1800341. [DOI: 10.1002/pmic.201800341] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/13/2018] [Revised: 01/18/2019] [Indexed: 01/22/2023]
Affiliation(s)
- Valerie C. Wasinger
- Bioanalytical Mass Spectrometry Facility Mark Wainwright Analytical Centre University of New South Wales Sydney NSW 2052 Australia
- Palaeontology, Geobiology and Earth Archives Research Centre University of New South Wales Sydney NSW 2052 Australia
| | - Darren Curnoe
- Palaeontology, Geobiology and Earth Archives Research Centre University of New South Wales Sydney NSW 2052 Australia
- ARC Centre of Excellence for Australian Biodiversity and Heritage University of New South Wales Sydney NSW 2052 Australia
| | - Sonia Bustamante
- Bioanalytical Mass Spectrometry Facility Mark Wainwright Analytical Centre University of New South Wales Sydney NSW 2052 Australia
| | - Raynold Mendoza
- Palaeontology, Geobiology and Earth Archives Research Centre University of New South Wales Sydney NSW 2052 Australia
- ARC Centre of Excellence for Australian Biodiversity and Heritage University of New South Wales Sydney NSW 2052 Australia
| | - Rasmi Shoocongdej
- Department of Archaeology Silpakorn University Bangkok 10200 Thailand
- Interaction between Prehistoric Population and Environments in Highland Pang Mapha Project Bangkok 10170 Thailand
| | - Lewis Adler
- Bioanalytical Mass Spectrometry Facility Mark Wainwright Analytical Centre University of New South Wales Sydney NSW 2052 Australia
| | - Andy Baker
- Palaeontology, Geobiology and Earth Archives Research Centre University of New South Wales Sydney NSW 2052 Australia
| | - Kanoknart Chintakanon
- Interaction between Prehistoric Population and Environments in Highland Pang Mapha Project Bangkok 10170 Thailand
- Advanced Dental Technology Center Thailand Science Park Amphoe Khlong Luang, Chang Wat Pathum Thani 12120 Thailand
| | - Ceridwen Boel
- Palaeontology, Geobiology and Earth Archives Research Centre University of New South Wales Sydney NSW 2052 Australia
- ARC Centre of Excellence for Australian Biodiversity and Heritage University of New South Wales Sydney NSW 2052 Australia
| | - Paul S.C. Tacon
- PERAHU Griffith Centre for Social and Cultural Research & School of Humanities Languages and Social Science Griffith University Gold Coast campus QLD 4222 Australia
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Wadsworth C, Buckley M. Characterization of Proteomes Extracted through Collagen-based Stable Isotope and Radiocarbon Dating Methods. J Proteome Res 2017; 17:429-439. [DOI: 10.1021/acs.jproteome.7b00624] [Citation(s) in RCA: 35] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Caroline Wadsworth
- Manchester Institute of Biotechnology, The University of Manchester, 131 Princess Street, Manchester M1 7DN, United Kingdom
| | - Michael Buckley
- Manchester Institute of Biotechnology, The University of Manchester, 131 Princess Street, Manchester M1 7DN, United Kingdom
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9
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Grundy H, Reece P, Buckley M, Solazzo C, Dowle A, Ashford D, Charlton A, Wadsley M, Collins M. A mass spectrometry method for the determination of the species of origin of gelatine in foods and pharmaceutical products. Food Chem 2016. [DOI: 10.1016/j.foodchem.2015.05.054] [Citation(s) in RCA: 33] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/03/2023]
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10
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Dallongeville S, Garnier N, Rolando C, Tokarski C. Proteins in Art, Archaeology, and Paleontology: From Detection to Identification. Chem Rev 2015; 116:2-79. [PMID: 26709533 DOI: 10.1021/acs.chemrev.5b00037] [Citation(s) in RCA: 82] [Impact Index Per Article: 9.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
Affiliation(s)
- Sophie Dallongeville
- Miniaturisation pour la Synthèse, l'Analyse & la Protéomique (MSAP), USR CNRS 3290, Université de Lille 1 Sciences et Technologies , 59655 Villeneuve d'Ascq Cedex, France
| | - Nicolas Garnier
- SARL Laboratoire Nicolas Garnier , 63270 Vic le Comte, France
| | - Christian Rolando
- Miniaturisation pour la Synthèse, l'Analyse & la Protéomique (MSAP), USR CNRS 3290, Université de Lille 1 Sciences et Technologies , 59655 Villeneuve d'Ascq Cedex, France
| | - Caroline Tokarski
- Miniaturisation pour la Synthèse, l'Analyse & la Protéomique (MSAP), USR CNRS 3290, Université de Lille 1 Sciences et Technologies , 59655 Villeneuve d'Ascq Cedex, France
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Claydon AJ, Grundy HH, Charlton AJ, Romero MR. Identification of novel peptides for horse meat speciation in highly processed foodstuffs. Food Addit Contam Part A Chem Anal Control Expo Risk Assess 2015; 32:1718-29. [DOI: 10.1080/19440049.2015.1075256] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/12/2023]
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12
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Hill RC, Wither MJ, Nemkov T, Barrett A, D'Alessandro A, Dzieciatkowska M, Hansen KC. Preserved Proteins from Extinct Bison latifrons Identified by Tandem Mass Spectrometry; Hydroxylysine Glycosides are a Common Feature of Ancient Collagen. Mol Cell Proteomics 2015; 14:1946-58. [PMID: 25948757 DOI: 10.1074/mcp.m114.047787] [Citation(s) in RCA: 66] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/22/2014] [Indexed: 11/06/2022] Open
Abstract
Bone samples from several vertebrates were collected from the Ziegler Reservoir fossil site, in Snowmass Village, Colorado, and processed for proteomics analysis. The specimens come from Pleistocene megafauna Bison latifrons, dating back ∼ 120,000 years. Proteomics analysis using a simplified sample preparation procedure and tandem mass spectrometry (MS/MS) was applied to obtain protein identifications. Several bioinformatics resources were used to obtain peptide identifications based on sequence homology to extant species with annotated genomes. With the exception of soil sample controls, all samples resulted in confident peptide identifications that mapped to type I collagen. In addition, we analyzed a specimen from the extinct B. latifrons that yielded peptide identifications mapping to over 33 bovine proteins. Our analysis resulted in extensive fibrillar collagen sequence coverage, including the identification of posttranslational modifications. Hydroxylysine glucosylgalactosylation, a modification thought to be involved in collagen fiber formation and bone mineralization, was identified for the first time in an ancient protein dataset. Meta-analysis of data from other studies indicates that this modification may be common in well-preserved prehistoric samples. Additional peptide sequences from extracellular matrix (ECM) and non-ECM proteins have also been identified for the first time in ancient tissue samples. These data provide a framework for analyzing ancient protein signatures in well-preserved fossil specimens, while also contributing novel insights into the molecular basis of organic matter preservation. As such, this analysis has unearthed common posttranslational modifications of collagen that may assist in its preservation over time. The data are available via ProteomeXchange with identifier PXD001827.
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Affiliation(s)
- Ryan C Hill
- From the ‡Department of Biochemistry and Molecular Genetics, University of Colorado Denver, Aurora, Colorado 80045, USA
| | - Matthew J Wither
- From the ‡Department of Biochemistry and Molecular Genetics, University of Colorado Denver, Aurora, Colorado 80045, USA
| | - Travis Nemkov
- From the ‡Department of Biochemistry and Molecular Genetics, University of Colorado Denver, Aurora, Colorado 80045, USA
| | - Alexander Barrett
- From the ‡Department of Biochemistry and Molecular Genetics, University of Colorado Denver, Aurora, Colorado 80045, USA
| | - Angelo D'Alessandro
- From the ‡Department of Biochemistry and Molecular Genetics, University of Colorado Denver, Aurora, Colorado 80045, USA
| | - Monika Dzieciatkowska
- From the ‡Department of Biochemistry and Molecular Genetics, University of Colorado Denver, Aurora, Colorado 80045, USA
| | - Kirk C Hansen
- From the ‡Department of Biochemistry and Molecular Genetics, University of Colorado Denver, Aurora, Colorado 80045, USA
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13
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Wadsworth C, Buckley M. Proteome degradation in fossils: investigating the longevity of protein survival in ancient bone. RAPID COMMUNICATIONS IN MASS SPECTROMETRY : RCM 2014; 28:605-15. [PMID: 24519823 PMCID: PMC4282581 DOI: 10.1002/rcm.6821] [Citation(s) in RCA: 80] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/14/2013] [Revised: 12/23/2013] [Accepted: 12/30/2013] [Indexed: 05/19/2023]
Abstract
RATIONALE We report the use of proteomics techniques to study how the fossil bone proteome changes in complexity over one million years. METHODS We include the attempted use of a previously unreported methodology in proteome research, to remove the dominant bone collagens using bacterial collagenase as well as conventional shotgun proteomics methodology following digestion with the protease trypsin. In this study we expand upon a set of 19 bovine sub-fossil specimens ranging over one and a half million years that had previously been shown to possess collagen, using a total of 46 LTQ-Orbitrap liquid chromatography/tandem mass spectrometry (LC/MS/MS) analyses containing 462,186 precursor ion analyses. RESULTS Although many types of proteins can typically be identified in recent bone, in degraded bone we observe a rapid loss of lower abundance proteins. Abundant serum proteins such as serum albumin and alpha-2-HS-glycoprotein appear to be more easily recovered in ancient bone, both being identified in specimens dating to the Early Pleistocene, the earliest period tested in this study. Proteins belonging to the leucine-rich repeat family such as lumican, biglycan and chondroadherin also survive well, possibly because of their interactions with bone collagen. CONCLUSIONS Of these 'survivor proteins' A2HSG shows a remarkable amount of sequence variation, making it potentially one of the most useful proteins to study for species identification and phylogenetic inference in archaeological and palaeontological bone.
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Affiliation(s)
- Caroline Wadsworth
- Faculty of Life Sciences, Manchester Institute of Biotechnology131 Princess Street, Manchester, M1 7DN, UK
| | - Mike Buckley
- *Correspondence to: M. Buckley, Faculty of Life Sciences, Manchester Institute of Biotechnology, 131 Princess Street, Manchester M1 7DN, UK., E-mail:
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14
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Bona A, Papai Z, Maasz G, Toth GA, Jambor E, Schmidt J, Toth C, Farkas C, Mark L. Mass spectrometric identification of ancient proteins as potential molecular biomarkers for a 2000-year-old osteogenic sarcoma. PLoS One 2014; 9:e87215. [PMID: 24475253 PMCID: PMC3903643 DOI: 10.1371/journal.pone.0087215] [Citation(s) in RCA: 29] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/29/2013] [Accepted: 12/26/2013] [Indexed: 11/18/2022] Open
Abstract
Osteosarcoma is the most common primary malignant tumor of bone usually occurring in young adolescent and children. This disease has a poor prognosis, because of the metastases in the period of tumor progression, which are usually developed previous to the clinical diagnosis. In this paper, a 2000-year-old ancient bone remain with osteogenic sarcoma was analyzed searching for tumor biomarkers which are closely related to this disease. After a specific extraction SDS-PAGE gel electrophoresis followed by tryptic digestion was performed. After the digestion the samples were measured using MALDI TOF/TOF MS. Healthy bone samples from same archaeological site were used as control samples. Our results show that in the pathological skeletal remain several well known tumor biomarkers are detected such as annexin A10, BCL-2-like protein, calgizzarin, rho GTPase-activating protein 7, HSP beta-6 protein, transferrin and vimentin compared to the control samples. The identified protein biomarkers can be useful in the discovery of malignant bone lesions such as osteosarcoma in the very early stage of the disease from paleoanthropological remains.
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Affiliation(s)
- Agnes Bona
- Department of Analytical Biochemistry, Institute of Biochemistry and Medical Chemistry, University of Pecs, Pecs, Hungary
| | - Zoltan Papai
- Department of Analytical Biochemistry, Institute of Biochemistry and Medical Chemistry, University of Pecs, Pecs, Hungary
| | - Gabor Maasz
- Department of Analytical Biochemistry, Institute of Biochemistry and Medical Chemistry, University of Pecs, Pecs, Hungary
- Janos Szentagothai Research Center, University of Pecs, Pecs, Hungary
- Imaging Center for Life and Material Sciences, University of Pecs, Pecs, Hungary
- PTE-MTA Human Reproduction Research Group, Pecs, Hungary
| | - Gabor A. Toth
- Institute of Biology, University of West Hungary, Szombathely, Hungary
| | - Eva Jambor
- Department of Analytical Biochemistry, Institute of Biochemistry and Medical Chemistry, University of Pecs, Pecs, Hungary
- Imaging Center for Life and Material Sciences, University of Pecs, Pecs, Hungary
| | - Janos Schmidt
- Department of Analytical Biochemistry, Institute of Biochemistry and Medical Chemistry, University of Pecs, Pecs, Hungary
- Janos Szentagothai Research Center, University of Pecs, Pecs, Hungary
- Imaging Center for Life and Material Sciences, University of Pecs, Pecs, Hungary
| | - Csaba Toth
- Department of Pathology, University Teaching Hospital Markusovszky, Szombathely, Hungary
| | - Csilla Farkas
- Department of Archaeology, Vas County Museums' Directorate, Szombathely, Hungary
| | - Laszlo Mark
- Department of Analytical Biochemistry, Institute of Biochemistry and Medical Chemistry, University of Pecs, Pecs, Hungary
- Janos Szentagothai Research Center, University of Pecs, Pecs, Hungary
- Imaging Center for Life and Material Sciences, University of Pecs, Pecs, Hungary
- PTE-MTA Human Reproduction Research Group, Pecs, Hungary
- * E-mail:
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15
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Balizs G, Weise C, Rozycki C, Opialla T, Sawada S, Zagon J, Lampen A. Determination of osteocalcin in meat and bone meal of bovine and porcine origin using matrix-assisted laser desorption ionization/time-of-flight mass spectrometry and high-resolution hybrid mass spectrometry. Anal Chim Acta 2011; 693:89-99. [DOI: 10.1016/j.aca.2011.03.027] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/10/2011] [Revised: 03/08/2011] [Accepted: 03/09/2011] [Indexed: 11/29/2022]
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16
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Buckley M, Collins M, Thomas-Oates J, Wilson JC. Species identification by analysis of bone collagen using matrix-assisted laser desorption/ionisation time-of-flight mass spectrometry. RAPID COMMUNICATIONS IN MASS SPECTROMETRY : RCM 2009; 23:3843-54. [PMID: 19899187 DOI: 10.1002/rcm.4316] [Citation(s) in RCA: 213] [Impact Index Per Article: 14.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/19/2023]
Abstract
Species identification of fragmentary bone, such as in rendered meat and bone meal or from archaeological sites, is often difficult in the absence of clear morphological markers. Here we present a robust method of analysing genus-specific collagen peptides by mass spectrometry simply by using solid-phase extraction (a C18 ZipTip) for peptide purification, rather than liquid chromatography/mass spectrometry (LC/MS). Analysis of the collagen from 32 different mammal species identified a total of 92 peptide markers that could be used for species identification, for example, in processed food and animal feed. A set of ancient (>100 ka@10 degrees C) bone samples was also analysed to show that the proposed method has applications to archaeological bone identification.
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Affiliation(s)
- Michael Buckley
- Department of Biology, University of York, Heslington, York YO10 5YW, UK.
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