1
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Dating the Paleolithic: Trapped charge methods and amino acid geochronology. Proc Natl Acad Sci U S A 2022; 119:e2109324119. [PMID: 36252044 PMCID: PMC9618083 DOI: 10.1073/pnas.2109324119] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Despite the vast array of different geochronological tools available, dating the Paleolithic remains one of the discipline’s greatest challenges. This review focuses on two different dating approaches: trapped charge and amino acid geochronology. While differing in their fundamental principles, both exploit time-dependent changes in signals found within crystals to generate a chronology for the material dated and hence, the associated deposits. Within each method, there is a diverse range of signals that can be analyzed, each covering different time ranges, applicable to different materials and suitable for different paleoenvironmental and archaeological contexts. This multiplicity of signals can at first sight appear confusing, but it is a fundamental strength of the techniques, allowing internal checks for consistency and providing more information than simply a chronology. For each technique, we present an overview of the basis for the time-dependent signals and the types of material that can be analyzed, with examples of their archaeological application, as well as their future potential.
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2
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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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3
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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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4
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The degradation of intracrystalline mollusc shell proteins: A proteomics study of Spondylus gaederopus. BIOCHIMICA ET BIOPHYSICA ACTA-PROTEINS AND PROTEOMICS 2021; 1869:140718. [PMID: 34506968 DOI: 10.1016/j.bbapap.2021.140718] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/31/2021] [Revised: 07/20/2021] [Accepted: 08/31/2021] [Indexed: 11/23/2022]
Abstract
Mollusc shells represent excellent systems for the preservation and retrieval of genuine biomolecules from archaeological or palaeontological samples. As a consequence, the post-mortem breakdown of intracrystalline mollusc shell proteins has been extensively investigated, particularly with regard to its potential use as a "molecular clock" for geochronological applications. But despite seventy years of ancient protein research, the fundamental aspects of diagenesis-induced changes to protein structures and sequences remain elusive. In this study we investigate the degradation of intracrystalline proteins by performing artificial degradation experiments on the shell of the thorny oyster, Spondylus gaederopus, which is particularly important for archaeological research. We used immunochemistry and tandem mass tag (TMT) quantitative proteomics to simultaneously track patterns of structural loss and of peptide bond hydrolysis. Powdered and bleached shell samples were heated in water at four different temperatures (80, 95, 110, 140 °C) for different time durations. The structural loss of carbohydrate and protein groups was investigated by immunochemical techniques (ELLA and ELISA) and peptide bond hydrolysis was studied by tracking the changes in protein/peptide relative abundances over time using TMT quantitative proteomics. We find that heating does not induce instant organic matrix decay, but first facilitates the uncoiling of cross-linked structures, thus improving matrix detection. We calculated apparent activation energies of structural loss: Ea (carbohydrate groups) = 104.7 kJ/mol, Ea (protein epitopes) = 104.4 kJ/mol, which suggests that secondary matrix structure degradation may proceed simultaneously with protein hydrolysis. While prolonged heating at 110 °C (10 days) results in complete loss of the structural signal, surviving peptide sequences were still observed. Eight hydrolysis-prone peptide bonds were identified in the top scoring shell sequence, the uncharacterised protein LOC117318053 from Pecten maximus. Interestingly, these were not the expected "weak" bonds based on published theoretical stabilities calculated for peptides in solution. This further confirms that intracrystalline protein degradation patterns are complex and that the overall microchemical environment plays an active role in protein stability. Our TMT approach represents a major stepping stone towards developing a model for studying protein diagenesis in biomineralised systems.
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5
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Martin KR, Waits LP, Parent CE. Teaching an Old Shell New Tricks: Extracting DNA from Current, Historical, and Ancient Mollusk Shells. Bioscience 2021. [DOI: 10.1093/biosci/biaa164] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Abstract
ABSTRACT
The use of unconventional DNA sources has increased because the acquisition of traditional samples can be invasive, destructive, or impossible. Mollusks are one group for which novel genetic sources are crucial, but methodology remains relatively undeveloped. Many species are important ecologically and in aquaculture production. However, mollusks have the highest number of extinctions of any taxonomic group. Traditionally, mollusk shell material was used for morphological research and only recently has been used in DNA studies. In the present article, we review the studies in which shell DNA was extracted and found that effective procedures consider taxon-specific biological characteristics, environmental conditions, laboratory methods, and the study objectives. Importantly, these factors cannot be considered in isolation because of their fundamental, sometimes reciprocal, relationships and influence in the long-term preservation and recovery of shell DNA. Successful recovery of shell DNA can facilitate research on pressing ecological and evolutionary questions and inform conservation strategies to protect molluscan diversity.
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Affiliation(s)
- Kelly R Martin
- Department of Biological Sciences, and Lisette Waits is a distinguished professor of wildlife resources and is head of the Fish and Wildlife Sciences Department, University of Idaho, Moscow, Idaho, United States
| | - Lisette P Waits
- Department of Biological Sciences, and Lisette Waits is a distinguished professor of wildlife resources and is head of the Fish and Wildlife Sciences Department, University of Idaho, Moscow, Idaho, United States
| | - Christine E Parent
- Department of Biological Sciences, and Lisette Waits is a distinguished professor of wildlife resources and is head of the Fish and Wildlife Sciences Department, University of Idaho, Moscow, Idaho, United States
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6
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Hendy J. Ancient protein analysis in archaeology. SCIENCE ADVANCES 2021; 7:7/3/eabb9314. [PMID: 33523896 PMCID: PMC7810370 DOI: 10.1126/sciadv.abb9314] [Citation(s) in RCA: 33] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/27/2020] [Accepted: 11/20/2020] [Indexed: 05/10/2023]
Abstract
The analysis of ancient proteins from paleontological, archeological, and historic materials is revealing insights into past subsistence practices, patterns of health and disease, evolution and phylogeny, and past environments. This review tracks the development of this field, discusses some of the major methodological strategies used, and synthesizes recent developments in archeological applications of ancient protein analysis. Moreover, this review highlights some of the challenges faced by the field and potential future directions, arguing that the development of minimally invasive or nondestructive techniques, strategies for protein authentication, and the integration of ancient protein analysis with other biomolecular techniques are important research strategies as this field grows.
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Affiliation(s)
- Jessica Hendy
- BioArCh, Department of Archaeology, University of York, York, UK
- Max Planck Institute for the Science of Human History, Jena, Germany.
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7
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Drake JL, Whitelegge JP, Jacobs DK. First sequencing of ancient coral skeletal proteins. Sci Rep 2020; 10:19407. [PMID: 33173075 PMCID: PMC7655939 DOI: 10.1038/s41598-020-75846-4] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/20/2020] [Accepted: 10/07/2020] [Indexed: 12/12/2022] Open
Abstract
Here we report the first recovery, sequencing, and identification of fossil biomineral proteins from a Pleistocene fossil invertebrate, the stony coral Orbicella annularis. This fossil retains total hydrolysable amino acids of a roughly similar composition to extracts from modern O. annularis skeletons, with the amino acid data rich in Asx (Asp + Asn) and Glx (Glu + Gln) typical of invertebrate skeletal proteins. It also retains several proteins, including a highly acidic protein, also known from modern coral skeletal proteomes that we sequenced by LC-MS/MS over multiple trials in the best-preserved fossil coral specimen. A combination of degradation or amino acid racemization inhibition of trypsin digestion appears to limit greater recovery. Nevertheless, our workflow determines optimal samples for effective sequencing of fossil coral proteins, allowing comparison of modern and fossil invertebrate protein sequences, and will likely lead to further improvements of the methods. Sequencing of endogenous organic molecules in fossil invertebrate biominerals provides an ancient record of composition, potentially clarifying evolutionary changes and biotic responses to paleoenvironments.
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Affiliation(s)
- Jeana L Drake
- Department of Ecology and Evolutionary Biology, University of California, Los Angeles, USA.
- Department of Earth, Planetary, and Space Sciences, University of California, Los Angeles, USA.
- Department of Marine Biology, University of Haifa, Haifa, Israel.
| | | | - David K Jacobs
- Department of Ecology and Evolutionary Biology, University of California, Los Angeles, USA.
- Department of Earth, Planetary, and Space Sciences, University of California, Los Angeles, USA.
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8
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Presslee S, Penkman K, Fischer R, Richards-Slidel E, Southon J, Hospitaleche CA, Collins M, MacPhee R. Assessment of different screening methods for selecting palaeontological bone samples for peptide sequencing. J Proteomics 2020; 230:103986. [PMID: 32941991 DOI: 10.1016/j.jprot.2020.103986] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/14/2020] [Revised: 07/24/2020] [Accepted: 09/10/2020] [Indexed: 10/23/2022]
Abstract
Ancient proteomics is being applied to samples dating further and further back in time, with many palaeontological specimens providing protein sequence data for phylogenetic analysis as well as protein degradation studies. However, fossils are a precious material and proteomic analysis is destructive and costly. In this paper we consider three different techniques (ATR-FTIR, MALDI-ToF MS and chiral AA analysis) to screen fossil material for potential protein preservation, aiming to maximise the proteomic information recovered and saving costly time consuming analyses which may produce low quality results. It was found that splitting factor and C/P indices from ATR-FTIR were not a reliable indicator of protein survival as they are confounded by secondary mineralisation of the fossil material. Both MALDI-ToF MS and chiral AA analysis results were able to successfully identify samples with surviving proteins, and it is suggested that one or both of these analyses be used for screening palaeontological specimens. SIGNIFICANCE: This study has shown both chiral amino acid analysis and MALDI-ToF MS are reliable screening methods for predicting protein survival in fossils. Both these methods are quick, cheap, minimally destructive (1 mg and 15 mg respectively) and can provide crucial additional information about the endogeneity of the surviving proteins. It is hoped that the use of these screening methods will encourage the examination of a wide range of palaeontological specimens for potential proteomic analysis. This in turn will give us a better understanding of protein survival far back in time and under different environmental conditions.
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Affiliation(s)
- Samantha Presslee
- BioArCh, Department of Archaeology, University of York, York, UK; BioArCh, Department of Chemistry, University of York, York, UK.
| | - Kirsty Penkman
- BioArCh, Department of Chemistry, University of York, York, UK
| | - Roman Fischer
- Target Discovery Institute, Nuffield Department of Medicine, University of Oxford, Oxford, UK
| | - Eden Richards-Slidel
- BioArCh, Department of Archaeology, University of York, York, UK; Section for Evolutionary Genomics, The Globe Institute, Faculty of Health, University of Copenhagen, Copenhagen, Denmark
| | - John Southon
- Department of Earth System Science, University of California, Irvine, USA
| | | | - Matthew Collins
- Section for Evolutionary Genomics, The Globe Institute, Faculty of Health, University of Copenhagen, Copenhagen, Denmark; McDonald Institute for Archaeological Research, University of Cambridge, Cambridge, UK
| | - Ross MacPhee
- Department of Mammalogy, American Museum of Natural History, New York, NY, USA
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9
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Ferreira S, Ashby R, Jeunen GJ, Rutherford K, Collins C, Todd EV, Gemmell NJ. DNA from mollusc shell: a valuable and underutilised substrate for genetic analyses. PeerJ 2020; 8:e9420. [PMID: 32821530 PMCID: PMC7396136 DOI: 10.7717/peerj.9420] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/10/2020] [Accepted: 06/03/2020] [Indexed: 12/14/2022] Open
Abstract
Mollusc shells are an abundant resource that have been long used to predict the structures of ancient ecological communities, examine evolutionary processes, reconstruct paleoenvironmental conditions, track and predict responses to climatic change, and explore the movement of hominids across the globe. Despite the ubiquity of mollusc shell in many environments, it remains relatively unexplored as a substrate for molecular genetic analysis. Here we undertook a series of experiments using the New Zealand endemic greenshell mussel, Perna canaliculus, to explore the utility of fresh, aged, beach-cast and cooked mollusc shell for molecular genetic analyses. We find that reasonable quantities of DNA (0.002-21.48 ng/mg shell) can be derived from aged, beach-cast and cooked mussel shell and that this can routinely provide enough material to undertake PCR analyses of mitochondrial and nuclear gene fragments. Mitochondrial PCR amplification had an average success rate of 96.5% from shell tissue extracted thirteen months after the animal's death. A success rate of 93.75% was obtained for cooked shells. Amplification of nuclear DNA (chitin synthase gene) was less successful (80% success from fresh shells, decreasing to 10% with time, and 75% from cooked shells). Our results demonstrate the promise of mollusc shell as a substrate for genetic analyses targeting both mitochondrial and nuclear genes.
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Affiliation(s)
- Sara Ferreira
- Department of Anatomy, University of Otago, Dunedin, New Zealand
| | - Rachael Ashby
- Invermay Agricultural Centre, AgResearch, Dunedin, New Zealand
| | - Gert-Jan Jeunen
- Department of Anatomy, University of Otago, Dunedin, New Zealand
| | - Kim Rutherford
- Department of Anatomy, University of Otago, Dunedin, New Zealand
| | | | - Erica V. Todd
- Department of Anatomy, University of Otago, Dunedin, New Zealand
| | - Neil J. Gemmell
- Department of Anatomy, University of Otago, Dunedin, New Zealand
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10
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Sakalauskaite J, Andersen SH, Biagi P, Borrello MA, Cocquerez T, Colonese AC, Dal Bello F, Girod A, Heumüller M, Koon H, Mandili G, Medana C, Penkman KE, Plasseraud L, Schlichtherle H, Taylor S, Tokarski C, Thomas J, Wilson J, Marin F, Demarchi B. 'Palaeoshellomics' reveals the use of freshwater mother-of-pearl in prehistory. eLife 2019; 8:45644. [PMID: 31060688 PMCID: PMC6542584 DOI: 10.7554/elife.45644] [Citation(s) in RCA: 22] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/30/2019] [Accepted: 04/20/2019] [Indexed: 01/14/2023] Open
Abstract
The extensive use of mollusc shell as a versatile raw material is testament to its importance in prehistoric times. The consistent choice of certain species for different purposes, including the making of ornaments, is a direct representation of how humans viewed and exploited their environment. The necessary taxonomic information, however, is often impossible to obtain from objects that are small, heavily worked or degraded. Here we propose a novel biogeochemical approach to track the biological origin of prehistoric mollusc shell. We conducted an in-depth study of archaeological ornaments using microstructural, geochemical and biomolecular analyses, including ‘palaeoshellomics’, the first application of palaeoproteomics to mollusc shells (and indeed to any invertebrate calcified tissue). We reveal the consistent use of locally-sourced freshwater mother-of-pearl for the standardized manufacture of ‘double-buttons’. This craft is found throughout Europe between 4200–3800 BCE, highlighting the ornament-makers’ profound knowledge of the biogeosphere and the existence of cross-cultural traditions. Just like people do today, prehistoric humans liked to adorn themselves with beautiful objects. Shells, from creatures like clams and snails, were used to decorate clothing or worn as jewelry at least as far back as 100,000 years ago. Later people used shells as the raw materials to make beads or bracelets. Learning where the shells came from may help scientists understand why prehistoric people chose certain shells and not others. It may also offer clues about how they used natural resources and the cultural significance of these objects. But identifying the shells is difficult because they lose many of their original distinctive features when worked into ornaments. New tools that use DNA or proteins to identify the raw materials used to craft ancient artifacts have emerged that may help. So far, scientists have mostly used these genomic and proteomic tools to identify the source of materials made from animal hide, ivory or bone – where collagen is the most abundant protein molecule. Yet it is more challenging to extract and characterize proteins or genetic material from mollusc shells. This is partly because the amount of proteins in shells is at least 300 times lower than in bone, and also because the makeup of proteins in shells is not as well-known as in collagen. Sakalauskaite et al. have now overcome these issues by combining the analytical tools used to study the proteins and mineral content of modern shells with those of ancient protein research. They then used this approach, which they named palaeoshellomics, to extract proteins from seven “double-buttons” – pearl-like ornaments crafted by prehistoric people in Europe. The double-buttons were made between 4200 and 3800 BC and found at archeological sites in Denmark, Germany and Romania. Comparing the extracted proteins to those from various mollusc shells showed that the double-buttons were made from freshwater mussels belonging to a group known as the Unionoida. The discovery helps settle a decade-long debate in archeology about the origin of the shells used to make double-buttons in prehistoric Europe. Ancient people often crafted ornaments from marine shells, because they were exotic and considered more prestigious. But the results on the double-buttons suggest instead that mother-of-pearl from fresh water shells was valued and used by groups throughout Europe, even those living in coastal areas. The palaeoshellomics technique used by Sakalauskaite et al. may now help identify the origins of shells from archeological and palaeontological sites.
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Affiliation(s)
- Jorune Sakalauskaite
- Department of Life Sciences and Systems Biology, University of Turin, Turin, Italy.,UMR CNRS 6282 Biogéosciences, University of Burgundy-Franche-Comté, Dijon, France
| | | | - Paolo Biagi
- Department of Asian and North African Studies, University of Ca' Foscari, Venice, Italy
| | | | - Théophile Cocquerez
- UMR CNRS 6282 Biogéosciences, University of Burgundy-Franche-Comté, Dijon, France
| | | | - Federica Dal Bello
- Department of Molecular Biotechnology and Health Sciences, University of Turin, Turin, Italy
| | | | - Marion Heumüller
- Niedersächsisches Landesamt für Denkmalpflege, Hannover, Germany
| | - Hannah Koon
- School of Archaeological and Forensic Sciences, University of Bradford, Bradford, United Kingdom
| | - Giorgia Mandili
- Department of Molecular Biotechnology and Health Sciences, University of Turin, Turin, Italy.,Centre for Experimental and Clinical Studies, University of Turin, Turin, Italy
| | - Claudio Medana
- Department of Molecular Biotechnology and Health Sciences, University of Turin, Turin, Italy
| | - Kirsty Eh Penkman
- Department of Chemistry, University of York, Heslington, United Kingdom
| | - Laurent Plasseraud
- Institute of Molecular Chemistry, ICMUB UMR CNRS 6302, University of Burgundy-Franche-Comté, Dijon, France
| | - Helmut Schlichtherle
- Landesamt für Denkmalpflege im Regierungspräsidium Stuttgart, Gaienhofen, Germany
| | - Sheila Taylor
- Department of Chemistry, University of York, Heslington, United Kingdom
| | - Caroline Tokarski
- Miniaturization for Synthesis, Analysis & Proteomics, USR CNRS 3290, University of Lille, Lille, France
| | - Jérôme Thomas
- UMR CNRS 6282 Biogéosciences, University of Burgundy-Franche-Comté, Dijon, France
| | - Julie Wilson
- Department of Mathematics, University of York, Heslington, United Kingdom
| | - Frédéric Marin
- UMR CNRS 6282 Biogéosciences, University of Burgundy-Franche-Comté, Dijon, France
| | - Beatrice Demarchi
- Department of Life Sciences and Systems Biology, University of Turin, Turin, Italy.,Department of Archaeology, University of York, Heslington, United Kingdom
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11
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Ayon NJ, Sharma AD, Gutheil WG. LC-MS/MS-Based Separation and Quantification of Marfey's Reagent Derivatized Proteinogenic Amino Acid DL-Stereoisomers. JOURNAL OF THE AMERICAN SOCIETY FOR MASS SPECTROMETRY 2019; 30:448-458. [PMID: 30421361 PMCID: PMC6417927 DOI: 10.1007/s13361-018-2093-9] [Citation(s) in RCA: 42] [Impact Index Per Article: 8.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/14/2018] [Revised: 10/15/2018] [Accepted: 10/15/2018] [Indexed: 05/31/2023]
Abstract
D-Amino acids are important biological molecules. Improved analytical methods for their resolution and quantification remain of keen interest. In this study, we investigated the use of Marfey's reagent (chiral) derivatization coupled with LC-MS/MS-based separation and detection of the resulting diastereomers for quantification of the 19 common L- and D-amino acids and glycine. Standard formic acid (pH 2)-based separations on reverse phase media were unable to separate all 19 amino acid DL pairs. In contrast, a water/acetonitrile/ammonium acetate (pH 6.5) solvent system allowed all 19 amino acid DL pairs to be chromatographically resolved on a 30 min gradient, with negative mode detection at pH 6.5 giving good sensitivity. Derivatization reaction rates between amino acids varied substantially, with overnight derivatization required for some amino acids. Chromatography at pH 6.5 combined with MS/MS quantification in negative mode demonstrated good linearity over a wide concentration range for all 20 amino acids. Matrix effects, assessed with an MRSA extract, were negligible. Marfey's derivatized analytes were stable for 24 h at room temperature. This method was demonstrated by determining the levels of these analytes in mid-log phase MRSA extracts. This approach provides for the chromatographic resolution and MS/MS-based quantification of all 20 common L- and D-amino acids in complex matrices. Graphical Abstract.
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Affiliation(s)
- Navid J Ayon
- Division of Pharmacology and Pharmaceutical Sciences, School of Pharmacy, University of Missouri-Kansas City, 2464 Charlotte Street, Kansas City, MO, 64108, USA
| | - Amar Deep Sharma
- Division of Pharmacology and Pharmaceutical Sciences, School of Pharmacy, University of Missouri-Kansas City, 2464 Charlotte Street, Kansas City, MO, 64108, USA
| | - William G Gutheil
- Division of Pharmacology and Pharmaceutical Sciences, School of Pharmacy, University of Missouri-Kansas City, 2464 Charlotte Street, Kansas City, MO, 64108, USA.
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12
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Giuffrida MG, Mazzoli R, Pessione E. Back to the past: deciphering cultural heritage secrets by protein identification. Appl Microbiol Biotechnol 2018; 102:5445-5455. [DOI: 10.1007/s00253-018-8963-z] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/23/2018] [Revised: 03/19/2018] [Accepted: 03/21/2018] [Indexed: 12/22/2022]
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13
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Bravenec AD, Ward KD, Ward TJ. Amino acid racemization and its relation to geochronology and archaeometry. J Sep Sci 2018; 41:1489-1506. [DOI: 10.1002/jssc.201701506] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/23/2017] [Revised: 02/15/2018] [Accepted: 02/15/2018] [Indexed: 11/11/2022]
Affiliation(s)
- Ardith D. Bravenec
- School of GeoSciences; Grant Institute; University of Edinburgh; Edinburgh UK
| | - Karen D. Ward
- Department of Chemistry and Biochemistry; Keck Center for Instrumental and Biochemical Comparative Archaeology; Millsaps College; Jackson MS USA
| | - Timothy J. Ward
- Department of Chemistry and Biochemistry; Keck Center for Instrumental and Biochemical Comparative Archaeology; Millsaps College; Jackson MS USA
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14
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Green EJ, Speller CF. Novel Substrates as Sources of Ancient DNA: Prospects and Hurdles. Genes (Basel) 2017; 8:E180. [PMID: 28703741 PMCID: PMC5541313 DOI: 10.3390/genes8070180] [Citation(s) in RCA: 30] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/30/2017] [Revised: 06/22/2017] [Accepted: 07/10/2017] [Indexed: 12/17/2022] Open
Abstract
Following the discovery in the late 1980s that hard tissues such as bones and teeth preserve genetic information, the field of ancient DNA analysis has typically concentrated upon these substrates. The onset of high-throughput sequencing, combined with optimized DNA recovery methods, has enabled the analysis of a myriad of ancient species and specimens worldwide, dating back to the Middle Pleistocene. Despite the growing sophistication of analytical techniques, the genetic analysis of substrates other than bone and dentine remain comparatively "novel". Here, we review analyses of other biological substrates which offer great potential for elucidating phylogenetic relationships, paleoenvironments, and microbial ecosystems including (1) archaeological artifacts and ecofacts; (2) calcified and/or mineralized biological deposits; and (3) biological and cultural archives. We conclude that there is a pressing need for more refined models of DNA preservation and bespoke tools for DNA extraction and analysis to authenticate and maximize the utility of the data obtained. With such tools in place the potential for neglected or underexploited substrates to provide a unique insight into phylogenetics, microbial evolution and evolutionary processes will be realized.
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Affiliation(s)
- Eleanor Joan Green
- BioArCh, Department of Archaeology, University of York, Wentworth Way, York YO10 5DD, UK.
| | - Camilla F Speller
- BioArCh, Department of Archaeology, University of York, Wentworth Way, York YO10 5DD, UK.
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Demarchi B, Hall S, Roncal-Herrero T, Freeman CL, Woolley J, Crisp MK, Wilson J, Fotakis A, Fischer R, Kessler BM, Rakownikow Jersie-Christensen R, Olsen JV, Haile J, Thomas J, Marean CW, Parkington J, Presslee S, Lee-Thorp J, Ditchfield P, Hamilton JF, Ward MW, Wang CM, Shaw MD, Harrison T, Domínguez-Rodrigo M, MacPhee RDE, Kwekason A, Ecker M, Kolska Horwitz L, Chazan M, Kröger R, Thomas-Oates J, Harding JH, Cappellini E, Penkman K, Collins MJ. Protein sequences bound to mineral surfaces persist into deep time. eLife 2016; 5. [PMID: 27668515 PMCID: PMC5039028 DOI: 10.7554/elife.17092] [Citation(s) in RCA: 101] [Impact Index Per Article: 12.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/21/2016] [Accepted: 08/17/2016] [Indexed: 12/14/2022] Open
Abstract
Proteins persist longer in the fossil record than DNA, but the longevity, survival mechanisms and substrates remain contested. Here, we demonstrate the role of mineral binding in preserving the protein sequence in ostrich (Struthionidae) eggshell, including from the palaeontological sites of Laetoli (3.8 Ma) and Olduvai Gorge (1.3 Ma) in Tanzania. By tracking protein diagenesis back in time we find consistent patterns of preservation, demonstrating authenticity of the surviving sequences. Molecular dynamics simulations of struthiocalcin-1 and -2, the dominant proteins within the eggshell, reveal that distinct domains bind to the mineral surface. It is the domain with the strongest calculated binding energy to the calcite surface that is selectively preserved. Thermal age calculations demonstrate that the Laetoli and Olduvai peptides are 50 times older than any previously authenticated sequence (equivalent to ~16 Ma at a constant 10°C). DOI:http://dx.doi.org/10.7554/eLife.17092.001 The pattern of chemical reactions that break down the molecules that make our bodies is still fairly mysterious. Archaeologists and geologists hope that dead organisms (or artefacts made from them) might not decay entirely, leaving behind clues to their lives. We know that some molecules are more resistant than others; for example, fats are tough and survive for a long time while DNA is degraded very rapidly. Proteins, which are made of chains of smaller molecules called amino acids, are usually sturdier than DNA. Since the amino acid sequence of a protein reflects the DNA sequence that encodes it, proteins in fossils can help researchers to reconstruct how extinct organisms are related in cases where DNA cannot be retrieved. Time, temperature, burial environment and the chemistry of the fossil all influence how quickly a protein decays. However, it is not clear what mechanisms slow down decay so that full protein sequences can be preserved and identified after millions of years. As a result, it is difficult to know where to look for these ancient sequences. In the womb of ostriches, several proteins are responsible for assembling the minerals that make up the ostrich eggshell. These proteins become trapped tightly within the mineral crystals themselves. In this situation, proteins can potentially be preserved over geological time. Demarchi et al. have now studied 3.8 million-year-old eggshells found close to the equator and, despite the extent to which the samples have degraded, discovered fully preserved protein sequences. Using a computer simulation method called molecular dynamics, Demarchi et al. calculated that the protein sequences that are able to survive the longest are stabilized by strong binding to the surface of the mineral crystals. The authenticity of these sequences was tested thoroughly using a combination of several approaches that Demarchi et al. recommend using as a standard for ancient protein studies. Overall, it appears that biominerals are an excellent source of ancient protein sequences because mineral binding ensures survival. A systematic survey of fossil biominerals from different environments is now needed to assess whether these biomolecules have the potential to act as barcodes for interpreting the evolution of organisms. DOI:http://dx.doi.org/10.7554/eLife.17092.002
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Affiliation(s)
- Beatrice Demarchi
- BioArCh, Department of Archaeology, University of York, York, United Kingdom
| | - Shaun Hall
- Department of Material Science and Engineering, University of Sheffield, Sheffield, United Kingdom
| | | | - Colin L Freeman
- Department of Material Science and Engineering, University of Sheffield, Sheffield, United Kingdom
| | - Jos Woolley
- BioArCh, Department of Archaeology, University of York, York, United Kingdom
| | - Molly K Crisp
- Department of Chemistry, University of York, York, United Kingdom
| | - Julie Wilson
- Department of Chemistry, University of York, York, United Kingdom.,Department of Mathematics, University of York, York, United Kingdom
| | - Anna Fotakis
- Centre for GeoGenetics, Natural History Museum of Denmark, University of Copenhagen, Copenhagen, Denmark
| | - Roman Fischer
- Advanced Proteomics Facility, Target Discovery Institute, Nuffield Department of Medicine, University of Oxford, Oxford, United Kingdom
| | - Benedikt M Kessler
- Advanced Proteomics Facility, Target Discovery Institute, Nuffield Department of Medicine, University of Oxford, Oxford, United Kingdom
| | | | - Jesper V Olsen
- Novo Nordisk Foundation Center for Protein Research, Faculty of Health Sciences, University of Copenhagen, Copenhagen, Denmark
| | - James Haile
- Research Laboratory for Archaeology and the History of Art, University of Oxford, Oxford, United Kingdom
| | - Jessica Thomas
- Centre for GeoGenetics, Natural History Museum of Denmark, University of Copenhagen, Copenhagen, Denmark.,Molecular Ecology and Fisheries Genetics Laboratory, School of Biological Sciences, Bangor University, Bangor, United Kingdom
| | - Curtis W Marean
- Institute of Human Origins, SHESC, Arizona State University, Tempe, United States.,Centre for Coastal Palaeoscience, Nelson Mandela Metropolitan University, Port Elizabeth, South Africa
| | - John Parkington
- Department of Archaeology, University of Cape Town, Cape Town, South Africa
| | - Samantha Presslee
- BioArCh, Department of Archaeology, University of York, York, United Kingdom
| | - Julia Lee-Thorp
- Research Laboratory for Archaeology and the History of Art, University of Oxford, Oxford, United Kingdom
| | - Peter Ditchfield
- Research Laboratory for Archaeology and the History of Art, University of Oxford, Oxford, United Kingdom
| | - Jacqueline F Hamilton
- Wolfson Atmospheric Chemistry Laboratories, Department of Chemistry, University of York, York, United Kingdom
| | - Martyn W Ward
- Wolfson Atmospheric Chemistry Laboratories, Department of Chemistry, University of York, York, United Kingdom
| | - Chunting Michelle Wang
- Wolfson Atmospheric Chemistry Laboratories, Department of Chemistry, University of York, York, United Kingdom
| | - Marvin D Shaw
- Wolfson Atmospheric Chemistry Laboratories, Department of Chemistry, University of York, York, United Kingdom
| | - Terry Harrison
- Center for the Study of Human Origins, Department of Anthropology, New York University, New York, United States
| | | | - Ross DE MacPhee
- Department of Mammalogy, American Museum of Natural History, New York, United States
| | | | - Michaela Ecker
- Research Laboratory for Archaeology and the History of Art, University of Oxford, Oxford, United Kingdom
| | - Liora Kolska Horwitz
- National Natural History Collections, Faculty of Life Sciences, The Hebrew University, Jerusalem, Israel
| | - Michael Chazan
- Department of Anthropology, University of Toronto, Toronto, Canada.,Evolutionary Studies Institute, University of the Witwatersrand, Braamfontein, South Africa
| | - Roland Kröger
- Department of Physics, University of York, York, United Kingdom
| | - Jane Thomas-Oates
- Department of Chemistry, University of York, York, United Kingdom.,Centre of Excellence in Mass Spectrometry, University of York, New York, United States
| | - John H Harding
- Department of Material Science and Engineering, University of Sheffield, Sheffield, United Kingdom
| | - Enrico Cappellini
- Centre for GeoGenetics, Natural History Museum of Denmark, University of Copenhagen, Copenhagen, Denmark
| | - Kirsty Penkman
- Department of Chemistry, University of York, York, United Kingdom
| | - Matthew J Collins
- BioArCh, Department of Archaeology, University of York, York, United Kingdom
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Aspartic acid racemization reveals a high turnover state in knee compared with hip osteoarthritic cartilage. Osteoarthritis Cartilage 2016; 24:374-81. [PMID: 26417696 PMCID: PMC4897591 DOI: 10.1016/j.joca.2015.09.003] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 01/06/2015] [Revised: 06/23/2015] [Accepted: 09/01/2015] [Indexed: 02/02/2023]
Abstract
OBJECTIVE We investigated tissue turnover in healthy and osteoarthritic cartilage. We challenge long held views that osteoarthritis (OA) is dominated by a similar turnover process in all joints and present evidence that hip and knee cartilage respond very differently to OA. METHODS d- and l-Aspartate (Asp) were quantified for whole cartilage, collagen and non-collagenous components of cartilage obtained at the time of joint replacement. We computed the Asp racemization ratio (Asp-RR = d/d + l Asp), reflecting the proportion of old to total protein, for each component. RESULTS Compared with hip OA, knee OA collagen fibrils (P < 0.0001), collagen (P = 0.007), and non-collagenous proteins (P = 0.0003) had significantly lower age-adjusted mean Asp-RRs consistent with elevated protein synthesis in knee OA. Knee OA collagen had a mean hydroxyproline/proline (H/P) ratio of 1.2 consistent with the presence of type III collagen whereas hip OA collagen had a mean H/P ratio of 0.99 consistent with type II collagen. Based on Asp-RR, the relative age was significantly different in knee and hip OA (P < 0.0005); on average OA knees were estimated to be 30 yrs 'younger', and OA hips 10 yrs 'older' than non-OA. CONCLUSIONS The metabolic response to OA was strikingly different by joint site. Knee OA cartilage evinced an anabolic response that appeared to be absent in hip OA cartilage. These results challenge the long held view that OA cartilage is capable of only minimal repair and that collagen loss is irreversible.
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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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18
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Demarchi B, O'Connor S, de Lima Ponzoni A, de Almeida Rocha Ponzoni R, Sheridan A, Penkman K, Hancock Y, Wilson J. An integrated approach to the taxonomic identification of prehistoric shell ornaments. PLoS One 2014; 9:e99839. [PMID: 24936797 PMCID: PMC4061022 DOI: 10.1371/journal.pone.0099839] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/14/2014] [Accepted: 05/17/2014] [Indexed: 11/18/2022] Open
Abstract
Shell beads appear to have been one of the earliest examples of personal adornments. Marine shells identified far from the shore evidence long-distance transport and imply networks of exchange and negotiation. However, worked beads lose taxonomic clues to identification, and this may be compounded by taphonomic alteration. Consequently, the significance of this key early artefact may be underestimated. We report the use of bulk amino acid composition of the stable intra-crystalline proteins preserved in shell biominerals and the application of pattern recognition methods to a large dataset (777 samples) to demonstrate that taxonomic identification can be achieved at genus level. Amino acid analyses are fast (<2 hours per sample) and micro-destructive (sample size <2 mg). Their integration with non-destructive techniques provides a valuable and affordable tool, which can be used by archaeologists and museum curators to gain insight into early exploitation of natural resources by humans. Here we combine amino acid analyses, macro- and microstructural observations (by light microscopy and scanning electron microscopy) and Raman spectroscopy to try to identify the raw material used for beads discovered at the Early Bronze Age site of Great Cornard (UK). Our results show that at least two shell taxa were used and we hypothesise that these were sourced locally.
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Affiliation(s)
- Beatrice Demarchi
- BioArCh, Department of Archaeology, University of York, York, United Kingdom
- * E-mail: (BD); (JW)
| | - Sonia O'Connor
- School of Life Sciences, University of Bradford, Bradford, United Kingdom
| | | | | | - Alison Sheridan
- National Museums Scotland, Chambers Street, Edinburgh, United Kingdom
| | - Kirsty Penkman
- BioArCh, Department of Chemistry, University of York, York, United Kingdom
| | - Y. Hancock
- Department of Physics, University of York, York, United Kingdom
- York Centre for Complex Systems Analysis (YCCSA), University of York, York, United Kingdom
| | - Julie Wilson
- Departments of Mathematics and Chemistry, University of York, York, United Kingdom
- York Centre for Complex Systems Analysis (YCCSA), University of York, York, United Kingdom
- * E-mail: (BD); (JW)
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Demarchi B, Collins M, Bergström E, Dowle A, Penkman K, Thomas-Oates J, Wilson J. New experimental evidence for in-chain amino acid racemization of serine in a model peptide. Anal Chem 2013; 85:5835-42. [PMID: 23705982 DOI: 10.1021/ac4005869] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/01/2023]
Abstract
The facile racemization of protein-bound amino acids plays an important role in the aging and pathologies of living tissues, and it can be exploited for protein geochronological studies in subfossil biominerals. However, the in-chain degradation pathways of amino acids are complex and difficult to elucidate. Serine has proven to be particularly elusive, and its ability to racemize as a peptide-bound residue (like asparagine and aspartic acid) has not been demonstrated. This study investigates the patterns of degradation of a model peptide (WNSVWAW) at elevated temperatures, quantifying the extent of racemization and peptide bond hydrolysis using reverse-phase high-performance liquid chromatography (RP-HPLC) and tracking the presence of degradation products by MALDI-MS. We provide direct evidence that, under these experimental conditions, both serine and asparagine are able to undergo racemization as internally bound residues, which shows their potential for initiating protein breakdown and provides an explanation for the presence of d-enantiomers in living mammalian tissues.
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Affiliation(s)
- Beatrice Demarchi
- BioArCh, Department of Archaeology, University of York, York YO10 5DD, United Kingdom.
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20
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Demarchi B, Rogers K, Fa D, Finlayson C, Milner N, Penkman K. Intra-crystalline protein diagenesis (IcPD) in Patella vulgata. Part I: Isolation and testing of the closed system. QUATERNARY GEOCHRONOLOGY 2013; 16:144-157. [PMID: 23956807 PMCID: PMC3743299 DOI: 10.1016/j.quageo.2012.03.016] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/21/2011] [Revised: 03/14/2012] [Accepted: 03/19/2012] [Indexed: 05/28/2023]
Abstract
This study successfully isolates a fraction of intra-crystalline proteins from shells of the marine gastropod Patella vulgata and assesses the suitability of these proteins for IcPD (Intra-crystalline Protein Diagenesis) geochronology. We discuss the mineralogical composition of this gastropod, investigated for the first time by X-ray diffraction mapping, and use the results to inform our sampling strategy. The potential of the calcitic rim and of a bulk sample (containing both apex and rim) of the shell to act as stable repositories for the intra-crystalline proteins during diagenesis is examined. The composition and the diagenetic behaviour of the intra-crystalline proteins isolated from different locations within the shell are compared, highlighting the necessity of targeting consistent sampling positions. We induced artificial diagenesis of both intra-crystalline and whole-shell proteins by conducting high-temperature experiments in hydrous environment; this allowed us to quantify the loss of amino acids by leaching and therefore evaluate the open- or closed-system behaviour of the different fractions of proteins. The results obtained provide further confirmation that patterns of diagenesis vary according to the protein sequence, structure, and location within or outside the intra-crystalline fraction. As Patella is frequently found in the fossil record, both in archaeological and geological contexts, the application of IcPD geochronology to this biomineral opens up the possibility to obtain reliable age information from a range of sites in different areas of the world.
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Affiliation(s)
- B. Demarchi
- BioArCh, Department of Chemistry, University of York, York YO10 5DD, UK
| | - K. Rogers
- Cranfield Forensic Institute, Cranfield University, Swindon SN6 8LA, UK
| | - D.A. Fa
- The Gibraltar Museum, 18–20 Bomb House Lane, Gibraltar
| | - C.J. Finlayson
- The Gibraltar Museum, 18–20 Bomb House Lane, Gibraltar
- Department of Social Sciences, University of Toronto at Scarborough, Toronto, ON, Canada, M1C 1A4
| | - N. Milner
- Department of Archaeology, University of York, King's Manor, York Y01 7EP, UK
| | - K.E.H. Penkman
- BioArCh, Department of Chemistry, University of York, York YO10 5DD, UK
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21
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Demarchi B, Collins M, Tomiak P, Davies B, Penkman K. Intra-crystalline protein diagenesis (IcPD) in Patella vulgata. Part II: Breakdown and temperature sensitivity. QUATERNARY GEOCHRONOLOGY 2013; 16:158-172. [PMID: 23956808 PMCID: PMC3743298 DOI: 10.1016/j.quageo.2012.08.001] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/28/2011] [Revised: 07/06/2012] [Accepted: 08/06/2012] [Indexed: 05/17/2023]
Abstract
Artificial diagenesis of the intra-crystalline proteins isolated from Patella vulgata was induced by isothermal heating at 140 °C, 110 °C and 80 °C. Protein breakdown was quantified for multiple amino acids, measuring the extent of peptide bond hydrolysis, amino acid racemisation and decomposition. The patterns of diagenesis are complex; therefore the kinetic parameters of the main reactions were estimated by two different methods: 1) a well-established approach based on fitting mathematical expressions to the experimental data, e.g. first-order rate equations for hydrolysis and power-transformed first-order rate equations for racemisation; and 2) an alternative model-free approach, which was developed by estimating a "scaling" factor for the independent variable (time) which produces the best alignment of the experimental data. This method allows the calculation of the relative reaction rates for the different temperatures of isothermal heating. High-temperature data were compared with the extent of degradation detected in sub-fossil Patella specimens of known age, and we evaluated the ability of kinetic experiments to mimic diagenesis at burial temperature. The results highlighted a difference between patterns of degradation at low and high temperature and therefore we recommend caution for the extrapolation of protein breakdown rates to low burial temperatures for geochronological purposes when relying solely on kinetic data.
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Affiliation(s)
- B. Demarchi
- BioArCh, Departments of Biology, Archaeology and Chemistry, University of York, York YO10 5DD, UK
- Corresponding author. Tel.: +44 (0) 1904 328559.
| | - M.J. Collins
- BioArCh, Departments of Biology, Archaeology and Chemistry, University of York, York YO10 5DD, UK
| | - P.J. Tomiak
- School of Earth Sciences, University of Bristol, Wills Memorial Building, Queen's Rd, Bristol BS8 1RJ, UK
| | - B.J. Davies
- Centre for Glaciology, Institute of Geography and Earth Sciences, Aberystwyth University, Llandinam Building, Penglais Campus, Aberystwyth SY23 3DB, UK
| | - K.E.H. Penkman
- BioArCh, Departments of Biology, Archaeology and Chemistry, University of York, York YO10 5DD, UK
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