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Lecrenier MC, Veys P, Fumière O, Berben G, Saegerman C, Baeten V. Official Feed Control Linked to the Detection of Animal Byproducts: Past, Present, and Future. JOURNAL OF AGRICULTURAL AND FOOD CHEMISTRY 2020; 68:8093-8103. [PMID: 32614586 DOI: 10.1021/acs.jafc.0c02718] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/11/2023]
Abstract
In the context of the expansion of the human population, availability of food, and in extension of animal feed, is a big issue. Favoring a circular economy by the valorization of byproducts is a sustainable way to be more efficient. Animal byproducts are an interesting source of feed materials due to their richness in proteins of high nutritional value. Prevention and control efforts have allowed a gradual lifting of the feed ban regarding the use of animal byproducts. Nevertheless, the challenge remains the development of analytical methods enabling a distinction between authorized and unauthorized feed materials. This Review focuses on the historical and epidemiological context of the official control, the evaluation of current and foreseen legislation, and the available methods of analysis for the detection of constituents of animal origin in feedingstuffs. It also underlines the analytical limitations of the approach and discusses some prospects of novel methods to ensure food and feed safety.
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Affiliation(s)
- Marie-Caroline Lecrenier
- Knowledge and Valorization of Agricultural Products Department, Walloon Agricultural Research Centre (CRA-W), Chaussée de Namur 24, 5030 Gembloux, Belgium
- Faculty of Veterinary Medicine, Fundamental and Applied Research for Animal and Health (FARAH) Center, Research Unit of Epidemiology and Risk Analysis Applied to Veterinary Sciences (UREAR-ULg), University of Liège (ULiège), Boulevard de Colonster 20 B42, 4000 Liège, Belgium
| | - Pascal Veys
- Knowledge and Valorization of Agricultural Products Department, Walloon Agricultural Research Centre (CRA-W), Chaussée de Namur 24, 5030 Gembloux, Belgium
| | - Olivier Fumière
- Knowledge and Valorization of Agricultural Products Department, Walloon Agricultural Research Centre (CRA-W), Chaussée de Namur 24, 5030 Gembloux, Belgium
| | - Gilbert Berben
- Knowledge and Valorization of Agricultural Products Department, Walloon Agricultural Research Centre (CRA-W), Chaussée de Namur 24, 5030 Gembloux, Belgium
| | - Claude Saegerman
- Faculty of Veterinary Medicine, Fundamental and Applied Research for Animal and Health (FARAH) Center, Research Unit of Epidemiology and Risk Analysis Applied to Veterinary Sciences (UREAR-ULg), University of Liège (ULiège), Boulevard de Colonster 20 B42, 4000 Liège, Belgium
| | - Vincent Baeten
- Knowledge and Valorization of Agricultural Products Department, Walloon Agricultural Research Centre (CRA-W), Chaussée de Namur 24, 5030 Gembloux, Belgium
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102
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van Huizen NA, Ijzermans JNM, Burgers PC, Luider TM. Collagen analysis with mass spectrometry. MASS SPECTROMETRY REVIEWS 2020; 39:309-335. [PMID: 31498911 DOI: 10.1002/mas.21600] [Citation(s) in RCA: 21] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/22/2017] [Revised: 07/17/2019] [Accepted: 07/17/2019] [Indexed: 06/10/2023]
Abstract
Mass spectrometry-based techniques can be applied to investigate collagen with respect to identification, quantification, supramolecular organization, and various post-translational modifications. The continuous interest in collagen research has led to a shift from techniques to analyze the physical characteristics of collagen to methods to study collagen abundance and modifications. In this review, we illustrate the potential of mass spectrometry for in-depth analyses of collagen.
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Affiliation(s)
- Nick A van Huizen
- Department of Neurology, Erasmus Medical Center, Rotterdam, The Netherlands
- Department of Surgery, Erasmus University Medical Center, 3015 CN, Rotterdam, The Netherlands
| | - Jan N M Ijzermans
- Department of Surgery, Erasmus University Medical Center, 3015 CN, Rotterdam, The Netherlands
| | - Peter C Burgers
- Department of Neurology, Erasmus Medical Center, Rotterdam, The Netherlands
| | - Theo M Luider
- Department of Neurology, Erasmus Medical Center, Rotterdam, The Netherlands
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103
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Hickinbotham S, Fiddyment S, Stinson TL, Collins MJ. How to get your goat: automated identification of species from MALDI-ToF spectra. Bioinformatics 2020; 36:3719-3725. [PMID: 32176274 PMCID: PMC7320604 DOI: 10.1093/bioinformatics/btaa181] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/29/2019] [Revised: 11/19/2019] [Accepted: 03/13/2020] [Indexed: 01/30/2023] Open
Abstract
Motivation Classification of archaeological animal samples is commonly achieved via manual examination of matrix-assisted laser desorption/ionization time-of-flight (MALDI-ToF) spectra. This is a time-consuming process which requires significant training and which does not produce a measure of confidence in the classification. We present a new, automated method for arriving at a classification of a MALDI-ToF sample, provided the collagen sequences for each candidate species are available. The approach derives a set of peptide masses from the sequence data for comparison with the sample data, which is carried out by cross-correlation. A novel way of combining evidence from multiple marker peptides is used to interpret the raw alignments and arrive at a classification with an associated confidence measure. Results To illustrate the efficacy of the approach, we tested the new method with a previously published classification of parchment folia from a copy of the Gospel of Luke, produced around 1120 C.E. by scribes at St Augustine’s Abbey in Canterbury, UK. In total, 80 of the 81 samples were given identical classifications by both methods. In addition, the new method gives a quantifiable level of confidence in each classification. Availability and implementation The software can be found at https://github.com/bioarch-sjh/bacollite, and can be installed in R using devtools. Supplementary information Supplementary data are available at Bioinformatics online.
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Affiliation(s)
| | - Sarah Fiddyment
- BioArch, University of York, York YO10 5DD, UK.,McDonald Institute for Archaeological Research, University of Cambridge, Cambridge, CB2 3ER, UK
| | | | - Matthew J Collins
- McDonald Institute for Archaeological Research, University of Cambridge, Cambridge, CB2 3ER, UK.,Evogenomics Section, University of Copenhagen, Copenhagen 1307 K, Denmark
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104
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Initial Upper Palaeolithic Homo sapiens from Bacho Kiro Cave, Bulgaria. Nature 2020; 581:299-302. [DOI: 10.1038/s41586-020-2259-z] [Citation(s) in RCA: 108] [Impact Index Per Article: 27.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/30/2019] [Accepted: 02/24/2020] [Indexed: 12/15/2022]
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105
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A 14C chronology for the Middle to Upper Palaeolithic transition at Bacho Kiro Cave, Bulgaria. Nat Ecol Evol 2020; 4:794-801. [DOI: 10.1038/s41559-020-1136-3] [Citation(s) in RCA: 48] [Impact Index Per Article: 12.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/30/2019] [Accepted: 02/03/2020] [Indexed: 11/09/2022]
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106
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Martisius NL, Welker F, Dogandžić T, Grote MN, Rendu W, Sinet-Mathiot V, Wilcke A, McPherron SJP, Soressi M, Steele TE. Non-destructive ZooMS identification reveals strategic bone tool raw material selection by Neandertals. Sci Rep 2020; 10:7746. [PMID: 32385291 PMCID: PMC7210944 DOI: 10.1038/s41598-020-64358-w] [Citation(s) in RCA: 14] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/25/2019] [Accepted: 04/14/2020] [Indexed: 02/02/2023] Open
Abstract
Five nearly identical fragments of specialized bone tools, interpreted as lissoirs (French for “smoothers”), have been found at two Middle Paleolithic sites in southwest France. The finds span three separate archaeological deposits, suggesting continuity in the behavior of late Neandertals. Using standard morphological assessments, we determined that the lissoirs were produced on ribs of medium-sized ungulates. However, since these bones are highly fragmented and anthropogenically modified, species determinations were challenging. Also, conservative curation policy recommends minimizing destructive sampling of rare, fragile, or small artifacts for molecular identification methods. To better understand raw material selection for these five lissoirs, we reassess their taxonomy using a non-destructive ZooMS methodology based on triboelectric capture of collagen. We sampled four storage containers and obtained identifiable MALDI-TOF MS collagen fingerprints, all indicative of the same taxonomic clade, which includes aurochs and bison (Bos sp. and Bison sp.). The fifth specimen, which was stored in a plastic bag, provided no useful MALDI-TOF MS spectra. We show that the choice of large bovid ribs in an archaeological layer dominated by reindeer (Rangifer tarandus) demonstrates strategic selection by these Neandertals. Furthermore, our results highlight the value of a promising technique for the non-destructive analysis of bone artifacts.
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Affiliation(s)
- Naomi L Martisius
- Department of Anthropology, University of California, Davis, Davis, CA, 95616-8522, USA.
| | - Frido Welker
- Evolutionary Genomics Section, Globe Institute, University of Copenhagen, Øster Farimagsgade 5, 1353, Copenhagen, Denmark.,Department of Human Evolution, Max Planck Institute for Evolutionary Anthropology, Deutscher Platz 6, D-04103, Leipzig, Germany
| | - Tamara Dogandžić
- Department of Human Evolution, Max Planck Institute for Evolutionary Anthropology, Deutscher Platz 6, D-04103, Leipzig, Germany.,Department of Anthropology, University of Pennsylvania, 3260 South Street, Philadelphia, PA, 19104-6398, USA
| | - Mark N Grote
- Department of Anthropology, University of California, Davis, Davis, CA, 95616-8522, USA
| | - William Rendu
- Centre National de la Recherche Scientifique, MCC, Préhistoire à l'Actuel, Cultures, Environnement, Anthropologie, UMR5199, Université de Bordeaux, FR-33615, Pessac, France
| | - Virginie Sinet-Mathiot
- Department of Human Evolution, Max Planck Institute for Evolutionary Anthropology, Deutscher Platz 6, D-04103, Leipzig, Germany
| | - Arndt Wilcke
- Fraunhofer Institute for Cell Therapy and Immunology, Perlickstraße 1, D-04013, Leipzig, Germany
| | - Shannon J P McPherron
- Department of Human Evolution, Max Planck Institute for Evolutionary Anthropology, Deutscher Platz 6, D-04103, Leipzig, Germany
| | - Marie Soressi
- Department of Human Evolution, Max Planck Institute for Evolutionary Anthropology, Deutscher Platz 6, D-04103, Leipzig, Germany.,Faculty of Archaeology, Leiden University, 2300 RA, Leiden, The Netherlands
| | - Teresa E Steele
- Department of Anthropology, University of California, Davis, Davis, CA, 95616-8522, USA.,Department of Human Evolution, Max Planck Institute for Evolutionary Anthropology, Deutscher Platz 6, D-04103, Leipzig, Germany
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107
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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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108
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Climate stability and societal decline on the margins of the Byzantine empire in the Negev Desert. Sci Rep 2020; 10:1512. [PMID: 32001740 PMCID: PMC6992700 DOI: 10.1038/s41598-020-58360-5] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/24/2019] [Accepted: 01/13/2020] [Indexed: 11/29/2022] Open
Abstract
Understanding past human settlement of inhospitable regions is one of the most intriguing puzzles in archaeological research, with implications for more sustainable use of marginal regions today. During the Byzantine period in the 4th century CE, large settlements were established in the arid region of the Negev Desert, Israel, but it remains unclear why it did so, and why the settlements were abandoned three centuries later. Previous theories proposed that the Negev was a “green desert” in the early 1st millennium CE, and that the Byzantine Empire withdrew from this region due to a dramatic climatic downturn. In the absence of a local climate archive correlated to the Byzantine/Early Islamic transition, testing this theory has proven challenging. We use stable isotopic indicators of animal dietary and mobility patterns to assess the extent of the vegetative cover in the desert. By doing so, we aim to detect possible climatic fluctuations that may have led to the abandonment of the Byzantine settlements. The findings show that the Negev Desert was not greener during the time period under investigation than it is today and that the composition of the animals’ diets, as well as their grazing mobility patterns, remained unchanged through the Byzantine/Early Islamic transition. Favoring a non-climatic explanation, we propose instead that the abandonment of the Negev Byzantine settlements was motivated by restructuring of the Empire’s territorial priorities.
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109
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Taylor WTT, Clark J, Bayarsaikhan J, Tuvshinjargal T, Jobe JT, Fitzhugh W, Kortum R, Spengler RN, Shnaider S, Seersholm FV, Hart I, Case N, Wilkin S, Hendy J, Thuering U, Miller B, Miller ARV, Picin A, Vanwezer N, Irmer F, Brown S, Abdykanova A, Shultz DR, Pham V, Bunce M, Douka K, Jones EL, Boivin N. Early Pastoral Economies and Herding Transitions in Eastern Eurasia. Sci Rep 2020; 10:1001. [PMID: 31969593 PMCID: PMC6976682 DOI: 10.1038/s41598-020-57735-y] [Citation(s) in RCA: 17] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/14/2019] [Accepted: 12/20/2019] [Indexed: 11/23/2022] Open
Abstract
While classic models for the emergence of pastoral groups in Inner Asia describe mounted, horse-borne herders sweeping across the Eurasian Steppes during the Early or Middle Bronze Age (ca. 3000–1500 BCE), the actual economic basis of many early pastoral societies in the region is poorly characterized. In this paper, we use collagen mass fingerprinting and ancient DNA analysis of some of the first stratified and directly dated archaeofaunal assemblages from Mongolia’s early pastoral cultures to undertake species identifications of this rare and highly fragmented material. Our results provide evidence for livestock-based, herding subsistence in Mongolia during the late 3rd and early 2nd millennia BCE. We observe no evidence for dietary exploitation of horses prior to the late Bronze Age, ca. 1200 BCE – at which point horses come to dominate ritual assemblages, play a key role in pastoral diets, and greatly influence pastoral mobility. In combination with the broader archaeofaunal record of Inner Asia, our analysis supports models for widespread changes in herding ecology linked to the innovation of horseback riding in Central Asia in the final 2nd millennium BCE. Such a framework can explain key broad-scale patterns in the movement of people, ideas, and material culture in Eurasian prehistory.
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Affiliation(s)
- William Timothy Treal Taylor
- CU Museum of Natural History/Department of Anthropology, CU 218, Boulder, CO, 80309, USA. .,Department of Archaeology, Max Planck Institute for the Science of Human History, 10 Kahlaische Str., Jena, 07745, Germany.
| | - Julia Clark
- Flinders University, Australia, Sturt Road, Bedford Park, South Australia, 5042, Australia
| | | | - Tumurbaatar Tuvshinjargal
- Graduate School of Human Development in Landscapes, University of Kiel, Johanna-Mestorf Str 2-6, R.156, D - 24118, Kiel, Germany
| | - Jessica Thompson Jobe
- Department of Geology and Geological Engineering, Colorado School of Mines, 1500 Illinois St., Golden, CO, 80401, USA
| | - William Fitzhugh
- Arctic Studies Center, Smithsonian National Museum of Natural History, Washington, D.C., 20560, USA
| | - Richard Kortum
- Department of Philosophy and Humanities, East Tennessee State University, 276 Gilbreath Dr, Johnson City, TN, 37614, USA
| | - Robert N Spengler
- Department of Archaeology, Max Planck Institute for the Science of Human History, 10 Kahlaische Str., Jena, 07745, Germany
| | - Svetlana Shnaider
- Institute of Archaeology and Ethnography, Siberian Branch Russian Academy of Science, 17 Lavrentieva Avenue, Novosibirsk, 630090, Russia.,Novosibirsk State University, 1, Pirogova Str., Novosibirsk, Russia
| | - Frederik Valeur Seersholm
- Trace and Environmental DNA (TrEnD) Laboratory, Curtin University, Kent Street, Bentley, WA, 6102, Australia
| | - Isaac Hart
- Department of Geography, University of Utah, 260 Central campus Drive Room 4625, Salt Lake City, UT, 84112, USA
| | - Nicholas Case
- Wyoming Geographic Information Science Center, Department of Geography, University of Wyoming, 1000 E. University Ave., Laramie, WY, 82071, USA
| | - Shevan Wilkin
- Department of Archaeology, Max Planck Institute for the Science of Human History, 10 Kahlaische Str., Jena, 07745, Germany
| | - Jessica Hendy
- Department of Archaeology, Max Planck Institute for the Science of Human History, 10 Kahlaische Str., Jena, 07745, Germany
| | - Ulrike Thuering
- Department of Archaeology, Max Planck Institute for the Science of Human History, 10 Kahlaische Str., Jena, 07745, Germany
| | - Bryan Miller
- Department of Archaeology, Max Planck Institute for the Science of Human History, 10 Kahlaische Str., Jena, 07745, Germany.,Faculty of History, University of Oxford, George Street, OX1 2RL, Oxford, UK
| | - Alicia R Ventresca Miller
- Department of Archaeology, Max Planck Institute for the Science of Human History, 10 Kahlaische Str., Jena, 07745, Germany.,Department of Anthropology, Museum of Anthropological Archaeology, University of Michigan, Ann Arbor, MI, 48109, USA
| | - Andrea Picin
- Department of Archaeology, Max Planck Institute for the Science of Human History, 10 Kahlaische Str., Jena, 07745, Germany
| | - Nils Vanwezer
- Department of Archaeology, Max Planck Institute for the Science of Human History, 10 Kahlaische Str., Jena, 07745, Germany
| | - Franziska Irmer
- Department of Archaeology, Max Planck Institute for the Science of Human History, 10 Kahlaische Str., Jena, 07745, Germany
| | - Samantha Brown
- Department of Archaeology, Max Planck Institute for the Science of Human History, 10 Kahlaische Str., Jena, 07745, Germany
| | - Aida Abdykanova
- Anthropology Program, American University of Central Asia, Aaly Tokombaev st. 7/6, 720060, Bishkek, Kyrgyzstan
| | - Daniel R Shultz
- Departments of Anthropology and History, McGill University, 855 Sherbrooke Street West, Montreal, Quebec, Canada, H3A 2T7
| | - Victoria Pham
- University of Sydney, Australia, Camperdown, NSW, 2006, Australia
| | - Michael Bunce
- Trace and Environmental DNA (TrEnD) Laboratory, Curtin University, Kent Street, Bentley, WA, 6102, Australia
| | - Katerina Douka
- Department of Archaeology, Max Planck Institute for the Science of Human History, 10 Kahlaische Str., Jena, 07745, Germany
| | - Emily Lena Jones
- Department of Anthropology, University of New Mexico, MSC01-1040, Albuquerque, NM, 87131, USA
| | - Nicole Boivin
- Department of Archaeology, Max Planck Institute for the Science of Human History, 10 Kahlaische Str., Jena, 07745, Germany
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110
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Abstract
Introduction: Despite an extensive published literature, skepticism over the claim of original biochemicals including proteins preserved in the fossil record persists and the issue remains controversial. Workers using many different techniques including mass spectrometry, X-ray, electron microscopy and optical spectroscopic techniques, have attempted to verify proteinaceous or other biochemicals that appear endogenous to fossils found throughout the geologic column.Areas covered: This paper presents a review of the relevant literature published over the last 50 years. A comparative survey of the reported techniques used is also given.Expert opinion: Morphological and molecular investigations show that original biochemistry is geologically extensive, geographically global, and taxonomically wide-ranging. The survival of endogenous organics in fossils remains the subject of widespread and increasing research investigation.
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Affiliation(s)
- Brian Thomas
- Mass Spectrometry Group, Department of Electrical Engineering and Electronics, University of Liverpool, Liverpool, UK
| | - Stephen Taylor
- Mass Spectrometry Group, Department of Electrical Engineering and Electronics, University of Liverpool, Liverpool, UK
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111
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Marković N, Stevanović O, Krstić N, Marinković D, Buckley M. A case study of vertebral fusion in a 19 th-century horse from Serbia. INTERNATIONAL JOURNAL OF PALEOPATHOLOGY 2019; 27:17-23. [PMID: 31550619 DOI: 10.1016/j.ijpp.2019.07.007] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/30/2019] [Revised: 07/13/2019] [Accepted: 07/13/2019] [Indexed: 06/10/2023]
Abstract
OBJECTIVE To evaluate the etiology of skeletal changes noted in equid vertebrae from a 19th- century context near Belgrade, Serbia. MATERIALS A vertebral column consisting of 15 fused thoracic vertebrae (T2-T16), with right ribs fused to T4 and T5 and small remnants of ribs articulating with T4, T5 and T6 on the left side were accidentally recovered during industrial exploitation of sand. METHODS The specimen was subjected to morphological analysis and collagen fingerprinting by mass spectrometry for species identification. In order to determine the absolute temporal context, radiocarbon dating was employed. Pathological changes were analyzed macroscopically and then underwent X-ray and (CT) imaging. RESULTS Species identification indicates that the vertebral column belonged to a domestic horse (Equus caballus) living in the early 19th century. Pathological changes included exuberant bone proliferation, fusion of small articulations, enthesopathy formation, complete fusion between the vertebral bodies, and ossification of the anterior longitudinal ligament. CONCLUSIONS Pathological changes represent signs of an advanced stage of vertebral fusion consistent with diffuse idiopathic skeletal hyperostosis (DISH). SIGNIFICANCE This case study provides a clear distinction between diffuse idiopathic skeletal hyperostosis (DISH) and other vertebral column diseases in equids. It also presents a new and significant contribution to the nascent discipline of animal paleopathology in present-day Serbia. LIMITATIONS Given that only 15 thoracic vertebrae were discovered, the impact of this disease on other parts of the horse skeleton remains unknown, as does the archaeological context of the remains. SUGGESTIONS FOR FURTHER RESEARCH Research into the frequency of DISH in equids, as well as the historical context of equine husbandry in Serbia will allow greater insight into the causes and effects of this pathological condition.
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Affiliation(s)
- Nemanja Marković
- Institute of Archaeology, Kneza Mihaila 35/IV, 11000, Belgrade, Serbia.
| | - Oliver Stevanović
- Veterinary clinic "BL vet" Banja Luka, Stepe Stepanovića 173, 78000, Banja Luka, Bosnia and Herzegovina
| | - Nikola Krstić
- Faculty of Veterinary Medicine, University of Belgrade, Bulevar Oslobođenja 18, 11000 Belgrade, Serbia
| | - Darko Marinković
- Faculty of Veterinary Medicine, University of Belgrade, Bulevar Oslobođenja 18, 11000 Belgrade, Serbia
| | - Michael Buckley
- Manchester Institute of Biotechnology, School of Earth and Environmental Sciences, The University of Manchester, 131 Princess Street, Manchester, M1 7DN, UK.
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112
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Swift JA, Bunce M, Dortch J, Douglass K, Faith JT, Fellows Yates JA, Field J, Haberle SG, Jacob E, Johnson CN, Lindsey E, Lorenzen ED, Louys J, Miller G, Mychajliw AM, Slon V, Villavicencio NA, Waters MR, Welker F, Wood R, Petraglia M, Boivin N, Roberts P. Micro Methods for Megafauna: Novel Approaches to Late Quaternary Extinctions and Their Contributions to Faunal Conservation in the Anthropocene. Bioscience 2019; 69:877-887. [PMID: 31719710 PMCID: PMC6829010 DOI: 10.1093/biosci/biz105] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/05/2023] Open
Abstract
Drivers of Late Quaternary megafaunal extinctions are relevant to modern conservation policy in a world of growing human population density, climate change, and faunal decline. Traditional debates tend toward global solutions, blaming either dramatic climate change or dispersals of Homo sapiens to new regions. Inherent limitations to archaeological and paleontological data sets often require reliance on scant, poorly resolved lines of evidence. However, recent developments in scientific technologies allow for more local, context-specific approaches. In the present article, we highlight how developments in five such methodologies (radiocarbon approaches, stable isotope analysis, ancient DNA, ancient proteomics, microscopy) have helped drive detailed analysis of specific megafaunal species, their particular ecological settings, and responses to new competitors or predators, climate change, and other external phenomena. The detailed case studies of faunal community composition, extinction chronologies, and demographic trends enabled by these methods examine megafaunal extinctions at scales appropriate for practical understanding of threats against particular species in their habitats today.
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Affiliation(s)
- Jillian A Swift
- Department of Archaeology, Max Planck Institute for the Science of Human History, Jena, Germany
- Anthropology Department of Bernice Pauahi Bishop Museum, Honolulu, Hawai’i
| | - Michael Bunce
- Trace and Environmental DNA Laboratory, School of Molecular and Life Sciences, Curtin University, Bentley, Western Australia, Australia
| | - Joe Dortch
- Centre for Rock Art Research and Management, University of Western Australia, Perth, Australia
| | - Kristina Douglass
- Department of Anthropology and with the Institutes for Energy and the Environment, The Pennsylvania State University, State College, Pennsylvania
| | - J Tyler Faith
- Natural History Museum of Utah and with the Department of Anthropology, University of Utah, Salt Lake City, Utah
| | - James A Fellows Yates
- Department of Archaeogenetics, Max Planck Institute for the Science of Human History, Jena, Germany
| | - Judith Field
- School of Biological, Earth, and Environmental Science, University of New South Wales, Sydney, Australia
| | - Simon G Haberle
- College of Asia and the Pacific and the School of Culture, History, and Language, Australian National University, Canberra, Australia
- Australian Research Council Centre of Excellence, Australian Biodiversity and Heritage, Wollongong, New South Wales, Australia
| | - Eileen Jacob
- Research Laboratory for Archaeology and the History of Art, University of Oxford, Oxford, England
| | - Chris N Johnson
- Australian Research Council Centre of Excellence, Australian Biodiversity and Heritage, Wollongong, New South Wales, Australia
- School of Natural Sciences, University of Tasmania, Hobart, Australia
| | - Emily Lindsey
- La Brea Tar Pits and Museum, part of the Natural History Museum, Los Angeles County, Los Angeles, California
| | - Eline D Lorenzen
- Natural History Museum of Denmark, University of Copenhagen, Copenhagen, Denmark
| | - Julien Louys
- Australian Research Center for Human Evolution, Environmental Futures Research Institute, Griffith University, Brisbane, Queensland, Australia
| | - Gifford Miller
- INSTAAR and Department of Geological Sciences, University of Colorado, Boulder
| | - Alexis M Mychajliw
- La Brea Tar Pits and Museum, part of the Natural History Museum, Los Angeles County, Los Angeles, California
| | - Viviane Slon
- Department of Evolutionary Genetics, Max Planck Institute for Evolutionary Anthropology, Leipzig, Germany
| | - Natalia A Villavicencio
- Departamento de Ecología, in the Facultad de Ciencias Biológicas, Pontificia Universidad Católica de Chile, Santiago, Chile
- Instituto de Ecología and Biodiversidad, Santiago, Chile
| | - Michael R Waters
- Center for the Study of the First Americans, the Department of Anthropology, Texas A&M University, College Station, Texas
| | - Frido Welker
- Evolutionary Genomics Section of the GLOBE Institute, University of Copenhagen, Copenhagen, Denmark, and with the Department of Human Evolution, Max Planck Institute for Evolutionary Anthropology, Leipzig, Germany
| | - Rachel Wood
- Research School of Earth Sciences, Australian National University, Canberra, Australia
| | - Michael Petraglia
- Department of Archaeology, Max Planck Institute for the Science of Human History, Jena, Germany
| | - Nicole Boivin
- Department of Archaeology, Max Planck Institute for the Science of Human History, Jena, Germany
| | - Patrick Roberts
- Department of Archaeology, Max Planck Institute for the Science of Human History, Jena, Germany
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113
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Harvey VL, LeFebvre MJ, deFrance SD, Toftgaard C, Drosou K, Kitchener AC, Buckley M. Preserved collagen reveals species identity in archaeological marine turtle bones from Caribbean and Florida sites. ROYAL SOCIETY OPEN SCIENCE 2019; 6:191137. [PMID: 31824722 PMCID: PMC6837194 DOI: 10.1098/rsos.191137] [Citation(s) in RCA: 16] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/29/2019] [Accepted: 10/04/2019] [Indexed: 05/03/2023]
Abstract
Advancements in molecular science are continually improving our knowledge of marine turtle biology and evolution. However, there are still considerable gaps in our understanding, such as past marine turtle distributions, which can benefit from advanced zooarchaeological analyses. Here, we apply collagen fingerprinting to 130 archaeological marine turtle bone samples up to approximately 2500 years old from the Caribbean and Florida's Gulf Coast for faunal identification, finding the vast majority of samples (88%) to contain preserved collagen despite deposition in the tropics. All samples can be identified to species-level with the exception of the Kemp's ridley (Lepidochelys kempii) and olive ridley (L. olivacea) turtles, which can be separated to genus level, having diverged from one another only approximately 5 Ma. Additionally, we identify a single homologous peptide that allows the separation of archaeological green turtle samples, Chelonia spp., into two distinct groups, which potentially signifies a difference in genetic stock. The majority of the archaeological samples are identified as green turtle (Chelonia spp.; 63%), with hawksbill (Eretmochelys imbricata; 17%) and ridley turtles (Lepidochelys spp.; 3%) making up smaller proportions of the assemblage. There were no molecular identifications of the loggerhead turtle (Caretta caretta) in the assemblage despite 9% of the samples being morphologically identified as such, highlighting the difficulties in relying on morphological identifications alone in archaeological remains. Finally, we present the first marine turtle molecular phylogeny using collagen (I) amino acid sequences and find our analyses match recent phylogenies based on nuclear and mitochondrial DNA. Our results highlight the advantage of using collagen fingerprinting to supplement morphological analyses of turtle bones and support the usefulness of this technique for assessing their past distributions across the Caribbean and Florida's Gulf Coast, especially in these tropical environments where DNA preservation may be poor.
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Affiliation(s)
- Virginia L. Harvey
- Manchester Institute of Biotechnology, School of Earth and Environmental Sciences, University of Manchester, 131 Princess Street, Manchester M1 7DN, UK
| | - Michelle J. LeFebvre
- Florida Museum of Natural History, University of Florida, Gainesville, FL 32611, USA
| | - Susan D. deFrance
- Department of Anthropology, University of Florida, Gainesville, FL 32611, USA
| | - Casper Toftgaard
- The SAXO Institute, University of Copenhagen, Karen Blixens Plads 8, 2300 København S, Denmark
- National Museum of Denmark, Nationalmuseet, Ny Vestergade 10, Prinsens Palæ, DK-1471, København K, Denmark
| | - Konstantina Drosou
- KNH Centre for Biomedical Egyptology, School of Biological Sciences, 99 Oxford Road, Manchester, M13 9PG, UK
| | - Andrew C. Kitchener
- Department of Natural Sciences, National Museums Scotland, Chambers Street, Edinburgh EH1 1JF, UK
- The University of Edinburgh, Institute of Geography, School of Geosciences, Drummond Street, Edinburgh, EH8 9XP, UK
| | - Michael Buckley
- Manchester Institute of Biotechnology, School of Earth and Environmental Sciences, University of Manchester, 131 Princess Street, Manchester M1 7DN, UK
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114
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Sinet-Mathiot V, Smith GM, Romandini M, Wilcke A, Peresani M, Hublin JJ, Welker F. Combining ZooMS and zooarchaeology to study Late Pleistocene hominin behaviour at Fumane (Italy). Sci Rep 2019; 9:12350. [PMID: 31451791 PMCID: PMC6710433 DOI: 10.1038/s41598-019-48706-z] [Citation(s) in RCA: 22] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/28/2019] [Accepted: 07/25/2019] [Indexed: 12/14/2022] Open
Abstract
Collagen type I fingerprinting (ZooMS) has recently been used to provide either palaeoenvironmental data or to identify additional hominin specimens in Pleistocene contexts, where faunal assemblages are normally highly fragmented. However, its potential to elucidate hominin subsistence behaviour has been unexplored. Here, ZooMS and zooarchaeology have been employed in a complementary approach to investigate bone assemblages from Final Mousterian and Uluzzian contexts at Fumane cave (Italy). Both approaches produced analogous species composition, but differ significantly in species abundance, particularly highlighted by a six fold-increase in the quantity of Bos/Bison remains in the molecularly identified component. Traditional zooarchaeological methods would therefore underestimate the proportion of Bos/Bison in these levels to a considerable extent. We suggest that this difference is potentially due to percussion-based carcass fragmentation of large Bos/Bison bone diaphyses. Finally, our data demonstrates high variability in species assignment to body size classes based on bone cortical thickness and fragment size. Thus, combining biomolecular and traditional zooarchaeological methods allows us to refine our understanding of bone assemblage composition associated with hominin occupation at Fumane.
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Affiliation(s)
- Virginie Sinet-Mathiot
- Department of Human Evolution, Max Planck Institute for Evolutionary Anthropology, Leipzig, Germany.
| | - Geoff M Smith
- Department of Human Evolution, Max Planck Institute for Evolutionary Anthropology, Leipzig, Germany
| | - Matteo Romandini
- University of Bologna, Department of Cultural Heritage, Ravenna, Italy.,University of Ferrara, Department of Humanities, Section of Prehistory and Anthropology, Ferrara, Italy
| | - Arndt Wilcke
- Fraunhofer Institute for Cell Therapy and Immunology, Leipzig, Germany
| | - Marco Peresani
- University of Ferrara, Department of Humanities, Section of Prehistory and Anthropology, Ferrara, Italy.
| | - Jean-Jacques Hublin
- Department of Human Evolution, Max Planck Institute for Evolutionary Anthropology, Leipzig, Germany
| | - Frido Welker
- Department of Human Evolution, Max Planck Institute for Evolutionary Anthropology, Leipzig, Germany. .,Section for Evolutionary Genomics, the Globe Institute, University of Copenhagen, Copenhagen, Denmark.
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115
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The Northern Route for Human dispersal in Central and Northeast Asia: New evidence from the site of Tolbor-16, Mongolia. Sci Rep 2019; 9:11759. [PMID: 31409814 PMCID: PMC6692324 DOI: 10.1038/s41598-019-47972-1] [Citation(s) in RCA: 27] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/09/2019] [Accepted: 07/26/2019] [Indexed: 11/21/2022] Open
Abstract
The fossil record suggests that at least two major human dispersals occurred across the Eurasian steppe during the Late Pleistocene. Neanderthals and Modern Humans moved eastward into Central Asia, a region intermittently occupied by the enigmatic Denisovans. Genetic data indicates that the Denisovans interbred with Neanderthals near the Altai Mountains (South Siberia) but where and when they met H. sapiens is yet to be determined. Here we present archaeological evidence that document the timing and environmental context of a third long-distance population movement in Central Asia, during a temperate climatic event around 45,000 years ago. The early occurrence of the Initial Upper Palaeolithic, a techno-complex whose sudden appearance coincides with the first occurrence of H. sapiens in the Eurasian steppes, establishes an essential archaeological link between the Siberian Altai and Northwestern China . Such connection between regions provides empirical ground to discuss contacts between local and exogenous populations in Central and Northeast Asia during the Late Pleistocene.
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116
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McGrath K, Rowsell K, Gates St-Pierre C, Tedder A, Foody G, Roberts C, Speller C, Collins M. Identifying Archaeological Bone via Non-Destructive ZooMS and the Materiality of Symbolic Expression: Examples from Iroquoian Bone Points. Sci Rep 2019; 9:11027. [PMID: 31363122 PMCID: PMC6667708 DOI: 10.1038/s41598-019-47299-x] [Citation(s) in RCA: 24] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/14/2019] [Accepted: 06/26/2019] [Indexed: 12/01/2022] Open
Abstract
Today, practical, functional and symbolic choices inform the selection of raw materials for worked objects. In cases where we can discern the origin of worked bone, tooth, ivory and antler objects in the past, we assume that similar choices are being made. However, morphological species identification of worked objects is often impossible due to the loss of identifying characteristics during manufacture. Here, we describe a novel non-destructive ZooMS (Zooarchaeology by Mass Spectrometry) method which was applied to bone points from Pre-Contact St. Lawrence Iroquoian village sites in southern Quebec, Canada. The traditional ZooMS technique requires destructive analysis of a sample, which can be problematic when dealing with artefacts. Here we instead extracted proteins from the plastic bags in which the points had been stored. ZooMS analysis revealed hitherto unexpected species, notably black bear (Ursus americanus) and human (Homo sapiens sapiens), used in point manufacture. These surprising results (confirmed through genomic sequencing) highlight the importance of advancing biomolecular research in artefact studies. Furthermore, they unexpectedly and exceptionally allow us to identify and explore the tangible, material traces of the symbolic relationship between bears and humans, central to past and present Iroquoian cosmology and mythology.
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Affiliation(s)
- Krista McGrath
- BioArCh, Department of Archaeology, University of York, York, UK.
| | - Keri Rowsell
- BioArCh, Department of Archaeology, University of York, York, UK.,London School of Economics and Political Science, London, UK
| | | | - Andrew Tedder
- School of Chemistry & Bioscience, University of Bradford, Bradford, UK
| | - George Foody
- Department of Biological and Geographical Sciences, School of Applied Sciences, University of Huddersfield, Huddersfield, UK
| | | | - Camilla Speller
- BioArCh, Department of Archaeology, University of York, York, UK.,Department of Anthropology, University of British Columbia, Vancouver, Canada
| | - Matthew Collins
- BioArCh, Department of Archaeology, University of York, York, UK.,EvoGenomics, Natural History Museum of Denmark, University of Copenhagen, Copenhagen, Denmark.,McDonald Institute for Archaeological Research, University of Cambridge, Cambridge, UK
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117
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Kuckova S, Cejnar P, Santrucek J, Hynek R. Characterization of proteins in cultural heritage using MALDI–TOF and LC–MS/MS mass spectrometric techniques. PHYSICAL SCIENCES REVIEWS 2019. [DOI: 10.1515/psr-2018-0011] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/22/2023]
Abstract
Abstract
Identification of proteinaceous materials in artworks is of high interest to restorers-conservators, art historians and archaeologists, because it helps to shed light on the used painting techniques, to attribute unknown artworks, to make conclusions on prehistoric diets, etc. The chapter is devoted to the mass spectrometry instrumentation, evaluation of obtained data and it is showing several examples of the application of matrix-assisted laser desorption/ionization–time-of-flight and liquid chromatography–electrospray ionization–quadrupole–time-of-flight mass spectrometers on cultural heritage samples.
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118
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Applications and challenges of forensic proteomics. Forensic Sci Int 2019; 297:350-363. [DOI: 10.1016/j.forsciint.2019.01.022] [Citation(s) in RCA: 20] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/16/2018] [Revised: 01/09/2019] [Accepted: 01/13/2019] [Indexed: 12/23/2022]
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119
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Di Maida G, Mannino MA, Krause-Kyora B, Jensen TZT, Talamo S. Radiocarbon dating and isotope analysis on the purported Aurignacian skeletal remains from Fontana Nuova (Ragusa, Italy). PLoS One 2019; 14:e0213173. [PMID: 30893326 PMCID: PMC6426221 DOI: 10.1371/journal.pone.0213173] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/09/2018] [Accepted: 02/16/2019] [Indexed: 01/13/2023] Open
Abstract
Proving voyaging at sea by Palaeolithic humans is a difficult archaeological task, even for short distances. In the Mediterranean, a commonly accepted sea crossing is that from the Italian Peninsula to Sicily by anatomically modern humans, purportedly of the Aurignacian culture. This claim, however, was only supported by the typological attribution to the Aurignacian of the lithic industries from the insular site of Fontana Nuova. AMS radiocarbon dating undertaken as part of our research shows that the faunal remains, previously considered Aurignacian, actually date to the Holocene. Absolute dating on dentinal collagen also attributes the human teeth from the site to the early Holocene, although we were unable to obtain ancient DNA to evaluate their ancestry. Ten radiocarbon dates on human and other taxa are comprised between 9910–9700 cal. BP and 8600–8480 cal. BP, indicating that Fontana Nuova was occupied by Mesolithic and not Aurignacian hunter-gatherers. Only a new study of the lithic assemblage could establish if the material from Fontana Nuova is a mixed collection that includes both late Upper Palaeolithic (Epigravettian) and Mesolithic artefacts, as can be suggested by taking into account both the results of our study and of the most recent reinterpretation of the lithics. Nevertheless, this research suggests that the notion that Aurignacian groups were present in Sicily should now be revised. Another outcome of our study is that we found that three specimens, attributed on grounds both of morphological and ZooMS identifications to Cervus elaphus, had δ13C values significantly higher than any available for such species in Europe.
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Affiliation(s)
- Gianpiero Di Maida
- Graduate School Human Development in Landscapes, CAU Kiel, Kiel, Germany.,Neanderthal Museum, Mettmann, Germany
| | - Marcello A Mannino
- Department of Archaeology and Heritage Studies, School of Culture and Society, Aarhus University, Højbjerg, Denmark.,Department of Human Evolution, Max Planck Institute for Evolutionary Anthropology, Leipzig, Germany
| | - Ben Krause-Kyora
- Institute of Clinical Molecular Biology, CAU Kiel, Kiel, Germany.,Max Planck Institute for the Science of Human History, Jena, Germany
| | - Theis Zetner Trolle Jensen
- Section for Evolutionary Genomics, Natural History Museum of Denmark, University of Copenhagen, Copenhagen, Denmark.,BioArCh, Department of Archaeology, University of York, York, United Kingdom
| | - Sahra Talamo
- Department of Human Evolution, Max Planck Institute for Evolutionary Anthropology, Leipzig, Germany
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120
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Jaouen K, Richards MP, Le Cabec A, Welker F, Rendu W, Hublin JJ, Soressi M, Talamo S. Exceptionally high δ 15N values in collagen single amino acids confirm Neandertals as high-trophic level carnivores. Proc Natl Acad Sci U S A 2019; 116:4928-4933. [PMID: 30782806 PMCID: PMC6421459 DOI: 10.1073/pnas.1814087116] [Citation(s) in RCA: 72] [Impact Index Per Article: 14.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022] Open
Abstract
Isotope and archeological analyses of Paleolithic food webs have suggested that Neandertal subsistence relied mainly on the consumption of large herbivores. This conclusion was primarily based on elevated nitrogen isotope ratios in Neandertal bone collagen and has been significantly debated. This discussion relies on the observation that similar high nitrogen isotopes values could also be the result of the consumption of mammoths, young animals, putrid meat, cooked food, freshwater fish, carnivores, or mushrooms. Recently, compound-specific C and N isotope analyses of bone collagen amino acids have been demonstrated to add significantly more information about trophic levels and aquatic food consumption. We undertook single amino acid C and N isotope analysis on two Neandertals, which were characterized by exceptionally high N isotope ratios in their bulk bone or tooth collagen. We report here both C and N isotope ratios on single amino acids of collagen samples for these two Neandertals and associated fauna. The samples come from two sites dating to the Middle to Upper Paleolithic transition period (Les Cottés and Grotte du Renne, France). Our results reinforce the interpretation of Neandertal dietary adaptations as successful top-level carnivores, even after the arrival of modern humans in Europe. They also demonstrate that high δ15N values of bone collagen can solely be explained by mammal meat consumption, as supported by archeological and zooarcheological evidence, without necessarily invoking explanations including the processing of food (cooking, fermenting), the consumption of mammoths or young mammals, or additional (freshwater fish, mushrooms) dietary protein sources.
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Affiliation(s)
- Klervia Jaouen
- Department of Human Evolution, Max Planck Institute for Evolutionary Anthropology, 04103 Leipzig, Germany;
| | - Michael P Richards
- Department of Archaeology, Simon Fraser University, Burnaby BC V5A 1S6, Canada
| | - Adeline Le Cabec
- Department of Human Evolution, Max Planck Institute for Evolutionary Anthropology, 04103 Leipzig, Germany
| | - Frido Welker
- Department of Human Evolution, Max Planck Institute for Evolutionary Anthropology, 04103 Leipzig, Germany
- Evolutionary Genomics, Natural History Museum of Denmark, University of Copenhagen, DK-1353 Copenhagen, Denmark
| | - William Rendu
- De la Préhistoire à l'Actuel: Culture, Environnement et Anthropologie, CNRS-University of Bordeaux, 33615 Pessac, France
| | - Jean-Jacques Hublin
- Department of Human Evolution, Max Planck Institute for Evolutionary Anthropology, 04103 Leipzig, Germany
- Chaire Internationale de Paléoanthropologie, Collège de France, 75005 Paris, France
| | - Marie Soressi
- Faculty of Archaeology, Leiden University, 2311 EZ Leiden, The Netherlands
| | - Sahra Talamo
- Department of Human Evolution, Max Planck Institute for Evolutionary Anthropology, 04103 Leipzig, Germany
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121
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Buckley M, Lawless C, Rybczynski N. Collagen sequence analysis of fossil camels, Camelops and c.f. Paracamelus, from the Arctic and sub-Arctic of Plio-Pleistocene North America. J Proteomics 2019; 194:218-225. [DOI: 10.1016/j.jprot.2018.11.014] [Citation(s) in RCA: 33] [Impact Index Per Article: 6.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/02/2018] [Revised: 11/02/2018] [Accepted: 11/19/2018] [Indexed: 11/27/2022]
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122
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Bradfield J. Identifying animal taxa used to manufacture bone tools during the Middle Stone Age at Sibudu, South Africa: Results of a CT-rendered histological analysis. PLoS One 2018; 13:e0208319. [PMID: 30496272 PMCID: PMC6264865 DOI: 10.1371/journal.pone.0208319] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/09/2018] [Accepted: 11/15/2018] [Indexed: 01/16/2023] Open
Abstract
This paper presents the histological characterisation of a selection of worked bone artefacts from Middle Stone Age layers at Sibudu cave, South Africa. Histographic rendering is achieved using high-resolution Computed Tomography, which is non-destructive and facilitates three-dimensional histologic analysis. Excellent congruency in image quality was achieved with previous studies using this method. The results show that most of the artefact fragments contain mostly primary lamellar tissue, which is the bone tissue best adapted to withstand impact stresses. This indicates that bone with greater elastic properties was chosen. Histological characterisation allows the identification of animal taxa. Based on the sample analysed in this paper, Perissodactyla bone was used predominantly in the older layers at the site. Artiodactyla are represented throughout but appear far more frequently in the later (post-Howiesons Poort onwards) layers. Some of the Artiodactyla specimens have high proportions of Haversian tissue, reducing elasticity. The higher percentages of Haversian tissue in the post-Howiesons Poort artefacts relative to Holocene examples from southern Africa suggests that people may have started experimenting with bone from different animal taxa at this time and had not yet learned to eliminate the mechanically weaker secondary tissue. Apart from mechanical considerations, possible cultural constraints governing raw material selection is also explored.
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Affiliation(s)
- Justin Bradfield
- Centre for Anthropological Research, University of Johannesburg, Johannesburg, South Africa
- Evolutionary Studies Institute and School of Geography, Archaeology and Environmental Studies, University of the Witwatersrand, Johannesburg, South Africa
- * E-mail:
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123
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Guiry E, Buckley M. Urban rats have less variable, higher protein diets. Proc Biol Sci 2018; 285:rspb.2018.1441. [PMID: 30333207 PMCID: PMC6234891 DOI: 10.1098/rspb.2018.1441] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/27/2018] [Accepted: 09/20/2018] [Indexed: 12/02/2022] Open
Abstract
Over the past 1000 years, rats (Rattus spp.) have become one of the most successful and prolific pests in human society. Despite their cosmopolitan distribution across six continents and ubiquity throughout the world's cities, rat urban ecology remains poorly understood. We investigate the role of human foods in brown rat (Rattus norvegicus) diets in urban and rural areas over a 100 year period (ca AD 1790–1890) in Toronto, Canada using stable carbon (δ13C) and nitrogen (δ15N) isotope analyses of archaeological remains. We found that rat diets from urban sites were of higher quality and were more homogeneous and stable over time. By contrast, in rural areas, they show a wide range of dietary niche specializations that directly overlap, and probably competed, with native omnivorous and herbivorous species. These results demonstrate a link between rodent diets and human population density, providing, to our knowledge, the first long-term dietary perspective on the relative value of different types of human settlements as rodent habitat. This study highlights the potential of using the historical and archaeological record to provide a retrospective on the urban ecology of commensal and synanthropic animals that could be useful for improving animal management and conservation strategies in urban areas.
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Affiliation(s)
- E Guiry
- Department of Anthropology, Trent University, 1600 W Bank Drive, Peterborough, Ontario, Canada K9 J 0G2 .,Department of Anthropology, University of British Columbia, 6303 NW Marine Drive, Vancouver, British Columbia, Canada V6T 1Z1
| | - M Buckley
- School of Earth and Environmental Sciences, Manchester Institute of Biotechnology, University of Manchester, 131 Princess Street, Manchester M1 7DN, UK
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124
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Steinhilber AE, Schmidt FF, Naboulsi W, Planatscher H, Niedzwiecka A, Zagon J, Braeuning A, Lampen A, Joos TO, Poetz O. Species Differentiation and Quantification of Processed Animal Proteins and Blood Products in Fish Feed Using an 8-Plex Mass Spectrometry-Based Immunoassay. JOURNAL OF AGRICULTURAL AND FOOD CHEMISTRY 2018; 66:10327-10335. [PMID: 30222351 DOI: 10.1021/acs.jafc.8b03934] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/08/2023]
Abstract
With the reintroduction of nonruminant processed animal proteins (PAPs) for use in aquaculture in 2013, there is a suitable alternative to replace expensive fish meal in fish feed. Nevertheless, since the bovine spongiform encephalopathy (BSE) crisis, the use of PAPs in feed is strictly regulated. To date, light microscopy and polymerase chain reaction are the official methods for proving the absence of illegal PAPs in feed. Due to their limitations, alternative methods for the quantitative species differentiation are needed. To address this issue, we developed and validated an 8-plex mass spectrometry-based immunoassay. The workflow comprises a tryptic digestion of PAPs and blood products in suspension, a cross-species immunoaffinity enrichment of 8 species-specific alpha-2-macroglobulin peptides using a group-specific antibody, and a subsequent analysis by ultrahigh-performance liquid chromatography coupled to tandem mass spectrometry for species identification and quantification. This workflow can be used to quantitatively determine the species origin in future feed authentication studies.
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Affiliation(s)
- Andreas E Steinhilber
- SIGNATOPE GmbH , 72770 Reutlingen , Germany
- NMI Natural and Medical Sciences Institute at the University of Tuebingen , 72770 Reutlingen , Germany
| | - Felix F Schmidt
- NMI Natural and Medical Sciences Institute at the University of Tuebingen , 72770 Reutlingen , Germany
| | | | | | - Alicia Niedzwiecka
- Department of Food Safety , German Federal Institute for Risk Assessment , 10589 Berlin , Germany
| | - Jutta Zagon
- Department of Food Safety , German Federal Institute for Risk Assessment , 10589 Berlin , Germany
| | - Albert Braeuning
- Department of Food Safety , German Federal Institute for Risk Assessment , 10589 Berlin , Germany
| | - Alfonso Lampen
- Department of Food Safety , German Federal Institute for Risk Assessment , 10589 Berlin , Germany
| | - Thomas O Joos
- NMI Natural and Medical Sciences Institute at the University of Tuebingen , 72770 Reutlingen , Germany
| | - Oliver Poetz
- SIGNATOPE GmbH , 72770 Reutlingen , Germany
- NMI Natural and Medical Sciences Institute at the University of Tuebingen , 72770 Reutlingen , Germany
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125
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Hendy J, Colonese AC, Franz I, Fernandes R, Fischer R, Orton D, Lucquin A, Spindler L, Anvari J, Stroud E, Biehl PF, Speller C, Boivin N, Mackie M, Jersie-Christensen RR, Olsen JV, Collins MJ, Craig OE, Rosenstock E. Ancient proteins from ceramic vessels at Çatalhöyük West reveal the hidden cuisine of early farmers. Nat Commun 2018; 9:4064. [PMID: 30283003 PMCID: PMC6170438 DOI: 10.1038/s41467-018-06335-6] [Citation(s) in RCA: 76] [Impact Index Per Article: 12.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/22/2018] [Accepted: 08/28/2018] [Indexed: 02/08/2023] Open
Abstract
The analysis of lipids (fats, oils and waxes) absorbed within archaeological pottery has revolutionized the study of past diets and culinary practices. However, this technique can lack taxonomic and tissue specificity and is often unable to disentangle signatures resulting from the mixing of different food products. Here, we extract ancient proteins from ceramic vessels from the West Mound of the key early farming site of Çatalhöyük in Anatolia, revealing that this community processed mixes of cereals, pulses, dairy and meat products, and that particular vessels may have been reserved for specialized foods (e.g., cow milk and milk whey). Moreover, we demonstrate that dietary proteins can persist on archaeological artefacts for at least 8000 years, and that this approach can reveal past culinary practices with more taxonomic and tissue-specific clarity than has been possible with previous biomolecular techniques.
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Affiliation(s)
- Jessica Hendy
- Department of Archaeology, Max Planck Institute for the Science of Human History, 07745, Jena, Germany. .,BioArCh, Department of Archaeology, University of York, York, YO10 5DD, UK.
| | - Andre C Colonese
- BioArCh, Department of Archaeology, University of York, York, YO10 5DD, UK
| | - Ingmar Franz
- Institute of Prehistoric and Protohistoric Archaeology, Christian-Albrechts-Universität zu Kiel, D-24098, Kiel, Germany
| | - Ricardo Fernandes
- Department of Archaeology, Max Planck Institute for the Science of Human History, 07745, Jena, Germany.,School of Archaeology, University of Oxford, Oxford, OX1 2PG, UK
| | - Roman Fischer
- Target Discovery Institute, University of Oxford, Oxford, OX3 7FZ, UK
| | - David Orton
- BioArCh, Department of Archaeology, University of York, York, YO10 5DD, UK
| | - Alexandre Lucquin
- BioArCh, Department of Archaeology, University of York, York, YO10 5DD, UK
| | - Luke Spindler
- BioArCh, Department of Archaeology, University of York, York, YO10 5DD, UK.,Oxford Radiocarbon Accelerator Unit, University of Oxford, 1 South Parks Road, Oxford, OX1 3TG, UK
| | - Jana Anvari
- Institute of Prehistoric Archaeology, Freie Universität Berlin, 14195, Berlin, Germany
| | - Elizabeth Stroud
- School of Archaeology, University of Oxford, Oxford, OX1 2PG, UK
| | - Peter F Biehl
- Department of Anthropology, University at Buffalo, Buffalo, NY, 14261-0026, USA
| | - Camilla Speller
- BioArCh, Department of Archaeology, University of York, York, YO10 5DD, UK.,Department of Anthropology, The University of British Columbia, Vancouver, BC, V6T 1Z1, Canada
| | - Nicole Boivin
- Department of Archaeology, Max Planck Institute for the Science of Human History, 07745, Jena, Germany
| | - Meaghan Mackie
- EvoGenomics, Natural History Museum of Denmark, University of Copenhagen, 2100, Copenhagen, Denmark.,Novo Nordisk Foundation Center for Protein Research, Faculty of Health and Medical Sciences, University of Copenhagen, 2200, Copenhagen, Denmark
| | - Rosa R Jersie-Christensen
- Novo Nordisk Foundation Center for Protein Research, Faculty of Health and Medical Sciences, University of Copenhagen, 2200, Copenhagen, Denmark
| | - Jesper V Olsen
- Novo Nordisk Foundation Center for Protein Research, Faculty of Health and Medical Sciences, University of Copenhagen, 2200, Copenhagen, Denmark
| | - Matthew J Collins
- BioArCh, Department of Archaeology, University of York, York, YO10 5DD, UK.,EvoGenomics, Natural History Museum of Denmark, University of Copenhagen, 2100, Copenhagen, Denmark
| | - Oliver E Craig
- BioArCh, Department of Archaeology, University of York, York, YO10 5DD, UK.
| | - Eva Rosenstock
- Institute of Prehistoric Archaeology, Freie Universität Berlin, 14195, Berlin, Germany.
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126
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Borić D, Higham T, Cristiani E, Dimitrijević V, Nehlich O, Griffiths S, Alexander C, Mihailović B, Filipović D, Allué E, Buckley M. High-Resolution AMS Dating of Architecture, Boulder Artworks and the Transition to Farming at Lepenski Vir. Sci Rep 2018; 8:14221. [PMID: 30242272 PMCID: PMC6155048 DOI: 10.1038/s41598-018-31884-7] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/14/2018] [Accepted: 08/21/2018] [Indexed: 11/09/2022] Open
Abstract
The archaeological site of Lepenski Vir is widely known after its remarkable stone art sculptures that represent a unique and unprecedented case of Holocene hunter-gatherer creativity. These artworks were found largely associated with equally unique trapezoidal limestone building floors around their centrally located rectangular stone-lined hearths. A debate has raged since the discovery of the site about the chronological place of various discovered features. While over years different views from that of the excavator about the stratigraphy and chronology of the site have been put forward, some major disagreements about the chronological position of the features that make this site a key point of reference in European Prehistory persist. Despite challenges of re-analyzing the site’s stratigraphy from the original excavation records, taphonomic problems, and issues of reservoir offsets when providing radiocarbon measurements on human and dog bones, our targeted AMS (Accelerator Mass Spectrometry) dating of various contexts from this site with the application of Bayesian statistical modelling allows us to propose with confidence a new and sound chronological framework and provide formal estimates for several key developments represented in the archaeological record of Lepenski Vir that help us in understanding the transition of last foragers to first farmers in southeast Europe as a whole.
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Affiliation(s)
- Dušan Borić
- The Italian Academy for Advanced Studies in America, Columbia University, 1161 Amsterdam Avenue, New York, NY, 10027, USA.
| | - Thomas Higham
- Oxford Radiocarbon Accelerator Unit, RLAHA, University of Oxford, Dyson Perrins Building, Oxford, OX1 3QY, UK
| | - Emanuela Cristiani
- DANTE Diet and Ancient Technology Laboratory, Sapienza University of Rome, Via Caserta 6, 00161, Rome, Italy
| | - Vesna Dimitrijević
- Department of Archaeology, University of Belgrade, Čika Ljubina 18-20, 11000, Belgrade, Serbia
| | - Olaf Nehlich
- Department of Anthropology, University of British Columbia, 6303 NW Marine Drive, Vancouver, BC, V6T 1Z1, Canada
| | - Seren Griffiths
- The School of Forensic and Applied Sciences, University of Central Lancashire, Preston, Lancashire, PR1 2HE, UK
| | | | | | - Dragana Filipović
- Institute for Balkan Studies, Serbian Academy of Sciences and Arts, Knez Mihailova 45, 11000, Belgrade, Serbia
| | - Ethel Allué
- Institut Català de Paleoecologia Humana i Evolució Social (IPHES), Campus Sescelades URV (Edifici W3), 43007, Tarragona, Spain.,Àrea de Prehistòria, Universitat Rovira i Virgili (URV), Av. Catalunya 35, 43002, Tarragona, Spain
| | - Michael Buckley
- Manchester Institute for Biotechnology, The University of Manchester, 131 Princess Street, Manchester, M1 7DN, UK
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127
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Estimation of collagen presence in dry bone using combined X-ray and neutron radiography. Appl Radiat Isot 2018; 139:141-145. [DOI: 10.1016/j.apradiso.2018.03.024] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/11/2017] [Revised: 03/25/2018] [Accepted: 03/28/2018] [Indexed: 11/22/2022]
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128
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Jarman KH, Heller NC, Jenson SC, Hutchison JR, Kaiser BLD, Payne SH, Wunschel DS, Merkley ED. Proteomics Goes to Court: A Statistical Foundation for Forensic Toxin/Organism Identification Using Bottom-Up Proteomics. J Proteome Res 2018; 17:3075-3085. [DOI: 10.1021/acs.jproteome.8b00212] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/19/2023]
Affiliation(s)
- Kristin H. Jarman
- Applied Statistics and Computational Modeling Group, Pacific Northwest National Laboratory, Richland, Washington 99352, United States
| | - Natalie C. Heller
- Applied Statistics and Computational Modeling Group, Pacific Northwest National Laboratory, Richland, Washington 99352, United States
| | - Sarah C. Jenson
- Chemical and Biological Signatures Group, Pacific Northwest National Laboratory, Richland, Washington 99352, United States
| | - Janine R. Hutchison
- Chemical and Biological Signatures Group, Pacific Northwest National Laboratory, Richland, Washington 99352, United States
| | - Brooke L. Deatherage Kaiser
- Chemical and Biological Signatures Group, Pacific Northwest National Laboratory, Richland, Washington 99352, United States
| | - Samuel H. Payne
- Biological Sciences Division, Environmental Molecular Sciences Laboratory, Pacific Northwest National Laboratory, Richland, Washington 99352, United States
| | - David S. Wunschel
- Chemical and Biological Signatures Group, Pacific Northwest National Laboratory, Richland, Washington 99352, United States
| | - Eric D. Merkley
- Chemical and Biological Signatures Group, Pacific Northwest National Laboratory, Richland, Washington 99352, United States
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129
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Rodrigues ASL, Charpentier A, Bernal-Casasola D, Gardeisen A, Nores C, Pis Millán JA, McGrath K, Speller CF. Forgotten Mediterranean calving grounds of grey and North Atlantic right whales: evidence from Roman archaeological records. Proc Biol Sci 2018; 285:20180961. [PMID: 30051821 PMCID: PMC6053924 DOI: 10.1098/rspb.2018.0961] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/30/2018] [Accepted: 06/20/2018] [Indexed: 11/12/2022] Open
Abstract
Right whales (Eubalaena glacialis) were extirpated from the eastern North Atlantic by commercial whaling. Grey whales (Eschrichtius robustus) disappeared from the entire North Atlantic in still-mysterious circumstances. Here, we test the hypotheses that both species previously occurred in the Mediterranean Sea, an area not currently considered part of their historical range. We used ancient DNA barcoding and collagen fingerprinting methods to taxonomically identify a rare set of 10 presumed whale bones from Roman and pre-Roman archaeological sites in the Strait of Gibraltar region, plus an additional bone from the Asturian coast. We identified three right whales, and three grey whales, demonstrating that the ranges of both of these species historically encompassed the Gibraltar region, probably including the Mediterranean Sea as calving grounds. Our results significantly extend the known range of the Atlantic grey whale, and suggest that 2000 years ago, right and grey whales were common when compared with other whale species. The disappearance of right and grey whales from the Mediterranean region is likely to have been accompanied by broader ecosystem impacts, including the disappearance of their predators (killer whales) and a reduction in marine primary productivity. The evidence that these two coastal and highly accessible species were present along the shores of the Roman Empire raises the hypothesis that they may have formed the basis of a forgotten whaling industry.
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Affiliation(s)
- Ana S L Rodrigues
- Centre d'Ecologie Fonctionnelle et Evolutive, UMR 5175 (CNRS-Université de Montpellier-UPVM-EPHE), 34293 Montpellier, France
| | - Anne Charpentier
- Centre d'Ecologie Fonctionnelle et Evolutive, UMR 5175 (CNRS-Université de Montpellier-UPVM-EPHE), 34293 Montpellier, France
| | - Darío Bernal-Casasola
- Faculty of Philosophy and Letters, Department of History, Geography and Philosophy, University of Cádiz, 11003 Cádiz, Spain
| | - Armelle Gardeisen
- Archéologie des Sociétés Méditerranéennes, UMR 5140 (CNRS-UPVM-MCC) and Labex Archimede IA-ANR-11-LABX-0032-01), Université Paul-Valéry Montpellier, 34199 Montpellier, France
| | - Carlos Nores
- Instituto de Recursos Naturales y Ordenación del Territorio, Universidad de Oviedo, Mieres 33600, Spain
| | - José Antonio Pis Millán
- Centro de Experimentación Pesquera, Dirección General de Pesca Marítima, Gobierno del Principado de Asturias, 33212 Gijón, Spain
| | - Krista McGrath
- BioArCh, Department of Archaeology, University of York, York YO10 5DD, UK
| | - Camilla F Speller
- BioArCh, Department of Archaeology, University of York, York YO10 5DD, UK
- Department of Anthropology, University of British Columbia, Vancouver, Canada V6T 1Z1
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130
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Hameed AM, Asiyanbi-H T, Idris M, Fadzillah N, Mirghani MES. A Review of Gelatin Source Authentication Methods. Trop Life Sci Res 2018; 29:213-227. [PMID: 30112151 PMCID: PMC6072727 DOI: 10.21315/tlsr2018.29.2.15] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Gelatin is a very popular pharmaceutical and food ingredient and the most studied ingredient in Halal researches. Interest in source gelatin authentication is based on religious and cultural beliefs, food fraud prevention and health issues. Seven gelatin authentication methods that have been developed include: nucleic acid based, immunochemical, electrophoretic analysis, spectroscopic, mass-spectrometric, chromatographic-chemometric and chemisorption methods. These methods are time consuming, and require capital intensive equipment with huge running cost. Reliability of gelatin authentication methods is challenged mostly by transformation of gelatin during processing and close similarities among gelatin structures. This review concisely presents findings and challenges in this research area and suggests needs for more researches on development of rapid authentication method and process-transformed gelatins.
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Affiliation(s)
- Ademola Monsur Hameed
- International Institute for Halal Research and Training, International Islamic University Malaysia, 53100 Gombak, Kuala Lumpur
| | - Tawakalit Asiyanbi-H
- Plant Science Department, North Dakota State University, Fargo, North Dakota, United States
| | - Munirat Idris
- International Institute for Halal Research and Training, International Islamic University Malaysia, 53100 Gombak, Kuala Lumpur
| | - Nurrulhidayah Fadzillah
- International Institute for Halal Research and Training, International Islamic University Malaysia, 53100 Gombak, Kuala Lumpur
| | - Mohamed Elwathig S Mirghani
- International Institute for Halal Research and Training, International Islamic University Malaysia, 53100 Gombak, Kuala Lumpur
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131
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Gu M, Buckley M. Semi-supervised machine learning for automated species identification by collagen peptide mass fingerprinting. BMC Bioinformatics 2018; 19:241. [PMID: 29940843 PMCID: PMC6019507 DOI: 10.1186/s12859-018-2221-3] [Citation(s) in RCA: 29] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/21/2017] [Accepted: 05/28/2018] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND Biomolecular methods for species identification are increasingly being utilised in the study of changing environments, both at the microscopic and macroscopic levels. High-throughput peptide mass fingerprinting has been largely applied to bacterial identification, but increasingly used to identify archaeological and palaeontological skeletal material to yield information on past environments and human-animal interaction. However, as applications move away from predominantly domesticate and the more abundant wild fauna to a much wider range of less common taxa that do not yet have genetically-derived sequence information, robust methods of species identification and biomarker selection need to be determined. RESULTS Here we developed a supervised machine learning algorithm for classifying the species of ancient remains based on collagen fingerprinting. The aim was to minimise requirements on prior knowledge of known species while yielding satisfactory sensitivity and specificity. The algorithm uses iterations of a modified random forest classifier with a similarity scoring system to expand its identified samples. We tested it on a set of 6805 spectra and found that a high level of accuracy can be achieved with a training set of five identified specimens per taxon. CONCLUSIONS This method consistently achieves higher accuracy than two-dimensional principal component analysis and similar accuracy with hierarchical clustering using optimised parameters, which greatly reduces requirements for human input. Within the vertebrata, we demonstrate that this method was able to achieve the taxonomic resolution of family or sub-family level whereas the genus- or species-level identification may require manual interpretation or further experiments. In addition, it also identifies additional species biomarkers than those previously published.
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Affiliation(s)
- Muxin Gu
- Michael Smith Building, Faculty of Biology, Medicine and Health, The University of Manchester, Manchester, M13 9PT, UK
| | - Michael Buckley
- Manchester Institute of Biotechnology, School of Earth and Environmental Sciences, The University of Manchester, 131 Princess Street, Manchester, M1 7DN, UK.
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132
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Brandt LØ, Haase K, Collins MJ. Species identification using ZooMS, with reference to the exploitation of animal resources in the medieval town of Odense. ACTA ACUST UNITED AC 2018. [DOI: 10.1080/21662282.2018.1468154] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/16/2022]
Affiliation(s)
| | - Kirstine Haase
- Centre for Urban Network Evolutions, Aarhus University, Aarhus, Denmark
- Department of Cultural Heritage, Odense City Museums, Odense, Denmark
| | - Matthew J. Collins
- EvoGenomics, Natural History Museum of Denmark, University of Copenhagen, Copenhagen, Denmark
- BioArCh, Department of Archaeology, University of York, York, UK
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133
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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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134
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Cappellini E, Prohaska A, Racimo F, Welker F, Pedersen MW, Allentoft ME, de Barros Damgaard P, Gutenbrunner P, Dunne J, Hammann S, Roffet-Salque M, Ilardo M, Moreno-Mayar JV, Wang Y, Sikora M, Vinner L, Cox J, Evershed RP, Willerslev E. Ancient Biomolecules and Evolutionary Inference. Annu Rev Biochem 2018; 87:1029-1060. [PMID: 29709200 DOI: 10.1146/annurev-biochem-062917-012002] [Citation(s) in RCA: 47] [Impact Index Per Article: 7.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Abstract
Over the past three decades, studies of ancient biomolecules-particularly ancient DNA, proteins, and lipids-have revolutionized our understanding of evolutionary history. Though initially fraught with many challenges, today the field stands on firm foundations. Researchers now successfully retrieve nucleotide and amino acid sequences, as well as lipid signatures, from progressively older samples, originating from geographic areas and depositional environments that, until recently, were regarded as hostile to long-term preservation of biomolecules. Sampling frequencies and the spatial and temporal scope of studies have also increased markedly, and with them the size and quality of the data sets generated. This progress has been made possible by continuous technical innovations in analytical methods, enhanced criteria for the selection of ancient samples, integrated experimental methods, and advanced computational approaches. Here, we discuss the history and current state of ancient biomolecule research, its applications to evolutionary inference, and future directions for this young and exciting field.
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Affiliation(s)
- Enrico Cappellini
- Centre for GeoGenetics, Natural History Museum of Denmark, University of Copenhagen, 1350 Copenhagen, Denmark; ,
| | - Ana Prohaska
- Department of Zoology, University of Cambridge, Cambridge CB2 3EJ, United Kingdom
| | - Fernando Racimo
- Centre for GeoGenetics, Natural History Museum of Denmark, University of Copenhagen, 1350 Copenhagen, Denmark; ,
| | - Frido Welker
- Natural History Museum of Denmark, University of Copenhagen, 1350 Copenhagen, Denmark.,Department of Human Evolution, Max Planck Institute for Evolutionary Anthropology, 04103 Leipzig, Germany
| | | | - Morten E Allentoft
- Centre for GeoGenetics, Natural History Museum of Denmark, University of Copenhagen, 1350 Copenhagen, Denmark; ,
| | - Peter de Barros Damgaard
- Centre for GeoGenetics, Natural History Museum of Denmark, University of Copenhagen, 1350 Copenhagen, Denmark; ,
| | - Petra Gutenbrunner
- Computational Systems Biochemistry, Max Planck Institute of Biochemistry, 82152 Martinsried, Germany
| | - Julie Dunne
- Organic Geochemistry Unit, School of Chemistry, University of Bristol, Bristol BS8 1TS, United Kingdom;
| | - Simon Hammann
- Organic Geochemistry Unit, School of Chemistry, University of Bristol, Bristol BS8 1TS, United Kingdom; .,Department of Anthropology and Archaeology, University of Bristol, Bristol BS8 1UU, United Kingdom
| | - Mélanie Roffet-Salque
- Organic Geochemistry Unit, School of Chemistry, University of Bristol, Bristol BS8 1TS, United Kingdom;
| | - Melissa Ilardo
- Centre for GeoGenetics, Natural History Museum of Denmark, University of Copenhagen, 1350 Copenhagen, Denmark; ,
| | - J Víctor Moreno-Mayar
- Centre for GeoGenetics, Natural History Museum of Denmark, University of Copenhagen, 1350 Copenhagen, Denmark; ,
| | - Yucheng Wang
- Centre for GeoGenetics, Natural History Museum of Denmark, University of Copenhagen, 1350 Copenhagen, Denmark; ,
| | - Martin Sikora
- Centre for GeoGenetics, Natural History Museum of Denmark, University of Copenhagen, 1350 Copenhagen, Denmark; ,
| | - Lasse Vinner
- Centre for GeoGenetics, Natural History Museum of Denmark, University of Copenhagen, 1350 Copenhagen, Denmark; ,
| | - Jürgen Cox
- Computational Systems Biochemistry, Max Planck Institute of Biochemistry, 82152 Martinsried, Germany
| | - Richard P Evershed
- Organic Geochemistry Unit, School of Chemistry, University of Bristol, Bristol BS8 1TS, United Kingdom;
| | - Eske Willerslev
- Centre for GeoGenetics, Natural History Museum of Denmark, University of Copenhagen, 1350 Copenhagen, Denmark; , .,Department of Zoology, University of Cambridge, Cambridge CB2 3EJ, United Kingdom.,Wellcome Trust Sanger Institute, Hinxton, Cambridgeshire CB10 1SA, United Kingdom
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135
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Hendy J, Welker F, Demarchi B, Speller C, Warinner C, Collins MJ. A guide to ancient protein studies. Nat Ecol Evol 2018; 2:791-799. [PMID: 29581591 DOI: 10.1038/s41559-018-0510-x] [Citation(s) in RCA: 106] [Impact Index Per Article: 17.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/29/2017] [Accepted: 02/19/2018] [Indexed: 12/24/2022]
Abstract
Palaeoproteomics is an emerging neologism used to describe the application of mass spectrometry-based approaches to the study of ancient proteomes. As with palaeogenomics (the study of ancient DNA), it intersects evolutionary biology, archaeology and anthropology, with applications ranging from the phylogenetic reconstruction of extinct species to the investigation of past human diets and ancient diseases. However, there is no explicit consensus at present regarding standards for data reporting, data validation measures or the use of suitable contamination controls in ancient protein studies. Additionally, in contrast to the ancient DNA community, no consolidated guidelines have been proposed by which researchers, reviewers and editors can evaluate palaeoproteomics data, in part due to the novelty of the field. Here we present a series of precautions and standards for ancient protein research that can be implemented at each stage of analysis, from sample selection to data interpretation. These guidelines are not intended to impose a narrow or rigid list of authentication criteria, but rather to support good practices in the field and to ensure the generation of robust, reproducible results. As the field grows and methodologies change, so too will best practices. It is therefore essential that researchers continue to provide necessary details on how data were generated and authenticated so that the results can be independently and effectively evaluated. We hope that these proposed standards of practice will help to provide a firm foundation for the establishment of palaeoproteomics as a viable and powerful tool for archaeologists, anthropologists and evolutionary biologists.
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Affiliation(s)
- Jessica Hendy
- Department of Archaeology, Max Planck Institute for the Science of Human History, Jena, Germany.
| | - Frido Welker
- Department of Human Evolution, Max Planck Institute for Evolutionary Anthropology, Leipzig, Germany. .,Natural History Museum of Denmark, University of Copenhagen, Copenhagen, Denmark.
| | - Beatrice Demarchi
- Department of Life Science and Systems Biology, University of Turin, Turin, Italy.,BioArCh, Department of Archaeology, University of York, York, UK
| | - Camilla Speller
- BioArCh, Department of Archaeology, University of York, York, UK
| | - Christina Warinner
- Department of Archaeogenetics, Max Planck Institute for the Science of Human History, Jena, Germany.,Department of Anthropology, University of Oklahoma, Norman, OK, USA.,Institute for Evolutionary Medicine, University of Zürich, Zürich, Switzerland
| | - Matthew J Collins
- Natural History Museum of Denmark, University of Copenhagen, Copenhagen, Denmark.,BioArCh, Department of Archaeology, University of York, York, UK
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136
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Steinhilber AE, Schmidt FF, Naboulsi W, Planatscher H, Niedzwiecka A, Zagon J, Braeuning A, Lampen A, Joos TO, Poetz O. Mass Spectrometry-Based Immunoassay for the Quantification of Banned Ruminant Processed Animal Proteins in Vegetal Feeds. Anal Chem 2018; 90:4135-4143. [PMID: 29470057 DOI: 10.1021/acs.analchem.8b00120] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/02/2023]
Abstract
The ban of processed animal proteins (PAPs) in feed for farmed animals introduced in 2001 was one of the main EU measures to control the bovine spongiform encephalopathy (BSE) crisis. Currently, microscopy and polymerase chain reaction (PCR) are the official methods for the detection of illegal PAPs in feed. However, the progressive release of the feed ban, recently with the legalization of nonruminant PAPs for the use in aquaculture, requires the development of alternative methods to determine the species origin and the source (legal or not). Additionally, discussions about the need for quantitative tests came up, particularly if the zero-tolerance-concept is replaced by introducing PAP thresholds. To address this issue, we developed and partially validated a multiplex mass spectrometry-based immunoassay to quantify ruminant specific peptides in vegetal cattle feed. The workflow comprises a new sample preparation procedure based on a tryptic digestion of PAPs in suspension, a subsequent immunoaffinity enrichment of the released peptides, and a LC-MS/MS-based analysis for peptide quantification using isotope labeled standard peptides. For the very first time, a mass spectrometry-based method is capable of detecting and quantifying illegal PAPs in animal feed over a concentration range of 4 orders of magnitude with a detection limit in the range of 0.1% to 1% (w/w).
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Affiliation(s)
- Andreas E Steinhilber
- NMI Natural and Medical Sciences Institute at the University of Tuebingen , 72770 Reutlingen , Germany
| | - Felix F Schmidt
- NMI Natural and Medical Sciences Institute at the University of Tuebingen , 72770 Reutlingen , Germany
| | | | | | | | - Jutta Zagon
- Federal Institute for Risk Assessment , 10589 Berlin , Germany
| | | | - Alfonso Lampen
- Federal Institute for Risk Assessment , 10589 Berlin , Germany
| | - Thomas O Joos
- NMI Natural and Medical Sciences Institute at the University of Tuebingen , 72770 Reutlingen , Germany
| | - Oliver Poetz
- NMI Natural and Medical Sciences Institute at the University of Tuebingen , 72770 Reutlingen , Germany.,SIGNATOPE GmbH , 72770 Reutlingen , Germany
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137
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Cleland TP, Schroeter ER. A Comparison of Common Mass Spectrometry Approaches for Paleoproteomics. J Proteome Res 2018; 17:936-945. [PMID: 29384680 DOI: 10.1021/acs.jproteome.7b00703] [Citation(s) in RCA: 41] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
The last two decades have seen a broad diversity of methods used to identify and/or characterize proteins in the archeological and paleontological record. Of these, mass spectrometry has opened an unprecedented window into the proteomes of the past, providing protein sequence data from long extinct animals as well as historical and prehistorical artifacts. Thus, application of mass spectrometry to fossil remains has become an attractive source for ancient molecular sequences with which to conduct evolutionary studies, particularly in specimens older than the proposed limit of amplifiable DNA detection. However, "mass spectrometry" covers a range of mass-based proteomic approaches, each of which utilize different technology and physical principles to generate unique types of data, with their own strengths and challenges. Here, we discuss a variety of mass spectrometry techniques that have or may be used to detect and characterize archeological and paleontological proteins, with a particular focus on MALDI-MS, LC-MS/MS, TOF-SIMS, and MSi. The main differences in their functionality, the types of data they produce, and the potential effects of diagenesis on their results are considered.
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Affiliation(s)
- Timothy P Cleland
- Museum Conservation Institute, Smithsonian Institution , Suitland, Maryland 20746, United States
| | - Elena R Schroeter
- Department of Biological Sciences, North Carolina State University , Raleigh, North Carolina 27695, United States
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138
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Szpak P, Buckley M, Darwent CM, Richards MP. Long-term ecological changes in marine mammals driven by recent warming in northwestern Alaska. GLOBAL CHANGE BIOLOGY 2018; 24:490-503. [PMID: 28850766 DOI: 10.1111/gcb.13880] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/23/2017] [Revised: 08/07/2017] [Accepted: 08/12/2017] [Indexed: 06/07/2023]
Abstract
Carbon and nitrogen isotopes analyses were performed on marine mammal bone collagen from three archaeological sites (ad 1170-1813) on Cape Espenberg (Kotzebue Sound, northwestern Alaska) as well as modern animals harvested from the same area to examine long-term trends in foraging ecology and sea ice productivity. We observed significant and dramatic changes in ringed seal stable isotope values between the early 19th and early 21st centuries, likely due to changing sea ice productivity and reduced delivery of organic matter to the benthos driven by recent warming in the Arctic. These data highlight the importance of the archaeological record for providing a long-term perspective on environmental variation and interpreting recent changes driven by anthropogenic processes.
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Affiliation(s)
- Paul Szpak
- Department of Anthropology, Trent University, Peterborough, ON, Canada
| | - Michael Buckley
- School of Earth and Environmental Sciences, Manchester Institute of Biotechnology, The University of Manchester, Manchester, UK
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139
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Central European Woolly Mammoth Population Dynamics: Insights from Late Pleistocene Mitochondrial Genomes. Sci Rep 2017; 7:17714. [PMID: 29255197 PMCID: PMC5735091 DOI: 10.1038/s41598-017-17723-1] [Citation(s) in RCA: 29] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/06/2017] [Accepted: 11/21/2017] [Indexed: 01/13/2023] Open
Abstract
The population dynamics of the Pleistocene woolly mammoth (Mammuthus primigenius) has been the subject of intensive palaeogenetic research. Although a large number of mitochondrial genomes across Eurasia have been reconstructed, the available data remains geographically sparse and mostly focused on eastern Eurasia. Thus, population dynamics in other regions have not been extensively investigated. Here, we use a multi-method approach utilising proteomic, stable isotope and genetic techniques to identify and generate twenty woolly mammoth mitochondrial genomes, and associated dietary stable isotopic data, from highly fragmentary Late Pleistocene material from central Europe. We begin to address region-specific questions regarding central European woolly mammoth populations, highlighting parallels with a previous replacement event in eastern Eurasia ten thousand years earlier. A high number of shared derived mutations between woolly mammoth mitochondrial clades are identified, questioning previous phylogenetic analysis and thus emphasizing the need for nuclear DNA studies to explicate the increasingly complex genetic history of the woolly mammoth.
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140
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141
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Devièse T, Karavanić I, Comeskey D, Kubiak C, Korlević P, Hajdinjak M, Radović S, Procopio N, Buckley M, Pääbo S, Higham T. Direct dating of Neanderthal remains from the site of Vindija Cave and implications for the Middle to Upper Paleolithic transition. Proc Natl Acad Sci U S A 2017; 114:10606-10611. [PMID: 28874524 PMCID: PMC5635904 DOI: 10.1073/pnas.1709235114] [Citation(s) in RCA: 43] [Impact Index Per Article: 6.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/06/2023] Open
Abstract
Previous dating of the Vi-207 and Vi-208 Neanderthal remains from Vindija Cave (Croatia) led to the suggestion that Neanderthals survived there as recently as 28,000-29,000 B.P. Subsequent dating yielded older dates, interpreted as ages of at least ∼32,500 B.P. We have redated these same specimens using an approach based on the extraction of the amino acid hydroxyproline, using preparative high-performance liquid chromatography (Prep-HPLC). This method is more efficient in eliminating modern contamination in the bone collagen. The revised dates are older than 40,000 B.P., suggesting the Vindija Neanderthals did not live more recently than others across Europe, and probably predate the arrival of anatomically modern humans in Eastern Europe. We applied zooarchaeology by mass spectrometry (ZooMS) to find additional hominin remains. We identified one bone that is Neanderthal, based on its mitochondrial DNA, and dated it directly to 46,200 ± 1,500 B.P. We also attempted to date six early Upper Paleolithic bone points from stratigraphic units G1, Fd/d+G1 and Fd/d, Fd. One bone artifact gave a date of 29,500 ± 400 B.P., while the remainder yielded no collagen. We additionally dated animal bone samples from units G1 and G1-G3 These dates suggest a co-occurrence of early Upper Paleolithic osseous artifacts, particularly split-based points, alongside the remains of Neanderthals is a result of postdepositional mixing, rather than an association between the two groups, although more work is required to show this definitively.
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Affiliation(s)
- Thibaut Devièse
- Oxford Radiocarbon Accelerator Unit, Research Laboratory for Archaeology and the History of Art, University of Oxford, Oxford OX1 3QY, United Kingdom;
| | - Ivor Karavanić
- Department of Archaeology, Faculty of Humanities and Social Sciences, University of Zagreb, HR-10000 Zagreb, Croatia
- Department of Anthropology, University of Wyoming, Laramie, WY 82071
| | - Daniel Comeskey
- Oxford Radiocarbon Accelerator Unit, Research Laboratory for Archaeology and the History of Art, University of Oxford, Oxford OX1 3QY, United Kingdom
| | - Cara Kubiak
- Oxford Radiocarbon Accelerator Unit, Research Laboratory for Archaeology and the History of Art, University of Oxford, Oxford OX1 3QY, United Kingdom
| | - Petra Korlević
- Department of Evolutionary Genetics, Max-Planck-Institute for Evolutionary Anthropology, D-04103 Leipzig, Germany
| | - Mateja Hajdinjak
- Department of Evolutionary Genetics, Max-Planck-Institute for Evolutionary Anthropology, D-04103 Leipzig, Germany
| | - Siniša Radović
- Institute for Quaternary Palaeontology and Geology, Croatian Academy of Sciences and Arts, HR-10000 Zagreb, Croatia
| | - Noemi Procopio
- Manchester Institute of Biotechnology, University of Manchester, Manchester M1 7DN, United Kingdom
| | - Michael Buckley
- Manchester Institute of Biotechnology, University of Manchester, Manchester M1 7DN, United Kingdom
| | - Svante Pääbo
- Department of Evolutionary Genetics, Max-Planck-Institute for Evolutionary Anthropology, D-04103 Leipzig, Germany
| | - Tom Higham
- Oxford Radiocarbon Accelerator Unit, Research Laboratory for Archaeology and the History of Art, University of Oxford, Oxford OX1 3QY, United Kingdom
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Prendergast ME, Buckley M, Crowther A, Frantz L, Eager H, Lebrasseur O, Hutterer R, Hulme-Beaman A, Van Neer W, Douka K, Veall MA, Quintana Morales EM, Schuenemann VJ, Reiter E, Allen R, Dimopoulos EA, Helm RM, Shipton C, Mwebi O, Denys C, Horton M, Wynne-Jones S, Fleisher J, Radimilahy C, Wright H, Searle JB, Krause J, Larson G, Boivin NL. Reconstructing Asian faunal introductions to eastern Africa from multi-proxy biomolecular and archaeological datasets. PLoS One 2017; 12:e0182565. [PMID: 28817590 PMCID: PMC5560628 DOI: 10.1371/journal.pone.0182565] [Citation(s) in RCA: 24] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/25/2017] [Accepted: 07/20/2017] [Indexed: 02/02/2023] Open
Abstract
Human-mediated biological exchange has had global social and ecological impacts. In sub-Saharan Africa, several domestic and commensal animals were introduced from Asia in the pre-modern period; however, the timing and nature of these introductions remain contentious. One model supports introduction to the eastern African coast after the mid-first millennium CE, while another posits introduction dating back to 3000 BCE. These distinct scenarios have implications for understanding the emergence of long-distance maritime connectivity, and the ecological and economic impacts of introduced species. Resolution of this longstanding debate requires new efforts, given the lack of well-dated fauna from high-precision excavations, and ambiguous osteomorphological identifications. We analysed faunal remains from 22 eastern African sites spanning a wide geographic and chronological range, and applied biomolecular techniques to confirm identifications of two Asian taxa: domestic chicken (Gallus gallus) and black rat (Rattus rattus). Our approach included ancient DNA (aDNA) analysis aided by BLAST-based bioinformatics, Zooarchaeology by Mass Spectrometry (ZooMS) collagen fingerprinting, and direct AMS (accelerator mass spectrometry) radiocarbon dating. Our results support a late, mid-first millennium CE introduction of these species. We discuss the implications of our findings for models of biological exchange, and emphasize the applicability of our approach to tropical areas with poor bone preservation.
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Affiliation(s)
- Mary E. Prendergast
- Radcliffe Institute for Advanced Study, Harvard University, Cambridge, MA, United States of America
- * E-mail:
| | - Michael Buckley
- Faculty of Life Sciences, University of Manchester, Manchester, United Kingdom
| | - Alison Crowther
- School of Social Science, The University of Queensland, Brisbane Queensland, Australia
| | - Laurent Frantz
- Palaeogenomics & Bio-Archaeology Research Network, Oxford University, Oxford, United Kingdom
- School of Biological and Chemical Sciences, Queen Mary University of London, Mile End Road, London, United Kingdom
| | - Heidi Eager
- Dept. Ecology and Evolutionary Biology, Cornell University, Ithaca, NY, United States of America
- Research Laboratory for Archaeology and the History of Art, Oxford University, Oxford, United Kingdom
| | - Ophélie Lebrasseur
- Palaeogenomics & Bio-Archaeology Research Network, Oxford University, Oxford, United Kingdom
| | - Rainer Hutterer
- Dept. Vertebrates, Zoologisches Forschungsmuseum Alexander Koenig, Bonn, Germany
| | | | - Wim Van Neer
- Royal Belgian Institute of Natural Sciences, Brussels, Belgium
- Dept. Biology, University of Leuven, Leuven, Belgium
| | - Katerina Douka
- Research Laboratory for Archaeology and the History of Art, Oxford University, Oxford, United Kingdom
| | - Margaret-Ashley Veall
- Research Laboratory for Archaeology and the History of Art, Oxford University, Oxford, United Kingdom
| | | | | | - Ella Reiter
- Institute for Archaeological Sciences, University of Tübingen, Tübingen, Germany
| | - Richard Allen
- Palaeogenomics & Bio-Archaeology Research Network, Oxford University, Oxford, United Kingdom
- Research Laboratory for Archaeology and the History of Art, Oxford University, Oxford, United Kingdom
| | - Evangelos A. Dimopoulos
- Palaeogenomics & Bio-Archaeology Research Network, Oxford University, Oxford, United Kingdom
| | | | - Ceri Shipton
- McDonald Institute for Archaeological Research, Cambridge, United Kingdom
- British Institute in Eastern Africa, Nairobi, Kenya
| | - Ogeto Mwebi
- Dept. Zoology, Osteology Section, National Museums of Kenya, Nairobi, Kenya
| | - Christiane Denys
- Dept. Systématique & Evolution, Muséum National d’Histoire Naturelle, Paris, France
| | - Mark Horton
- Dept. Archaeology and Anthropology, University of Bristol, Bristol, United Kingdom
| | | | - Jeffrey Fleisher
- Dept. Anthropology, Rice University, Houston, United States of America
| | - Chantal Radimilahy
- Musée d’Art et d’Archéologie, Université d’Antananarivo, Antananarivo, Madagascar
| | - Henry Wright
- Museum of Anthropology, University of Michigan, Ann Arbor, United States of America
- Santa Fe Institute, Santa Fe NM, United States of America
| | - Jeremy B. Searle
- Dept. Ecology and Evolutionary Biology, Cornell University, Ithaca, NY, United States of America
| | - Johannes Krause
- Institute for Archaeological Sciences, University of Tübingen, Tübingen, Germany
- Max Planck Institute for the Science of Human History, Jena, Germany
| | - Greger Larson
- Palaeogenomics & Bio-Archaeology Research Network, Oxford University, Oxford, United Kingdom
| | - Nicole L. Boivin
- Max Planck Institute for the Science of Human History, Jena, Germany
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Deeply divergent archaic mitochondrial genome provides lower time boundary for African gene flow into Neanderthals. Nat Commun 2017; 8:16046. [PMID: 28675384 PMCID: PMC5500885 DOI: 10.1038/ncomms16046] [Citation(s) in RCA: 116] [Impact Index Per Article: 16.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/28/2016] [Accepted: 05/23/2017] [Indexed: 12/19/2022] Open
Abstract
Ancient DNA is revealing new insights into the genetic relationship between Pleistocene hominins and modern humans. Nuclear DNA indicated Neanderthals as a sister group of Denisovans after diverging from modern humans. However, the closer affinity of the Neanderthal mitochondrial DNA (mtDNA) to modern humans than Denisovans has recently been suggested as the result of gene flow from an African source into Neanderthals before 100,000 years ago. Here we report the complete mtDNA of an archaic femur from the Hohlenstein–Stadel (HST) cave in southwestern Germany. HST carries the deepest divergent mtDNA lineage that splits from other Neanderthals ∼270,000 years ago, providing a lower boundary for the time of the putative mtDNA introgression event. We demonstrate that a complete Neanderthal mtDNA replacement is feasible over this time interval even with minimal hominin introgression. The highly divergent HST branch is indicative of greater mtDNA diversity during the Middle Pleistocene than in later periods. Ancient DNA keeps expanding our understanding of complex genetic relationships between Pleistocene hominins. Here, Posth and colleagues analyse the mitochondrial genome of an archaic human that diverged from other Neanderthals ∼270,000 years ago, providing the minimum age for an African introgression into Neanderthals.
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Welker F, Smith GM, Hutson JM, Kindler L, Garcia-Moreno A, Villaluenga A, Turner E, Gaudzinski-Windheuser S. Middle Pleistocene protein sequences from the rhinoceros genus Stephanorhinus and the phylogeny of extant and extinct Middle/Late Pleistocene Rhinocerotidae. PeerJ 2017; 5:e3033. [PMID: 28316883 PMCID: PMC5354071 DOI: 10.7717/peerj.3033] [Citation(s) in RCA: 40] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/09/2016] [Accepted: 01/26/2017] [Indexed: 11/20/2022] Open
Abstract
Background Ancient protein sequences are increasingly used to elucidate the phylogenetic relationships between extinct and extant mammalian taxa. Here, we apply these recent developments to Middle Pleistocene bone specimens of the rhinoceros genus Stephanorhinus. No biomolecular sequence data is currently available for this genus, leaving phylogenetic hypotheses on its evolutionary relationships to extant and extinct rhinoceroses untested. Furthermore, recent phylogenies based on Rhinocerotidae (partial or complete) mitochondrial DNA sequences differ in the placement of the Sumatran rhinoceros (Dicerorhinus sumatrensis). Therefore, studies utilising ancient protein sequences from Middle Pleistocene contexts have the potential to provide further insights into the phylogenetic relationships between extant and extinct species, including Stephanorhinus and Dicerorhinus. Methods ZooMS screening (zooarchaeology by mass spectrometry) was performed on several Late and Middle Pleistocene specimens from the genus Stephanorhinus, subsequently followed by liquid chromatography-tandem mass spectrometry (LC-MS/MS) to obtain ancient protein sequences from a Middle Pleistocene Stephanorhinus specimen. We performed parallel analysis on a Late Pleistocene woolly rhinoceros specimen and extant species of rhinoceroses, resulting in the availability of protein sequence data for five extant species and two extinct genera. Phylogenetic analysis additionally included all extant Perissodactyla genera (Equus, Tapirus), and was conducted using Bayesian (MrBayes) and maximum-likelihood (RAxML) methods. Results Various ancient proteins were identified in both the Middle and Late Pleistocene rhinoceros samples. Protein degradation and proteome complexity are consistent with an endogenous origin of the identified proteins. Phylogenetic analysis of informative proteins resolved the Perissodactyla phylogeny in agreement with previous studies in regards to the placement of the families Equidae, Tapiridae, and Rhinocerotidae. Stephanorhinus is shown to be most closely related to the genera Coelodonta and Dicerorhinus. The protein sequence data further places the Sumatran rhino in a clade together with the genus Rhinoceros, opposed to forming a clade with the black and white rhinoceros species. Discussion The first biomolecular dataset available for Stephanorhinus places this genus together with the extinct genus Coelodonta and the extant genus Dicerorhinus. This is in agreement with morphological studies, although we are unable to resolve the order of divergence between these genera based on the protein sequences available. Our data supports the placement of the genus Dicerorhinus in a clade together with extant Rhinoceros species. Finally, the availability of protein sequence data for both extinct European rhinoceros genera allows future investigations into their geographic distribution and extinction chronologies.
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Affiliation(s)
- Frido Welker
- Department of Human Evolution, Max Planck Institute for Evolutionary Anthropology, Leipzig, Germany; BioArCh, Department of Archaeology, University of York, York, UK
| | - Geoff M Smith
- MONREPOS Archaeological Research Centre and Museum for Human Behavioural Evolution, RGZM, Neuwied, Germany; Department of Anthropology, University of California Davis, Davis, CA, USA
| | - Jarod M Hutson
- MONREPOS Archaeological Research Centre and Museum for Human Behavioural Evolution, RGZM, Neuwied, Germany; Current affiliation: Department of Paleobiology, Smithsonian Institution, Washington, D.C., USA
| | - Lutz Kindler
- MONREPOS Archaeological Research Centre and Museum for Human Behavioural Evolution, RGZM, Neuwied, Germany; Department of Pre- and Protohistoric Archaeology, Institute of Ancient Studies, Johannes-Gutenberg Universität Mainz, Mainz, Germany
| | - Alejandro Garcia-Moreno
- MONREPOS Archaeological Research Centre and Museum for Human Behavioural Evolution, RGZM , Neuwied , Germany
| | - Aritza Villaluenga
- MONREPOS Archaeological Research Centre and Museum for Human Behavioural Evolution, RGZM , Neuwied , Germany
| | - Elaine Turner
- MONREPOS Archaeological Research Centre and Museum for Human Behavioural Evolution, RGZM , Neuwied , Germany
| | - Sabine Gaudzinski-Windheuser
- MONREPOS Archaeological Research Centre and Museum for Human Behavioural Evolution, RGZM, Neuwied, Germany; Department of Pre- and Protohistoric Archaeology, Institute of Ancient Studies, Johannes-Gutenberg Universität Mainz, Mainz, Germany
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146
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Schroeter ER, DeHart CJ, Cleland TP, Zheng W, Thomas PM, Kelleher NL, Bern M, Schweitzer MH. Expansion for the Brachylophosaurus canadensis Collagen I Sequence and Additional Evidence of the Preservation of Cretaceous Protein. J Proteome Res 2017; 16:920-932. [PMID: 28111950 PMCID: PMC5401637 DOI: 10.1021/acs.jproteome.6b00873] [Citation(s) in RCA: 61] [Impact Index Per Article: 8.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/10/2023]
Abstract
Sequence data from biomolecules such as DNA and proteins, which provide critical information for evolutionary studies, have been assumed to be forever outside the reach of dinosaur paleontology. Proteins, which are predicted to have greater longevity than DNA, have been recovered from two nonavian dinosaurs, but these results remain controversial. For proteomic data derived from extinct Mesozoic organisms to reach their greatest potential for investigating questions of phylogeny and paleobiology, it must be shown that peptide sequences can be reliably and reproducibly obtained from fossils and that fragmentary sequences for ancient proteins can be increasingly expanded. To test the hypothesis that peptides can be repeatedly detected and validated from fossil tissues many millions of years old, we applied updated extraction methodology, high-resolution mass spectrometry, and bioinformatics analyses on a Brachylophosaurus canadensis specimen (MOR 2598) from which collagen I peptides were recovered in 2009. We recovered eight peptide sequences of collagen I: two identical to peptides recovered in 2009 and six new peptides. Phylogenetic analyses place the recovered sequences within basal archosauria. When only the new sequences are considered, B. canadensis is grouped more closely to crocodylians, but when all sequences (current and those reported in 2009) are analyzed, B. canadensis is placed more closely to basal birds. The data robustly support the hypothesis of an endogenous origin for these peptides, confirm the idea that peptides can survive in specimens tens of millions of years old, and bolster the validity of the 2009 study. Furthermore, the new data expand the coverage of B. canadensis collagen I (a 33.6% increase in collagen I alpha 1 and 116.7% in alpha 2). Finally, this study demonstrates the importance of reexamining previously studied specimens with updated methods and instrumentation, as we obtained roughly the same amount of sequence data as the previous study with substantially less sample material. Data are available via ProteomeXchange with identifier PXD005087.
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Affiliation(s)
- Elena R. Schroeter
- Department of Biological Sciences, North Carolina State University, Raleigh, North Carolina 27695, United States
| | - Caroline J. DeHart
- National Resource for Translational and Developmental Proteomics, Northwestern University, Evanston, Illinois 60208, United States
| | - Timothy P. Cleland
- Department of Chemistry, University of Texas-Austin, Austin, Texas 78712, United States
| | - Wenxia Zheng
- Department of Biological Sciences, North Carolina State University, Raleigh, North Carolina 27695, United States
| | - Paul M. Thomas
- National Resource for Translational and Developmental Proteomics, Northwestern University, Evanston, Illinois 60208, United States
| | - Neil L. Kelleher
- National Resource for Translational and Developmental Proteomics, Northwestern University, Evanston, Illinois 60208, United States
| | - Marshall Bern
- Protein Metrics, San Carlos, California 94070, United States
| | - Mary H. Schweitzer
- Department of Biological Sciences, North Carolina State University, Raleigh, North Carolina 27695, United States
- North Carolina Museum of Natural Sciences, Raleigh, North Carolina 27601, United States
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147
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Zhai Y, Zhu Z, Zhu Y, Qian D, Liu R, Peng Y, Ding Y, Ouyang Z, Duan JA. Characterization of Collagen Peptides in Elaphuri Davidiani Cornu Aqueous Extract with Proliferative Activity on Osteoblasts Using Nano-Liquid Chromatography in Tandem with Orbitrap Mass Spectrometry. Molecules 2017; 22:molecules22010166. [PMID: 28117676 PMCID: PMC6155669 DOI: 10.3390/molecules22010166] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/03/2016] [Revised: 12/26/2016] [Accepted: 01/12/2017] [Indexed: 11/16/2022] Open
Abstract
First documented in Shennong Bencao Jing (about 200 B.C.–200 A.D.), Elaphuri Davidiani Cornu (EDC) has been recorded for its effects in strengthening bones and balancing other aspects of overall health for approximately 2000 years. In the present study, our aim was to investigate which are the components of the active EDC fraction by a peptidomic strategy. We explored the extent to which EDC increases the proliferation of osteoblasts by measuring the elevations in osteonectin and type I collagen mRNA levels and characterized it using nano-flow liquid chromatography in tandem with orbitrap mass spectrometry. In total, 272 peptide sequences from collagens were determined. “Hot regions” in parent proteins determined by peptide heat maps which indicated that amino acid sequences in the regions might undergo proteolysis easily and generate peptides. Among the identified peptides, 90.2% were hydrophilic, and the molecular weight of 97.1% of identified peptides was lower than 2000 Da. According to these results, EDC collagen-derived peptides were easily analyzed and identified. Moreover, this methodology is feasible to characterize the active peptides matrices originated from collagen hydrolysates or some other animal horn- derived TCMs.
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Affiliation(s)
- Yanjuan Zhai
- Jiangsu Collaborative Innovation Center of Chinese Medicinal Resources Industrialization, and National and Local Collaborative Engineering Center of Chinese Medicinal Resources Industrialization and Formulae Innovative Medicine, Nanjing University of Chinese Medicine, Nanjing 210023, China.
| | - Zhenhua Zhu
- Jiangsu Collaborative Innovation Center of Chinese Medicinal Resources Industrialization, and National and Local Collaborative Engineering Center of Chinese Medicinal Resources Industrialization and Formulae Innovative Medicine, Nanjing University of Chinese Medicine, Nanjing 210023, China.
| | - Yue Zhu
- Jiangsu Collaborative Innovation Center of Chinese Medicinal Resources Industrialization, and National and Local Collaborative Engineering Center of Chinese Medicinal Resources Industrialization and Formulae Innovative Medicine, Nanjing University of Chinese Medicine, Nanjing 210023, China.
| | - Dawei Qian
- Jiangsu Collaborative Innovation Center of Chinese Medicinal Resources Industrialization, and National and Local Collaborative Engineering Center of Chinese Medicinal Resources Industrialization and Formulae Innovative Medicine, Nanjing University of Chinese Medicine, Nanjing 210023, China.
| | - Rui Liu
- Jiangsu Collaborative Innovation Center of Chinese Medicinal Resources Industrialization, and National and Local Collaborative Engineering Center of Chinese Medicinal Resources Industrialization and Formulae Innovative Medicine, Nanjing University of Chinese Medicine, Nanjing 210023, China.
| | - Yunru Peng
- Jiangsu Provincial Academy of Chinese Medicine, Nanjing 210028, China.
| | - Yuhua Ding
- Jiangsu Dafeng Milu National Nature Reserve, Dafeng 224136, China.
| | - Zhen Ouyang
- School of Food and Biological Engineering, Jiangsu University, Zhenjiang 212013, China.
| | - Jin-Ao Duan
- Jiangsu Collaborative Innovation Center of Chinese Medicinal Resources Industrialization, and National and Local Collaborative Engineering Center of Chinese Medicinal Resources Industrialization and Formulae Innovative Medicine, Nanjing University of Chinese Medicine, Nanjing 210023, China.
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148
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Affiliation(s)
- Noemi Procopio
- Manchester
Institute of Biotechnology, The University of Manchester, 131 Princess
Street, Manchester M1 7DN, U.K
| | - Michael Buckley
- Manchester
Institute of Biotechnology, The University of Manchester, 131 Princess
Street, Manchester M1 7DN, U.K
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149
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Schroeter ER, DeHart CJ, Schweitzer MH, Thomas PM, Kelleher NL. Bone protein "extractomics": comparing the efficiency of bone protein extractions of Gallus gallus in tandem mass spectrometry, with an eye towards paleoproteomics. PeerJ 2016; 4:e2603. [PMID: 27812413 PMCID: PMC5088622 DOI: 10.7717/peerj.2603] [Citation(s) in RCA: 32] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/21/2016] [Accepted: 09/20/2016] [Indexed: 11/22/2022] Open
Abstract
Proteomic studies of bone require specialized extraction protocols to demineralize and solubilize proteins from within the bone matrix. Although various protocols exist for bone protein recovery, little is known about how discrete steps in each protocol affect the subset of the bone proteome recovered by mass spectrometry (MS) analyses. Characterizing these different “extractomes” will provide critical data for development of novel and more efficient protein extraction methodologies for fossils. Here, we analyze 22 unique sub-extractions of chicken bone and directly compare individual extraction components for their total protein yield and diversity and coverage of bone proteins identified by MS. We extracted proteins using different combinations and ratios of demineralizing reagents, protein-solubilizing reagents, and post-extraction buffer removal methods, then evaluated tryptic digests from 20 µg aliquots of each fraction by tandem MS/MS on a 12T FT-ICR mass spectrometer. We compared total numbers of peptide spectral matches, peptides, and proteins identified from each fraction, the redundancy of protein identifications between discrete steps of extraction methods, and the sequence coverage obtained for select, abundant proteins. Although both alpha chains of collagen I (the most abundant protein in bone) were found in all fractions, other collagenous and non-collagenous proteins (e.g., apolipoprotein, osteonectin, hemoglobin) were differentially identified. We found that when a standardized amount of extracted proteins was analyzed, extraction steps that yielded the most protein (by weight) from bone were often not the ones that produced the greatest diversity of bone proteins, or the highest degree of protein coverage. Generally, the highest degrees of diversity and coverage were obtained from demineralization fractions, and the proteins found in the subsequent solubilization fractions were highly redundant with those in the previous fraction. Based on these data, we identify future directions and parameters to consider (e.g., proteins targeted, amount of sample required) when applying discrete parts of these protocols to fossils.
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Affiliation(s)
- Elena R Schroeter
- Department of Biological Sciences, North Carolina State University , Raleigh , NC , United States
| | - Caroline J DeHart
- Proteomics Center of Excellence and Departments of Chemistry, Molecular Biosciences, and the Feinberg School of Medicine, Northwestern University , Evanston , IL , United States
| | - Mary H Schweitzer
- Department of Biological Sciences, North Carolina State University , Raleigh , NC , United States
| | - Paul M Thomas
- Proteomics Center of Excellence and Departments of Chemistry, Molecular Biosciences, and the Feinberg School of Medicine, Northwestern University , Evanston , IL , United States
| | - Neil L Kelleher
- Proteomics Center of Excellence and Departments of Chemistry, Molecular Biosciences, and the Feinberg School of Medicine, Northwestern University , Evanston , IL , United States
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150
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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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