1
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Drumheller SK, Boyd CA, Barnes BMS, Householder ML. Biostratinomic alterations of an Edmontosaurus "mummy" reveal a pathway for soft tissue preservation without invoking "exceptional conditions". PLoS One 2022; 17:e0275240. [PMID: 36223345 PMCID: PMC9555629 DOI: 10.1371/journal.pone.0275240] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/06/2022] [Accepted: 09/12/2022] [Indexed: 11/05/2022] Open
Abstract
Removal or protection from biostratinomic agents of decomposition, such as predators and scavengers, is widely seen as a requirement for high-quality preservation of soft tissues in the fossil record. In this context, extremely rapid burial is an oft-cited mechanism for shielding remains from degradation, but not all fossils fit nicely into this paradigm. Dinosaurian mummies in particular seemingly require two mutually exclusive taphonomic processes to preserve under that framework: desiccation and rapid burial. Here we present a recently prepared Edmontosaurus mummy that reveals an alternate fossilization pathway for resistant soft tissues (e.g., skin and nails). While the skin on this specimen is well-preserved in three dimensions and contains biomarkers, it is deflated and marked by the first documented examples of injuries consistent with carnivore activity on dinosaurian soft tissue during the perimortem interval. Incomplete scavenging of the carcass provided a route for the gases, fluids, and microbes associated with decomposition to escape, allowing more durable soft tissues to persist through the weeks to months required for desiccation prior to entombment and fossilization. This pathway is consistent with actualistic observations and explains why dinosaurian skin, while rare, is more commonly preserved than expected if extreme circumstances were required for its preservation. More broadly, our assumptions guide specimen collection and research, and the presence of soft tissues and biomolecules in fossils that demonstrably were not rapidly buried, such as this mummy, suggests that such types of evidence may be substantially more common than previously assumed.
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Affiliation(s)
- Stephanie K. Drumheller
- Department of Earth and Planetary Sciences, University of Tennessee–Knoxville, Knoxville, Tennessee, United States of America
- * E-mail: (SKD); (CAB)
| | - Clint A. Boyd
- Fossil Resource Management Program, North Dakota Geological Survey, Bismarck, North Dakota, United States of America
- * E-mail: (SKD); (CAB)
| | - Becky M. S. Barnes
- Fossil Resource Management Program, North Dakota Geological Survey, Bismarck, North Dakota, United States of America
| | - Mindy L. Householder
- State Historical Society of North Dakota, Bismarck, North Dakota, United States of America
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2
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Ullmann PV, Macauley K, Ash RD, Shoup B, Scannella JB. Taphonomic and Diagenetic Pathways to Protein Preservation, Part I: The Case of Tyrannosaurus rex Specimen MOR 1125. BIOLOGY 2021; 10:1193. [PMID: 34827186 PMCID: PMC8614911 DOI: 10.3390/biology10111193] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/21/2021] [Revised: 11/12/2021] [Accepted: 11/14/2021] [Indexed: 04/08/2023]
Abstract
Many recent reports have demonstrated remarkable preservation of proteins in fossil bones dating back to the Permian. However, preservation mechanisms that foster the long-term stability of biomolecules and the taphonomic circumstances facilitating them remain largely unexplored. To address this, we examined the taphonomic and geochemical history of Tyrannosaurus rex specimen Museum of the Rockies (MOR) 1125, whose right femur and tibiae were previously shown to retain still-soft tissues and endogenous proteins. By combining taphonomic insights with trace element compositional data, we reconstruct the postmortem history of this famous specimen. Our data show that following prolonged, subaqueous decay in an estuarine channel, MOR 1125 was buried in a coarse sandstone wherein its bones fossilized while interacting with oxic and potentially brackish early-diagenetic groundwaters. Once its bones became stable fossils, they experienced minimal further chemical alteration. Comparisons with other recent studies reveal that oxidizing early-diagenetic microenvironments and diagenetic circumstances which restrict exposure to percolating pore fluids elevate biomolecular preservation potential by promoting molecular condensation reactions and hindering chemical alteration, respectively. Avoiding protracted interactions with late-diagenetic pore fluids is also likely crucial. Similar studies must be conducted on fossil bones preserved under diverse paleoenvironmental and diagenetic contexts to fully elucidate molecular preservation pathways.
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Affiliation(s)
- Paul V. Ullmann
- Department of Geology, Rowan University, Glassboro, NJ 08028, USA;
| | - Kyle Macauley
- Department of Geology, Rowan University, Glassboro, NJ 08028, USA;
| | - Richard D. Ash
- Department of Geology, University of Maryland, College Park, MD 20742, USA;
| | - Ben Shoup
- Absaroka Energy & Environmental Solutions, Buffalo, WY 82834, USA;
| | - John B. Scannella
- Museum of the Rockies, Montana State University, Bozeman, MT 59717, USA;
- Department of Earth Sciences, Montana State University, Bozeman, MT 59717, USA
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3
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Hierarchical biota-level and taxonomic controls on the chemistry of fossil melanosomes revealed using synchrotron X-ray fluorescence. Sci Rep 2020; 10:8970. [PMID: 32488139 PMCID: PMC7265528 DOI: 10.1038/s41598-020-65868-3] [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: 11/18/2019] [Accepted: 05/12/2020] [Indexed: 12/22/2022] Open
Abstract
Fossil melanosomes, micron-sized granules rich in melanin in vivo, provide key information for investigations of the original coloration, taxonomy and internal anatomy of fossil vertebrates. Such studies rely, in part, on analysis of the inorganic chemistry of preserved melanosomes and an understanding of melanosome chemical taphonomy. The extent to which the preserved chemistry of fossil melanosomes is biased by biotic and abiotic factors is, however, unknown. Here we report the discovery of hierarchical controls on the inorganic chemistry of melanosomes from fossil vertebrates from nine biotas. The chemical data are dominated by a strong biota-level signal, indicating that the primary taphonomic control is the diagenetic history of the host sediment. This extrinsic control is superimposed by a biological, tissue-level control; tissue-specific chemical variation is most likely to survive in fossils where the inorganic chemistry of preserved melanosomes is distinct from that of the host sediment. Comparative analysis of our data for fossil and modern amphibians reveals that most fossil specimens show tissue-specific melanosome chemistries that differ from those of extant analogues, strongly suggesting alteration of original melanosome chemistry. Collectively, these findings form a predictive tool for the identification of fossil deposits with well-preserved melanosomes amenable to studies of fossil colour and anatomy.
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4
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Kane IA, Clare MA, Miramontes E, Wogelius R, Rothwell JJ, Garreau P, Pohl F. Seafloor microplastic hotspots controlled by deep-sea circulation. Science 2020; 368:1140-1145. [PMID: 32354839 DOI: 10.1126/science.aba5899] [Citation(s) in RCA: 238] [Impact Index Per Article: 59.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/16/2019] [Accepted: 04/09/2020] [Indexed: 01/23/2023]
Abstract
Although microplastics are known to pervade the global seafloor, the processes that control their dispersal and concentration in the deep sea remain largely unknown. Here, we show that thermohaline-driven currents, which build extensive seafloor sediment accumulations, can control the distribution of microplastics and create hotspots with the highest concentrations reported for any seafloor setting (190 pieces per 50 grams). Previous studies propose that microplastics are transported to the seafloor by vertical settling from surface accumulations; here, we demonstrate that the spatial distribution and ultimate fate of microplastics are strongly controlled by near-bed thermohaline currents (bottom currents). These currents are known to supply oxygen and nutrients to deep-sea benthos, suggesting that deep-sea biodiversity hotspots are also likely to be microplastic hotspots.
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Affiliation(s)
- Ian A Kane
- School of Earth and Environmental Sciences, University of Manchester, Manchester M13 9PL, UK.
| | - Michael A Clare
- National Oceanography Centre, University of Southampton Waterfront Campus, Southampton SO14 3ZH, UK
| | - Elda Miramontes
- Faculty of Geosciences, University of Bremen, 28359 Bremen, Germany.,MARUM-Center for Marine Environmental Sciences, University of Bremen, 28359 Bremen, Germany
| | - Roy Wogelius
- School of Earth and Environmental Sciences, University of Manchester, Manchester M13 9PL, UK
| | - James J Rothwell
- Department of Geography, University of Manchester, Manchester M13 9PL, UK
| | - Pierre Garreau
- IFREMER, Univ. Brest, CNRS UMR 6523, IRD, Laboratoire d'Océanographie Physique et Spatiale (LOPS), IUEM, 29280, Plouzané, France
| | - Florian Pohl
- Department of Earth Sciences, Durham University, Durham DH1 3LE, UK
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5
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Slater TS, McNamara ME, Orr PJ, Foley TB, Ito S, Wakamatsu K. Taphonomic experiments resolve controls on the preservation of melanosomes and keratinous tissues in feathers. PALAEONTOLOGY 2020; 63:103-115. [PMID: 32025055 PMCID: PMC6988486 DOI: 10.1111/pala.12445] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 02/04/2019] [Accepted: 05/15/2019] [Indexed: 06/10/2023]
Abstract
Fossils are a key source of data on the evolution of feather structure and function through deep time, but their ability to resolve macroevolutionary questions is compromised by an incomplete understanding of their taphonomy. Critically, the relative preservation potential of two key feather components, melanosomes and keratinous tissue, is not fully resolved. Recent studies suggesting that melanosomes are preferentially preserved conflict with observations that melanosomes preserve in fossil feathers as external moulds in an organic matrix. To date, there is no model to explain the latter mode of melanosome preservation. We addressed these issues by degrading feathers in systematic taphonomic experiments incorporating decay, maturation and oxidation in isolation and combination. Our results reveal that the production of mouldic melanosomes requires interactions with an oxidant and is most likely to occur prior to substantial maturation. This constrains the taphonomic conditions under which melanosomes are likely to be fossilized. Critically, our experiments also confirm that keratinous feather structures have a higher preservation potential than melanosomes under a range of diagenetic conditions, supporting hitherto controversial hypotheses that fossil feathers can retain degraded keratinous structures.
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Affiliation(s)
- Tiffany S. Slater
- School of Biological, Earth & Environmental SciencesUniversity College CorkCorkIreland
| | - Maria E. McNamara
- School of Biological, Earth & Environmental SciencesUniversity College CorkCorkIreland
| | - Patrick J. Orr
- UCDSchool of Earth SciencesUniversity College DublinDublinIreland
| | - Tara B. Foley
- Department of Anatomy & NeuroscienceUniversity College CorkCorkIreland
| | - Shosuke Ito
- Department of ChemistryFujita Health University School of Health SciencesToyoakeAichiJapan
| | - Kazumasa Wakamatsu
- Department of ChemistryFujita Health University School of Health SciencesToyoakeAichiJapan
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6
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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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7
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Barbi M, Bell PR, Fanti F, Dynes JJ, Kolaceke A, Buttigieg J, Coulson IM, Currie PJ. Integumentary structure and composition in an exceptionally well-preserved hadrosaur (Dinosauria: Ornithischia). PeerJ 2019; 7:e7875. [PMID: 31637130 PMCID: PMC6800526 DOI: 10.7717/peerj.7875] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/27/2019] [Accepted: 09/11/2019] [Indexed: 12/19/2022] Open
Abstract
Preserved labile tissues (e.g., skin, muscle) in the fossil record of terrestrial vertebrates are increasingly becoming recognized as an important source of biological and taphonomic information. Here, we combine a variety of synchrotron radiation techniques with scanning electron and optical microscopy to elucidate the structure of 72 million-year-old squamous (scaly) skin from a hadrosaurid dinosaur from the Late Cretaceous of Alberta, Canada. Scanning electron and optical microscopy independently reveal that the three-dimensionally preserved scales are associated with a band of carbon-rich layers up to a total thickness of ∼75 microns, which is topographically and morphologically congruent with the stratum corneum in modern reptiles. Compositionally, this band deviates from that of the surrounding sedimentary matrix; Fourier-transform infrared spectroscopy and soft X-ray spectromicroscopy analyses indicate that carbon appears predominantly as carbonyl in the skin. The regions corresponding to the integumentary layers are distinctively enriched in iron compared to the sedimentary matrix and appear with kaolinite-rich laminae. These hosting carbonyl-rich layers are apparently composed of subcircular bodies resembling preserved cell structures. Each of these structures is encapsulated by calcite/vaterite, with iron predominantly concentrated at its center. The presence of iron, calcite/vaterite and kaolinite may, independently or collectively, have played important roles in the preservation of the layered structures.
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Affiliation(s)
- Mauricio Barbi
- Department of Physics, University of Regina, Regina, Saskatchewan, Canada
| | - Phil R Bell
- School of Environmental and Rural Science, University of New England, Armidale, New South Wales, Australia
| | - Federico Fanti
- Dipartimento di Scienze Biologiche, Geologiche e Ambientali, Alma Mater Studiorum, Università di Bologna, Bologna, Italy.,Museo Geologico Giovanni Capellini, Università di Bologna, Bologna, Italy
| | - James J Dynes
- Canadian Light Source Inc., University of Saskatchewan, Saskatoon, Saskatchewan, Canada
| | - Anezka Kolaceke
- Department of Physics, University of Regina, Regina, Saskatchewan, Canada
| | - Josef Buttigieg
- Department of Biology, University of Regina, Regina, Saskatchewan, Canada
| | - Ian M Coulson
- Department of Geology, University of Regina, Regina, Saskatchewan, Canada
| | - Philip J Currie
- Biological Sciences, University of Alberta, Edmonton, Alberta, Canada
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8
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Fichtner M, Schuster S, Stark H. Determination of scoring functions for protein damage susceptibility. Biosystems 2019; 187:104035. [PMID: 31614190 DOI: 10.1016/j.biosystems.2019.104035] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/07/2019] [Revised: 09/18/2019] [Accepted: 09/18/2019] [Indexed: 12/15/2022]
Abstract
Protein damage (partly followed by protein aggregation) plays a significant role in ageing, cancer and in neurodegenerative and other diseases. It is known that the proteinogenic amino acids differ in their susceptibility to non-enzymatic modification, such as hydroxylation, peroxidation, chlorination etc. In a novel bioinformatics approach, we introduce measures to quantify the susceptibility of the 20 standard proteinogenic amino acids to such modification. Based on these amino acid scores, we calculated different susceptibilities for 116,387 proteins, testing various scoring approaches. These approaches are based on review articles, text mining and a combination of both. We also show an application by combining the score information with a tool for visualization.
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Affiliation(s)
- Maximilian Fichtner
- Matthias Schleiden Institute, Department of Bioinformatics, Friedrich Schiller University Jena, Ernst-Abbe-Platz 2, 07743 Jena, Germany.
| | - Stefan Schuster
- Matthias Schleiden Institute, Department of Bioinformatics, Friedrich Schiller University Jena, Ernst-Abbe-Platz 2, 07743 Jena, Germany
| | - Heiko Stark
- Matthias Schleiden Institute, Department of Bioinformatics, Friedrich Schiller University Jena, Ernst-Abbe-Platz 2, 07743 Jena, Germany; Institute of Zoology and Evolutionary Research, Friedrich Schiller University Jena, Erbertstraße 1, 07743 Jena, Germany
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9
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Pan Y, Hu L, Zhao T. Applications of chemical imaging techniques in paleontology. Natl Sci Rev 2019; 6:1040-1053. [PMID: 34691967 PMCID: PMC8291642 DOI: 10.1093/nsr/nwy107] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/03/2018] [Revised: 09/19/2018] [Accepted: 10/09/2018] [Indexed: 01/24/2023] Open
Abstract
Chemical imaging techniques, based on a combination of microscopy and spectroscopy, are designed to analyse the composition and spatial distribution of heterogeneous chemical complexes within a sample. Over the last few decades, it has become an increasingly popular tool for characterizing trace elements, isotopic information and organic biomarkers (molecular biosignatures) found in fossils. Here, we introduce the analytical principle of each technique and the interpretation of the chemical signals, followed by a review of the main applications of these techniques in paleontology. We also demonstrate that each technique is associated with pros and cons, and the current limitations and obstacles associated with the use of each specific technique should be taken into account before being applied to fossil samples. Finally, we propose that, due to the rapid advances in the available technology and overall trends towards more multi-disciplinary studies in paleontology, chemical imaging techniques can be expected to have broader applications in paleontology in the near future.
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Affiliation(s)
- Yanhong Pan
- CAS Key Laboratory of Economic Stratigraphy and Palaeogeography, Nanjing Institute of Geology and Palaeontology and Center for Excellence in Life and Paleoenvironment, Chinese Academy of Sciences, Nanjing 210008, China
| | - Liang Hu
- CAS Key Laboratory of Economic Stratigraphy and Palaeogeography, Nanjing Institute of Geology and Palaeontology and Center for Excellence in Life and Paleoenvironment, Chinese Academy of Sciences, Nanjing 210008, China.,University of Chinese Academy of Sciences, Beijing 100049, China
| | - Tao Zhao
- State Key Laboratory of Palaeobiology and Stratigraphy, Nanjing Institute of Geology and Palaeontology and Center for Excellence in Life and Paleoenvironment, Chinese Academy of Sciences, Nanjing 210008, China
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10
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Tissue-specific geometry and chemistry of modern and fossilized melanosomes reveal internal anatomy of extinct vertebrates. Proc Natl Acad Sci U S A 2019; 116:17880-17889. [PMID: 31427524 PMCID: PMC6731645 DOI: 10.1073/pnas.1820285116] [Citation(s) in RCA: 20] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022] Open
Abstract
Recent reports of nonintegumentary melanosomes in fossils hint at functions for melanin beyond color production, but the biology and evolution of internal melanins are poorly understood. Our results show that internal melanosomes are widespread in diverse fossil and modern vertebrates and have tissue-specific geometries and metal chemistries. Tissue-specific chemical signatures can persist in fossils despite some diagenetic overprint, allowing the reconstruction of internal soft-tissue anatomy in fossil vertebrates, and suggest that links between melanin and metal regulation have deep evolutionary origins in vertebrates. Recent discoveries of nonintegumentary melanosomes in extant and fossil amphibians offer potential insights into the physiological functions of melanin not directly related to color production, but the phylogenetic distribution and evolutionary history of these internal melanosomes has not been characterized systematically. Here, we present a holistic method to discriminate among melanized tissues by analyzing the anatomical distribution, morphology, and chemistry of melanosomes in various tissues in a phylogenetically broad sample of extant and fossil vertebrates. Our results show that internal melanosomes in all extant vertebrates analyzed have tissue-specific geometries and elemental signatures. Similar distinct populations of preserved melanosomes in phylogenetically diverse vertebrate fossils often map onto specific anatomical features. This approach also reveals the presence of various melanosome-rich internal tissues in fossils, providing a mechanism for the interpretation of the internal anatomy of ancient vertebrates. Collectively, these data indicate that vertebrate melanins share fundamental physiological roles in homeostasis via the scavenging and sequestering of metals and suggest that intimate links between melanin and metal metabolism in vertebrates have deep evolutionary origins.
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11
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Georgiou R, Gueriau P, Sahle CJ, Bernard S, Mirone A, Garrouste R, Bergmann U, Rueff JP, Bertrand L. Carbon speciation in organic fossils using 2D to 3D x-ray Raman multispectral imaging. SCIENCE ADVANCES 2019; 5:eaaw5019. [PMID: 31497643 PMCID: PMC6716953 DOI: 10.1126/sciadv.aaw5019] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/23/2019] [Accepted: 07/25/2019] [Indexed: 05/30/2023]
Abstract
The in situ two-dimensional (2D) and 3D imaging of the chemical speciation of organic fossils is an unsolved problem in paleontology and cultural heritage. Here, we use x-ray Raman scattering (XRS)-based imaging at the carbon K-edge to form 2D and 3D images of the carbon chemistry in two exceptionally preserved specimens, a fossil plant dating back from the Carboniferous and an ancient insect entrapped in 53-million-year-old amber. The 2D XRS imaging of the plant fossil reveals a homogeneous chemical composition with micrometric "pockets" of preservation, likely inherited from its geological history. The 3D XRS imaging of the insect cuticle displays an exceptionally well preserved remaining chemical signature typical of polysaccharides such as chitin around a largely hollowed-out inclusion. Our results open up new perspectives for in situ chemical speciation imaging of fossilized organic materials, with the potential to enhance our understanding of organic specimens and their paleobiology.
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Affiliation(s)
- Rafaella Georgiou
- IPANEMA, CNRS, ministère de la culture, Université de Versailles Saint-Quentin-en-Yvelines, Université Paris-Saclay, BP 48 St. Aubin, 91192 Gif-sur-Yvette, France
- Synchrotron SOLEIL, l’Orme des Merisiers, BP 48 St. Aubin, 91192 Gif-sur-Yvette, France
| | - Pierre Gueriau
- IPANEMA, CNRS, ministère de la culture, Université de Versailles Saint-Quentin-en-Yvelines, Université Paris-Saclay, BP 48 St. Aubin, 91192 Gif-sur-Yvette, France
- Institute of Earth Sciences, University of Lausanne, Géopolis, CH-1015 Lausanne, Switzerland
| | - Christoph J. Sahle
- ESRF–The European Synchrotron, 71, avenue des Martyrs, CS 40220, 38043 Grenoble, France
| | - Sylvain Bernard
- Muséum National d’Histoire Naturelle, Sorbonne Université, UMR CNRS 7590, IRD, Institut de Minéralogie, de Physique des Matériaux et de Cosmochimie (IMPMC), 75005 Paris, France
| | - Alessandro Mirone
- ESRF–The European Synchrotron, 71, avenue des Martyrs, CS 40220, 38043 Grenoble, France
| | - Romain Garrouste
- Institut de Systématique Evolution Biodiversité (ISYEB), UMR 7205 MNHN/CNRS/Sorbonne Univ./EPHE/Univ. Antilles, Muséum National d’Histoire Naturelle, 57 rue Cuvier, CP 50, F-75005 Paris, France
| | - Uwe Bergmann
- Stanford PULSE Institute, SLAC National Accelerator Laboratory, Menlo Park, CA, USA
| | - Jean-Pascal Rueff
- Synchrotron SOLEIL, l’Orme des Merisiers, BP 48 St. Aubin, 91192 Gif-sur-Yvette, France
- Sorbonne Université, CNRS, Laboratoire de Chimie Physique–Matière et Rayonnement, LCPMR, F-75005 Paris, France
| | - Loïc Bertrand
- IPANEMA, CNRS, ministère de la culture, Université de Versailles Saint-Quentin-en-Yvelines, Université Paris-Saclay, BP 48 St. Aubin, 91192 Gif-sur-Yvette, France
- Synchrotron SOLEIL, l’Orme des Merisiers, BP 48 St. Aubin, 91192 Gif-sur-Yvette, France
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12
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Manning PL, Edwards NP, Bergmann U, Anné J, Sellers WI, van Veelen A, Sokaras D, Egerton VM, Alonso-Mori R, Ignatyev K, van Dongen BE, Wakamatsu K, Ito S, Knoll F, Wogelius RA. Pheomelanin pigment remnants mapped in fossils of an extinct mammal. Nat Commun 2019; 10:2250. [PMID: 31113945 PMCID: PMC6529433 DOI: 10.1038/s41467-019-10087-2] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/15/2017] [Accepted: 04/09/2019] [Indexed: 11/17/2022] Open
Abstract
Recent progress has been made in paleontology with respect to resolving pigmentation in fossil material. Morphological identification of fossilized melanosomes has been one approach, while a second methodology using chemical imaging and spectroscopy has also provided critical information particularly concerning eumelanin (black pigment) residue. In this work we develop the chemical imaging methodology to show that organosulfur-Zn complexes are indicators of pheomelanin (red pigment) in extant and fossil soft tissue and that the mapping of these residual biochemical compounds can be used to restore melanin pigment distribution in a 3 million year old extinct mammal species (Apodemus atavus). Synchotron Rapid Scanning X-ray Fluorescence imaging showed that the distributions of Zn and organic S are correlated within this fossil fur just as in pheomelanin-rich modern integument. Furthermore, Zn coordination chemistry within this fossil fur is closely comparable to that determined from pheomelanin-rich fur and hair standards. The non-destructive methods presented here provide a protocol for detecting residual pheomelanin in precious specimens.
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Affiliation(s)
- Phillip L Manning
- University of Manchester, School of Earth and Environmental Sciences, Interdisciplinary Centre for Ancient Life, Manchester, M13 9PL, UK
- Department of Geology and Environmental Geoscience, College of Charleston, 66 George St, Charleston, SC, 29424, USA
| | - Nicholas P Edwards
- Stanford Synchrotron Radiation Lightsource, SLAC National Accelerator Laboratory, Menlo Park, CA, 94025, USA
| | - Uwe Bergmann
- Stanford PULSE Institute, SLAC National Accelerator Laboratory, Menlo Park, CA, 94025, USA
| | - Jennifer Anné
- The Children's Museum of Indianpolis, 3000 N Meridian St, Indianapolis, IN, 46208, USA
| | - William I Sellers
- University of Manchester, School of Earth and Environmental Sciences, Interdisciplinary Centre for Ancient Life, Manchester, M13 9PL, UK
| | - Arjen van Veelen
- University of Southampton, Faculty of Engineering and Physical Sciences, Southampton, SO17 1BJ, UK
| | - Dimosthenis Sokaras
- Stanford Synchrotron Radiation Lightsource, SLAC National Accelerator Laboratory, Menlo Park, CA, 94025, USA
| | - Victoria M Egerton
- University of Manchester, School of Earth and Environmental Sciences, Interdisciplinary Centre for Ancient Life, Manchester, M13 9PL, UK
- The Children's Museum of Indianpolis, 3000 N Meridian St, Indianapolis, IN, 46208, USA
| | - Roberto Alonso-Mori
- Linac Coherent Light Source, SLAC National Accelerator Laboratory, Menlo Park, CA, 94025, USA
| | | | - Bart E van Dongen
- University of Manchester, School of Earth and Environmental Sciences, Interdisciplinary Centre for Ancient Life, Manchester, M13 9PL, UK
| | - Kazumasa Wakamatsu
- Department of Chemistry, Fujita Health University School of Health Sciences, Toyoake, Aichi, 470-1192, Japan
| | - Shosuke Ito
- Department of Chemistry, Fujita Health University School of Health Sciences, Toyoake, Aichi, 470-1192, Japan
| | - Fabien Knoll
- University of Manchester, School of Earth and Environmental Sciences, Interdisciplinary Centre for Ancient Life, Manchester, M13 9PL, UK
- ARAID-Fundación Conjunto Paleontológico de Teruel-Dinópolis, 44002, Teruel, Spain
| | - Roy A Wogelius
- University of Manchester, School of Earth and Environmental Sciences, Williamson Research Centre for Molecular Environmental Science & Interdisciplinary Centre for Ancient Life, Manchester, M13 9PL, UK.
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13
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Biochemistry and adaptive colouration of an exceptionally preserved juvenile fossil sea turtle. Sci Rep 2017; 7:13324. [PMID: 29042651 PMCID: PMC5645316 DOI: 10.1038/s41598-017-13187-5] [Citation(s) in RCA: 26] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/17/2017] [Accepted: 09/19/2017] [Indexed: 12/27/2022] Open
Abstract
The holotype (MHM-K2) of the Eocene cheloniine Tasbacka danica is arguably one of the best preserved juvenile fossil sea turtles on record. Notwithstanding compactional flattening, the specimen is virtually intact, comprising a fully articulated skeleton exposed in dorsal view. MHM-K2 also preserves, with great fidelity, soft tissue traces visible as a sharply delineated carbon film around the bones and marginal scutes along the edge of the carapace. Here we show that the extraordinary preservation of the type of T. danica goes beyond gross morphology to include ultrastructural details and labile molecular components of the once-living animal. Haemoglobin-derived compounds, eumelanic pigments and proteinaceous materials retaining the immunological characteristics of sauropsid-specific β-keratin and tropomyosin were detected in tissues containing remnant melanosomes and decayed keratin plates. The preserved organics represent condensed remains of the cornified epidermis and, likely also, deeper anatomical features, and provide direct chemical evidence that adaptive melanism – a biological means used by extant sea turtle hatchlings to elevate metabolic and growth rates – had evolved 54 million years ago.
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14
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Cellular preservation of musculoskeletal specializations in the Cretaceous bird Confuciusornis. Nat Commun 2017; 8:14779. [PMID: 28327586 PMCID: PMC5364438 DOI: 10.1038/ncomms14779] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/14/2016] [Accepted: 02/02/2017] [Indexed: 01/10/2023] Open
Abstract
The hindlimb of theropod dinosaurs changed appreciably in the lineage leading to extant birds, becoming more ‘crouched' in association with changes to body shape and gait dynamics. This postural evolution included anatomical changes of the foot and ankle, altering the moment arms and control of the muscles that manipulated the tarsometatarsus and digits, but the timing of these changes is unknown. Here, we report cellular-level preservation of tendon- and cartilage-like tissues from the lower hindlimb of Early Cretaceous Confuciusornis. The digital flexor tendons passed through cartilages, cartilaginous cristae and ridges on the plantar side of the distal tibiotarsus and proximal tarsometatarsus, as in extant birds. In particular, fibrocartilaginous and cartilaginous structures on the plantar surface of the ankle joint of Confuciusornis may indicate a more crouched hindlimb posture. Recognition of these specialized soft tissues in Confuciusornis is enabled by our combination of imaging and chemical analyses applied to an exceptionally preserved fossil. Birds have a more crouched posture compared to their theropod dinosaur ancestors. Here, Jiang and colleagues describe a lower hindlimb of the Early Cretaceous bird Confuciusornis with soft tissues apparently preserved even as molecules, indicating a somewhat more modern posture in ancient birds.
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15
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Edwards NP, van Veelen A, Anné J, Manning PL, Bergmann U, Sellers WI, Egerton VM, Sokaras D, Alonso-Mori R, Wakamatsu K, Ito S, Wogelius RA. Elemental characterisation of melanin in feathers via synchrotron X-ray imaging and absorption spectroscopy. Sci Rep 2016; 6:34002. [PMID: 27658854 PMCID: PMC5034265 DOI: 10.1038/srep34002] [Citation(s) in RCA: 40] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/15/2016] [Accepted: 09/02/2016] [Indexed: 11/29/2022] Open
Abstract
Melanin is a critical component of biological systems, but the exact chemistry of melanin is still imprecisely known. This is partly due to melanin’s complex heterogeneous nature and partly because many studies use synthetic analogues and/or pigments extracted from their natural biological setting, which may display important differences from endogenous pigments. Here we demonstrate how synchrotron X-ray analyses can non-destructively characterise the elements associated with melanin pigment in situ within extant feathers. Elemental imaging shows that the distributions of Ca, Cu and Zn are almost exclusively controlled by melanin pigment distribution. X-ray absorption spectroscopy demonstrates that the atomic coordination of zinc and sulfur is different within eumelanised regions compared to pheomelanised regions. This not only impacts our fundamental understanding of pigmentation in extant organisms but also provides a significant contribution to the evidence-based colour palette available for reconstructing the appearance of fossil organisms.
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Affiliation(s)
- Nicholas P Edwards
- University of Manchester, School of Earth and Environmental Sciences, Williamson Research Centre for Molecular Environmental Science, M13 9PL, UK.,University of Manchester, School of Earth and Environmental Sciences, Interdisciplinary Centre for Ancient Life, Manchester M13 9PL, UK
| | - Arjen van Veelen
- University of Manchester, School of Earth and Environmental Sciences, Williamson Research Centre for Molecular Environmental Science, M13 9PL, UK.,University of Manchester, School of Earth and Environmental Sciences, Interdisciplinary Centre for Ancient Life, Manchester M13 9PL, UK
| | - Jennifer Anné
- University of Manchester, School of Earth and Environmental Sciences, Williamson Research Centre for Molecular Environmental Science, M13 9PL, UK.,University of Manchester, School of Earth and Environmental Sciences, Interdisciplinary Centre for Ancient Life, Manchester M13 9PL, UK
| | - Phillip L Manning
- University of Manchester, School of Earth and Environmental Sciences, Interdisciplinary Centre for Ancient Life, Manchester M13 9PL, UK.,College of Charleston, Department of Geology and Environmental Geosciences, Charleston, SC, 29424, USA
| | - Uwe Bergmann
- Stanford PULSE Institute, SLAC National Accelerator Laboratory, Menlo Park, CA, 94025, USA
| | - William I Sellers
- University of Manchester, School of Earth and Environmental Sciences, Williamson Research Centre for Molecular Environmental Science, M13 9PL, UK.,University of Manchester, School of Earth and Environmental Sciences, Interdisciplinary Centre for Ancient Life, Manchester M13 9PL, UK
| | - Victoria M Egerton
- University of Manchester, School of Earth and Environmental Sciences, Interdisciplinary Centre for Ancient Life, Manchester M13 9PL, UK.,College of Charleston, Department of Geology and Environmental Geosciences, Charleston, SC, 29424, USA
| | - Dimosthenis Sokaras
- Stanford Synchrotron Radiation Lightsource, SLAC National Accelerator Laboratory, Menlo Park, CA 94025, USA
| | - Roberto Alonso-Mori
- Linac Coherent Lightsource, SLAC National Accelerator Laboratory, Menlo Park, CA, 94025, USA
| | - Kazumasa Wakamatsu
- Department of Chemistry, Fujita Health University, School of Health Sciences, Toyoake, Aichi 470-1192, Japan
| | - Shosuke Ito
- Department of Chemistry, Fujita Health University, School of Health Sciences, Toyoake, Aichi 470-1192, Japan
| | - Roy A Wogelius
- University of Manchester, School of Earth and Environmental Sciences, Williamson Research Centre for Molecular Environmental Science, M13 9PL, UK.,University of Manchester, School of Earth and Environmental Sciences, Interdisciplinary Centre for Ancient Life, Manchester M13 9PL, UK
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16
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17
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McNamara ME, van Dongen BE, Lockyer NP, Bull I, Orr PJ. Fossilization of melanosomes via sulfurization. PALAEONTOLOGY 2016; 59:337-350. [PMID: 27499556 PMCID: PMC4957269 DOI: 10.1111/pala.12238] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 07/12/2015] [Accepted: 02/22/2016] [Indexed: 06/06/2023]
Abstract
Fossil melanin granules (melanosomes) are an important resource for inferring the evolutionary history of colour and its functions in animals. The taphonomy of melanin and melanosomes, however, is incompletely understood. In particular, the chemical processes responsible for melanosome preservation have not been investigated. As a result, the origins of sulfur-bearing compounds in fossil melanosomes are difficult to resolve. This has implications for interpretations of original colour in fossils based on potential sulfur-rich phaeomelanosomes. Here we use pyrolysis gas chromatography mass spectrometry (Py-GCMS), fourier transform infrared spectroscopy (FTIR) and time of flight secondary ion mass spectrometry (ToF-SIMS) to assess the mode of preservation of fossil microstructures, confirmed as melanosomes based on the presence of melanin, preserved in frogs from the Late Miocene Libros biota (NE Spain). Our results reveal a high abundance of organosulfur compounds and non-sulfurized fatty acid methyl esters in both the fossil tissues and host sediment; chemical signatures in the fossil tissues are inconsistent with preservation of phaeomelanin. Our results reflect preservation via the diagenetic incorporation of sulfur, i.e. sulfurization (natural vulcanization), and other polymerization processes. Organosulfur compounds and/or elevated concentrations of sulfur have been reported from melanosomes preserved in various invertebrate and vertebrate fossils and depositional settings, suggesting that preservation through sulfurization is likely to be widespread. Future studies of sulfur-rich fossil melanosomes require that the geochemistry of the host sediment is tested for evidence of sulfurization in order to constrain interpretations of potential phaeomelanosomes and thus of original integumentary colour in fossils.
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Affiliation(s)
- Maria E. McNamara
- School of Biological, Earth and Environmental SciencesUniversity College CorkNorth MallCorkIreland
| | - Bart E. van Dongen
- School of Earth, Atmospheric and Environmental SciencesWilliamson Research Centre for Molecular Environmental ScienceUniversity of ManchesterOxford RoadManchesterM13 9PLUK
| | - Nick P. Lockyer
- School of ChemistryManchester Institute of BiotechnologyUniversity of Manchester131 Princess StManchesterM13 9PLUK
| | - Ian D. Bull
- Organic Geochemistry UnitSchool of ChemistryUniversity of BristolBristolBS8 1TSUK
| | - Patrick J. Orr
- UCD School of Earth SciencesUniversity College DublinBelfield Dublin 4Ireland
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18
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Oliveira NC, Silva JH, Barros OA, Pinheiro AP, Santana W, Saraiva AAF, Ferreira OP, Freire PTC, Paula AJ. Large-Field Electron Imaging and X-ray Elemental Mapping Unveil the Morphology, Structure, and Fractal Features of a Cretaceous Fossil at the Centimeter Scale. Anal Chem 2015; 87:10088-95. [DOI: 10.1021/acs.analchem.5b02815] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Naiara C. Oliveira
- Solid-Biological
Interface Group (SolBIN), Departamento de Física, Universidade Federal do Ceará, P.O. Box 6030, 60455-900 Fortaleza, Ceará, Brazil
| | - João H. Silva
- Universidade Federal do Cariri, Cidade Universitária, 63048-080 Juazeiro do Norte, Ceará, Brazil
| | | | | | - William Santana
- Sistematic
Zoology Laboratory (LSZ), Pró-Reitoria de Pesquisa e Pós-Graduação, Universidade Sagrado Coração (USC), 17011-160 Bauru, São Paulo, Brazil
| | | | | | | | - Amauri J. Paula
- Solid-Biological
Interface Group (SolBIN), Departamento de Física, Universidade Federal do Ceará, P.O. Box 6030, 60455-900 Fortaleza, Ceará, Brazil
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19
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Lindgren J, Sjövall P, Carney RM, Cincotta A, Uvdal P, Hutcheson SW, Gustafsson O, Lefèvre U, Escuillié F, Heimdal J, Engdahl A, Gren JA, Kear BP, Wakamatsu K, Yans J, Godefroit P. Molecular composition and ultrastructure of Jurassic paravian feathers. Sci Rep 2015; 5:13520. [PMID: 26311035 PMCID: PMC4550916 DOI: 10.1038/srep13520] [Citation(s) in RCA: 39] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/10/2015] [Accepted: 07/29/2015] [Indexed: 11/17/2022] Open
Abstract
Feathers are amongst the most complex epidermal structures known, and they have a well-documented evolutionary trajectory across non-avian dinosaurs and basal birds. Moreover, melanosome-like microbodies preserved in association with fossil plumage have been used to reconstruct original colour, behaviour and physiology. However, these putative ancient melanosomes might alternatively represent microorganismal residues, a conflicting interpretation compounded by a lack of unambiguous chemical data. We therefore used sensitive molecular imaging, supported by multiple independent analytical tests, to demonstrate that the filamentous epidermal appendages in a new specimen of the Jurassic paravian Anchiornis comprise remnant eumelanosomes and fibril-like microstructures, preserved as endogenous eumelanin and authigenic calcium phosphate. These results provide novel insights into the early evolution of feathers at the sub-cellular level, and unequivocally determine that melanosomes can be preserved in fossil feathers.
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Affiliation(s)
- Johan Lindgren
- Department of Geology, Lund University, 223 62 Lund, Sweden
| | - Peter Sjövall
- SP Technical Research Institute of Sweden, Chemistry, Materials and Surfaces, 501 15 Borås, Sweden
| | - Ryan M Carney
- Department of Ecology and Evolutionary Biology, Brown University, Providence, Rhode Island 02906, USA
| | - Aude Cincotta
- Operational Direction 'Earth and History of Life', Royal Belgian Institute of Natural Sciences, 1000 Brussels, Belgium.,Department of Geology, University of Namur, 5000 Namur, Belgium
| | - Per Uvdal
- MAX-IV laboratory, Lund University, 221 00 Lund, Sweden.,Chemical Physics, Department of Chemistry, Lund University, 221 00 Lund, Sweden
| | - Steven W Hutcheson
- Department of Cell Biology and Molecular Genetics, University of Maryland, College Park, Maryland 20742, USA
| | - Ola Gustafsson
- Department of Biology, Lund University, 223 62 Lund, Sweden
| | - Ulysse Lefèvre
- Operational Direction 'Earth and History of Life', Royal Belgian Institute of Natural Sciences, 1000 Brussels, Belgium.,Department of Geology, Liège University, 4000 Liège, Belgium
| | | | - Jimmy Heimdal
- MAX-IV laboratory, Lund University, 221 00 Lund, Sweden
| | | | - Johan A Gren
- Department of Geology, Lund University, 223 62 Lund, Sweden
| | - Benjamin P Kear
- Museum of Evolution, Uppsala University, 752 36 Uppsala, Sweden.,Palaeobiology Programme, Department of Earth Sciences, Uppsala University, 752 36 Uppsala, Sweden
| | - Kazumasa Wakamatsu
- Department of Chemistry, Fujita Health University School of Health Sciences, Toyoake, Aichi 470-1192, Japan
| | - Johan Yans
- Department of Geology, University of Namur, 5000 Namur, Belgium
| | - Pascal Godefroit
- Operational Direction 'Earth and History of Life', Royal Belgian Institute of Natural Sciences, 1000 Brussels, Belgium
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20
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Hill RC, Wither MJ, Nemkov T, Barrett A, D'Alessandro A, Dzieciatkowska M, Hansen KC. Preserved Proteins from Extinct Bison latifrons Identified by Tandem Mass Spectrometry; Hydroxylysine Glycosides are a Common Feature of Ancient Collagen. Mol Cell Proteomics 2015; 14:1946-58. [PMID: 25948757 DOI: 10.1074/mcp.m114.047787] [Citation(s) in RCA: 66] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/22/2014] [Indexed: 11/06/2022] Open
Abstract
Bone samples from several vertebrates were collected from the Ziegler Reservoir fossil site, in Snowmass Village, Colorado, and processed for proteomics analysis. The specimens come from Pleistocene megafauna Bison latifrons, dating back ∼ 120,000 years. Proteomics analysis using a simplified sample preparation procedure and tandem mass spectrometry (MS/MS) was applied to obtain protein identifications. Several bioinformatics resources were used to obtain peptide identifications based on sequence homology to extant species with annotated genomes. With the exception of soil sample controls, all samples resulted in confident peptide identifications that mapped to type I collagen. In addition, we analyzed a specimen from the extinct B. latifrons that yielded peptide identifications mapping to over 33 bovine proteins. Our analysis resulted in extensive fibrillar collagen sequence coverage, including the identification of posttranslational modifications. Hydroxylysine glucosylgalactosylation, a modification thought to be involved in collagen fiber formation and bone mineralization, was identified for the first time in an ancient protein dataset. Meta-analysis of data from other studies indicates that this modification may be common in well-preserved prehistoric samples. Additional peptide sequences from extracellular matrix (ECM) and non-ECM proteins have also been identified for the first time in ancient tissue samples. These data provide a framework for analyzing ancient protein signatures in well-preserved fossil specimens, while also contributing novel insights into the molecular basis of organic matter preservation. As such, this analysis has unearthed common posttranslational modifications of collagen that may assist in its preservation over time. The data are available via ProteomeXchange with identifier PXD001827.
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Affiliation(s)
- Ryan C Hill
- From the ‡Department of Biochemistry and Molecular Genetics, University of Colorado Denver, Aurora, Colorado 80045, USA
| | - Matthew J Wither
- From the ‡Department of Biochemistry and Molecular Genetics, University of Colorado Denver, Aurora, Colorado 80045, USA
| | - Travis Nemkov
- From the ‡Department of Biochemistry and Molecular Genetics, University of Colorado Denver, Aurora, Colorado 80045, USA
| | - Alexander Barrett
- From the ‡Department of Biochemistry and Molecular Genetics, University of Colorado Denver, Aurora, Colorado 80045, USA
| | - Angelo D'Alessandro
- From the ‡Department of Biochemistry and Molecular Genetics, University of Colorado Denver, Aurora, Colorado 80045, USA
| | - Monika Dzieciatkowska
- From the ‡Department of Biochemistry and Molecular Genetics, University of Colorado Denver, Aurora, Colorado 80045, USA
| | - Kirk C Hansen
- From the ‡Department of Biochemistry and Molecular Genetics, University of Colorado Denver, Aurora, Colorado 80045, USA
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21
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Edwards NP, Manning PL, Bergmann U, Larson PL, van Dongen BE, Sellers WI, Webb SM, Sokaras D, Alonso-Mori R, Ignatyev K, Barden HE, van Veelen A, Anné J, Egerton VM, Wogelius RA. Leaf metallome preserved over 50 million years. Metallomics 2014; 6:774-82. [PMID: 24804302 DOI: 10.1039/c3mt00242j] [Citation(s) in RCA: 32] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Large-scale Synchrotron Rapid Scanning X-ray Fluorescence (SRS-XRF) elemental mapping and X-ray absorption spectroscopy are applied here to fossil leaf material from the 50 Mya Green River Formation (USA) in order to improve our understanding of the chemistry of fossilized plant remains. SRS-XRF of fossilized animals has previously shown that bioaccumulated trace metals and sulfur compounds may be preserved in their original distributions and these elements can also act as biomarkers for specific biosynthetic pathways. Similar spatially resolved chemical data for fossilized plants is sparsely represented in the literature despite the multitude of other chemical studies performed. Here, synchrotron data from multiple specimens consistently show that fossil leaves possess chemical inventories consisting of organometallic and organosulfur compounds that: (1) map discretely within the fossils, (2) resolve fine scale biological structures, and (3) are distinct from embedding sedimentary matrices. Additionally, the chemical distributions in fossil leaves are directly comparable to those of extant leaves. This evidence strongly suggests that a significant fraction of the chemical inventory of the examined fossil leaf material is derived from the living organisms and that original bioaccumulated elements have been preserved in situ for 50 million years. Chemical information of this kind has so far been unknown for fossilized plants and could for the first time allow the metallome of extinct flora to be studied.
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22
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Anné J, Edwards NP, Wogelius RA, Tumarkin-Deratzian AR, Sellers WI, van Veelen A, Bergmann U, Sokaras D, Alonso-Mori R, Ignatyev K, Egerton VM, Manning PL. Synchrotron imaging reveals bone healing and remodelling strategies in extinct and extant vertebrates. J R Soc Interface 2014; 11:20140277. [PMID: 24806709 PMCID: PMC4032541 DOI: 10.1098/rsif.2014.0277] [Citation(s) in RCA: 43] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Current understanding of bone healing and remodelling strategies in vertebrates has traditionally relied on morphological observations through the histological analysis of thin sections. However, chemical analysis may also be used in such interpretations, as different elements are known to be absorbed and used by bone for different physiological purposes such as growth and healing. These chemical signatures are beyond the detection limit of most laboratory-based analytical techniques (e.g. scanning electron microscopy). However, synchrotron rapid scanning–X-ray fluorescence (SRS–XRF) is an elemental mapping technique that uniquely combines high sensitivity (ppm), excellent sample resolution (20–100 µm) and the ability to scan large specimens (decimetre scale) approximately 3000 times faster than other mapping techniques. Here, we use SRS–XRF combined with microfocus elemental mapping (2–20 µm) to determine the distribution and concentration of trace elements within pathological and normal bone of both extant and extinct archosaurs (Cathartes aura and Allosaurus fragilis). Results reveal discrete chemical inventories within different bone tissue types and preservation modes. Chemical inventories also revealed detail of histological features not observable in thin section, including fine structures within the interface between pathological and normal bone as well as woven texture within pathological tissue.
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Affiliation(s)
- Jennifer Anné
- School of Earth, Atmospheric and Environmental Sciences, University of Manchester, Williamson Building, Oxford Road, , Manchester M13 9PL, UK
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23
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Conrad JL, Head JJ, Carrano MT. Unusual Soft-Tissue Preservation of a Crocodile Lizard (Squamata, Shinisauria) From the Green River Formation (Eocene) and Shinisaur Relationships. Anat Rec (Hoboken) 2014; 297:545-59. [DOI: 10.1002/ar.22868] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/15/2013] [Accepted: 06/24/2013] [Indexed: 11/07/2022]
Affiliation(s)
- Jack L. Conrad
- Anatomy Department; NYIT College of Osteopathic Medicine, Northern Boulevard; Old Westbury New York
- Department of Vertebrate Paleontology; American Museum of Natural History; New York
| | - Jason J. Head
- Department of Earth and Atmospheric Sciences; Hall, University of Nebraska-Lincoln; Lincoln Nebraska
| | - Matthew T. Carrano
- Department of Paleobiology; Smithsonian Institution, National Museum of Natural History; Washington District Of Columbia
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24
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Gueriau P, Mocuta C, Dutheil DB, Cohen SX, Thiaudière D, Charbonnier S, Clément G, Bertrand L. Trace elemental imaging of rare earth elements discriminates tissues at microscale in flat fossils. PLoS One 2014; 9:e86946. [PMID: 24489809 PMCID: PMC3906100 DOI: 10.1371/journal.pone.0086946] [Citation(s) in RCA: 33] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/24/2013] [Accepted: 12/15/2013] [Indexed: 11/18/2022] Open
Abstract
The interpretation of flattened fossils remains a major challenge due to compression of their complex anatomies during fossilization, making critical anatomical features invisible or hardly discernible. Key features are often hidden under greatly preserved decay prone tissues, or an unpreparable sedimentary matrix. A method offering access to such anatomical features is of paramount interest to resolve taxonomic affinities and to study fossils after a least possible invasive preparation. Unfortunately, the widely-used X-ray micro-computed tomography, for visualizing hidden or internal structures of a broad range of fossils, is generally inapplicable to flattened specimens, due to the very high differential absorbance in distinct directions. Here we show that synchrotron X-ray fluorescence spectral raster-scanning coupled to spectral decomposition or a much faster Kullback-Leibler divergence based statistical analysis provides microscale visualization of tissues. We imaged exceptionally well-preserved fossils from the Late Cretaceous without needing any prior delicate preparation. The contrasting elemental distributions greatly improved the discrimination of skeletal elements material from both the sedimentary matrix and fossilized soft tissues. Aside content in alkaline earth elements and phosphorus, a critical parameter for tissue discrimination is the distinct amounts of rare earth elements. Local quantification of rare earths may open new avenues for fossil description but also in paleoenvironmental and taphonomical studies.
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Affiliation(s)
- Pierre Gueriau
- CR2P, UMR 7207 CNRS, MNHN, UPMC, Paris, France
- IPANEMA, USR 3461 CNRS, MCC, Gif-sur-Yvette, France
- * E-mail: (PG); (LB)
| | | | | | | | | | | | | | | | - Loïc Bertrand
- IPANEMA, USR 3461 CNRS, MCC, Gif-sur-Yvette, France
- Synchrotron SOLEIL, Gif-sur-Yvette, France
- * E-mail: (PG); (LB)
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25
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Buckley M, Melton ND, Montgomery J. Proteomics analysis of ancient food vessel stitching reveals >4000-year-old milk protein. RAPID COMMUNICATIONS IN MASS SPECTROMETRY : RCM 2013; 27:531-538. [PMID: 23322659 DOI: 10.1002/rcm.6481] [Citation(s) in RCA: 30] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/10/2012] [Revised: 11/27/2012] [Accepted: 11/28/2012] [Indexed: 06/01/2023]
Abstract
RATIONALE The 19th century excavation of an exceptionally well-preserved Early Bronze Age high status log-coffin burial from northern England, dated to 2200-2020 BC, yielded a 'food residue' collected from the inside of an accompanying bark vessel. This residue contained fibrous stitching that was used to hold the bark walls of the vessel together, first described as animal sinews, although the surviving material clearly contains animal hairs. Protein sequencing by soft ionisation mass spectrometry should identify the proteins that constitute the material, as well as the animal species from which they derive. METHODS Peptide mass fingerprinting (PMF) by MALDI-TOF-MS combined with liquid chromatography-ESI-LTQ-MS/MS was used to identify low-abundance proteins as well as the dominant proteins in the sample. RESULTS These proteomics techniques revealed the dominant proteins as deriving from the fibrous keratins (both types 1 and 2) and collagens (types 1 and 3), specifically those indicative of a bovine source. However, several peptide sequences diagnostic of bovine α-S1-casein were also observed, indicating that traces of milk had been preserved within the >4000-year-old fibrous residue. CONCLUSIONS The presence of this food vessel that once contained milk within a burial of high status is suggestive of the importance placed on these secondary products. It is perhaps more remarkable that this information was retrieved not only from material of such antiquity, but also from an excavation that occurred nearly 200 years ago.
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Affiliation(s)
- Michael Buckley
- Manchester Institute of Biotechnology, Faculty of Life Sciences, University of Manchester, Manchester, UK.
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26
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Bergmann U, Manning PL, Wogelius RA. Chemical mapping of paleontological and archeological artifacts with synchrotron X-rays. ANNUAL REVIEW OF ANALYTICAL CHEMISTRY (PALO ALTO, CALIF.) 2012; 5:361-89. [PMID: 22524223 DOI: 10.1146/annurev-anchem-062011-143019] [Citation(s) in RCA: 23] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/12/2023]
Abstract
The application of the recently developed synchrotron rapid scanning X-ray fluorescence (SRS-XRF) technique to the mapping of large objects is the focus of this review. We discuss the advantages of SRS-XRF over traditional systems and the use of other synchrotron radiation (SR) techniques to provide corroborating spectroscopic and diffraction analyses during the same analytical session. After reviewing routine techniques used to analyze precious specimens, we present several case studies that show how SR-based methods have been successfully applied in archeology and paleontology. For example, SRS-XRF imaging of a seventh-century Qur'ān palimpsest and an overpainted original opera score from Luigi Cherubini is described. We also review the recent discovery of soft-tissue residue in fossils of Archaeopteryx and an ancient reptile, as well as work that has successfully resolved the remnants of pigment in Confuciusornis sanctus, a 120-million-year-old fossil of the oldest documented bird with a fully derived avian beak.
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Affiliation(s)
- Uwe Bergmann
- Linac Coherent Light Source, SLAC National Accelerator Laboratory, Menlo Park, California 94025, USA.
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27
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Barden HE, Wogelius RA, Li D, Manning PL, Edwards NP, van Dongen BE. Morphological and geochemical evidence of eumelanin preservation in the feathers of the Early Cretaceous bird, Gansus yumenensis. PLoS One 2011; 6:e25494. [PMID: 22022404 PMCID: PMC3192724 DOI: 10.1371/journal.pone.0025494] [Citation(s) in RCA: 32] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/20/2011] [Accepted: 09/05/2011] [Indexed: 11/19/2022] Open
Abstract
Recent studies have shown evidence for the preservation of colour in fossilized soft tissues by imaging melanosomes, melanin pigment containing organelles. This study combines geochemical analyses with morphological observations to investigate the preservation of melanosomes and melanin within feathers of the Early Cretaceous bird, Gansus yumenensis. Scanning electron microscopy reveals structures concordant with those previously identified as eumelanosomes within visually dark areas of the feathers but not in lighter areas or sedimentary matrices. Fourier transform infrared analyses show different spectra for the feathers and their matrices; melanic functional groups appear in the feather including carboxylic acid and ketone groups that are not seen in the matrix. When mapped, the carboxylic acid group absorption faithfully replicates the visually dark areas of the feathers. Electron Paramagnetic Resonance spectroscopy of one specimen demonstrates the presence of organic signals but proved too insensitive to resolve melanin. Pyrolysis gas chromatography mass spectrometry shows a similar distribution of aliphatic material within both feathers that are different from those of their respective matrices. In combination, these techniques strongly suggest that not only do the feathers contain endogenous organic material, but that both geochemical and morphological evidence supports the preservation of original eumelanic pigment residue.
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Affiliation(s)
- Holly E Barden
- School of Earth Atmospheric and Environmental Sciences and Williamson Research Centre for Molecular Environmental Science, University of Manchester, Manchester, United Kingdom.
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