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Morton-Hayward AL, Anderson RP, Saupe EE, Larson G, Cosmidis JG. Human brains preserve in diverse environments for at least 12 000 years. Proc Biol Sci 2024; 291:20232606. [PMID: 38503334 PMCID: PMC10950470 DOI: 10.1098/rspb.2023.2606] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/20/2023] [Accepted: 02/26/2024] [Indexed: 03/21/2024] Open
Abstract
The brain is thought to be among the first human organs to decompose after death. The discovery of brains preserved in the archaeological record is therefore regarded as unusual. Although mechanisms such as dehydration, freezing, saponification, and tanning are known to allow for the preservation of the brain on short time scales in association with other soft tissues (≲4000 years), discoveries of older brains, especially in the absence of other soft tissues, are rare. Here, we collated an archive of more than 4400 human brains preserved in the archaeological record across approximately 12 000 years, more than 1300 of which constitute the only soft tissue preserved amongst otherwise skeletonized remains. We found that brains of this type persist on time scales exceeding those preserved by other means, which suggests an unknown mechanism may be responsible for preservation particular to the central nervous system. The untapped archive of preserved ancient brains represents an opportunity for bioarchaeological studies of human evolution, health and disease.
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Affiliation(s)
- Alexandra L. Morton-Hayward
- Department of Earth Sciences, University of Oxford, Oxford, UK
- Target Discovery Institute, University of Oxford, Oxford, UK
| | - Ross P. Anderson
- Department of Earth Sciences, University of Oxford, Oxford, UK
- All Souls College, University of Oxford, Oxford, UK
| | - Erin E. Saupe
- Department of Earth Sciences, University of Oxford, Oxford, UK
| | - Greger Larson
- Palaeogenomics and Bio-Archaeology Research Network, School of Archaeology, University of Oxford, Oxford, UK
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2
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Tahoun M, Engeser M, Svolacchia L, Sander PM, Müller CE. Molecular Taphonomy of Heme: Chemical Degradation of Hemin under Presumed Fossilization Conditions. Molecules 2023; 28:4887. [PMID: 37446548 DOI: 10.3390/molecules28134887] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/26/2023] [Revised: 06/16/2023] [Accepted: 06/18/2023] [Indexed: 07/15/2023] Open
Abstract
The metalloporphyrin heme acts as the oxygen-complexing prosthetic group of hemoglobin in blood. Heme has been noted to survive for many millions of years in fossils. Here, we investigate its stability and degradation under various conditions expected to occur during fossilization. Oxidative, reductive, aerobic, and anaerobic conditions were studied at neutral and alkaline pH values. Elevated temperatures were applied to accelerate degradation. High-performance liquid chromatography coupled to tandem mass spectrometry (HPLC-MS/MS) identified four main degradation products. The vinyl residues are oxidized to formyl and further to carboxylate groups. In the presence of air or H2O2, cleavage of the tetrapyrrole ring occurs, and hematinic acid is formed. The highest stability of heme was observed under anaerobic reductive conditions (half-life 9.5 days), while the lowest stability was found in the presence of H2O2 (half-life 1 min). We confirmed that the iron cation plays a crucial role in degradation, since protoporphyrin IX, lacking iron, remained significantly more stable. Under anaerobic, reductive conditions, the above-mentioned degradation products were not observed, suggesting a different degradation pathway. To our knowledge, this is the first molecular taphonomy study on heme, which will be useful for understanding its fate during fossilization.
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Affiliation(s)
- Mariam Tahoun
- PharmaCenter Bonn & Pharmaceutical Institute, Department of Pharmaceutical & Medicinal Chemistry, University of Bonn, An der Immenburg 4, 53121 Bonn, Germany
| | - Marianne Engeser
- Kekulé Institute for Organic Chemistry and Biochemistry, University of Bonn, 53121 Bonn, Germany
| | - Luca Svolacchia
- PharmaCenter Bonn & Pharmaceutical Institute, Department of Pharmaceutical & Medicinal Chemistry, University of Bonn, An der Immenburg 4, 53121 Bonn, Germany
| | - Paul Martin Sander
- Section Paleontology, Institute of Geosciences, University of Bonn, 53115 Bonn, Germany
| | - Christa E Müller
- PharmaCenter Bonn & Pharmaceutical Institute, Department of Pharmaceutical & Medicinal Chemistry, University of Bonn, An der Immenburg 4, 53121 Bonn, Germany
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3
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Scaramanga J, Reiss MJ. Evolutionary stasis: creationism, evolution and climate change in the Accelerated Christian Education curriculum. CULTURAL STUDIES OF SCIENCE EDUCATION 2023; 18:1-19. [PMID: 37360053 PMCID: PMC10191816 DOI: 10.1007/s11422-023-10187-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/31/2022] [Accepted: 03/29/2023] [Indexed: 06/28/2023]
Abstract
There has been little consideration in the science education literature of schools or curricula that advocate creationism. Accelerated Christian Education (ACE) is among the world's largest providers of creationist science materials with a curriculum divided into a system of workbooks which students complete at their own speed. This article examines the ways in which ACE presents particular areas of science that it considers to be contentious, namely evolution and climate change. The ACE curriculum has recently been rewritten, and we show that, like previous editions, the current curriculum relies on rote memorisation to the exclusion of other styles of learning, and that information presented is often misleading or distorted. Religious explanations of natural phenomena are sometimes given in place of scientific ones, and creationist assumptions are inserted into lessons not directly related to evolution or the Big Bang. Those who reject creationism are depicted as making an immoral choice. ACE's recent curricula also add material denying the role of humans in climate change. It is argued that both the teaching methods and content of the ACE curriculum place students at an educational disadvantage.
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Umamaheswaran R, Dutta S, Prasad GVR, Khan MA, Kumar S, Bera S, Patnaik R. The diagenetic fate of collagen as revealed by analytical pyrolysis of fossil fish scales from deep time. GEOBIOLOGY 2023; 21:378-389. [PMID: 36529852 DOI: 10.1111/gbi.12537] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/09/2022] [Revised: 11/30/2022] [Accepted: 12/03/2022] [Indexed: 06/17/2023]
Abstract
The mechanism of protein degradation has remained a topic of debate (specifically concerning their preservation in deep time), which has recently been invigorated due to multiple published reports of preservation ranging from Miocene to the Triassic that potentially challenge the convention that protein preservation beyond the Cenozoic is extremely uncommon or is expected to be absent altogether, and thus have attracted skepticism. In this paper, we analyze fossil fish scales from the Cretaceous, Jurassic, and Triassic using comprehensive pyrolysis gas chromatography coupled with time-of-flight mass spectrometry and compare the pyrolytic products so obtained with a well-preserved fish scale from Late Pliocene, in an attempt to better understand the effects of diagenesis on protein degradation at the molecular level through deep time. We find that the Pliocene fish scale displays a large number of N-bearing pyrolytic products, including abundant substituted cyclic 2,5-diketopiperazines (2,5-DKPs) which are diagnostic products of peptide and amino acid pyrolysis. We identify N-bearing compounds in the Mesozoic fish scales-however, among the 2,5-DKPs that were identified in the Pliocene scale, only diketodipyrrole (or cyclo (Pyr-Pyr)) is present in the Mesozoic scales. We discuss the implications of N-bearing pyrolytic products with emphasis on 2,5-DKPs in geological samples and conclude that the discrepancy in abundance and variety of N-bearing products between Pliocene and Mesozoic scales indicates that the protein component in the latter has been extensively diagenetically altered, while a suite of DKPs such as in the former would imply stronger evidence to indicate preservation of protein. We conclude that analytical pyrolysis is an effective tool for detecting preservation of intact proteins, as well as for providing insights into their degradation mechanisms, and can potentially be utilized to assign proteinaceous origin to a fossil sample of unknown affinity.
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Affiliation(s)
- Raman Umamaheswaran
- Department of Earth Sciences, Indian Institute of Technology Bombay, Mumbai, India
| | - Suryendu Dutta
- Department of Earth Sciences, Indian Institute of Technology Bombay, Mumbai, India
| | - Guntupalli V R Prasad
- Department of Geology, Centre for Advanced Studies, University of Delhi, New Delhi, India
| | - Mahasin Ali Khan
- Department of Botany, Siddho-Kanho-Birsa University, Purulia, India
| | - Sumit Kumar
- Department of Earth Sciences, Indian Institute of Technology Bombay, Mumbai, India
| | - Subir Bera
- Department of Botany, University of Calcutta, Kolkata, India
| | - Rajeev Patnaik
- Department of Geology, Panjab University, Chandigarh, India
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De La Garza RG, Madsen H, Sjövall P, Osbӕck F, Zheng W, Jarenmark M, Schweitzer MH, Engdahl A, Uvdal P, Eriksson ME, Lindgren J. An ancestral hard-shelled sea turtle with a mosaic of soft skin and scutes. Sci Rep 2022; 12:22655. [PMID: 36587051 PMCID: PMC9805447 DOI: 10.1038/s41598-022-26941-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/20/2022] [Accepted: 12/22/2022] [Indexed: 01/01/2023] Open
Abstract
The transition from terrestrial to marine environments by secondarily aquatic tetrapods necessitates a suite of adaptive changes associated with life in the sea, e.g., the scaleless skin in adult individuals of the extant leatherback turtle. A partial, yet exceptionally preserved hard-shelled (Pan-Cheloniidae) sea turtle with extensive soft-tissue remains, including epidermal scutes and a virtually complete flipper outline, was recently recovered from the Eocene Fur Formation of Denmark. Examination of the fossilized limb tissue revealed an originally soft, wrinkly skin devoid of scales, together with organic residues that contain remnant eumelanin pigment and inferred epidermal transformation products. Notably, this stem cheloniid-unlike its scaly living descendants-combined scaleless limbs with a bony carapace covered in scutes. Our findings show that the adaptive transition to neritic waters by the ancestral pan-chelonioids was more complex than hitherto appreciated, and included at least one evolutionary lineage with a mosaic of integumental features not seen in any living turtle.
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Affiliation(s)
| | | | - Peter Sjövall
- grid.450998.90000 0004 0438 1242Materials and Production, RISE Research Institutes of Sweden, Borås, Sweden
| | - Frank Osbӕck
- grid.502431.10000 0004 4914 0813Museum Salling, Fur Museum, Skive, Denmark
| | - Wenxia Zheng
- grid.40803.3f0000 0001 2173 6074Department of Biological Sciences, North Carolina State University, Raleigh, NC USA
| | - Martin Jarenmark
- grid.4514.40000 0001 0930 2361Department of Geology, Lund University, Lund, Sweden
| | - Mary H. Schweitzer
- grid.4514.40000 0001 0930 2361Department of Geology, Lund University, Lund, Sweden ,grid.40803.3f0000 0001 2173 6074Department of Biological Sciences, North Carolina State University, Raleigh, NC USA ,grid.421582.80000 0001 2226 059XNorth Carolina Museum of Natural Sciences, Raleigh, NC USA
| | - Anders Engdahl
- grid.4514.40000 0001 0930 2361Medical Microspectroscopy, Biomedical Center, Lund University, Lund, Sweden
| | - Per Uvdal
- grid.4514.40000 0001 0930 2361Department of Chemistry, Lund University, Lund, Sweden
| | - Mats E. Eriksson
- grid.4514.40000 0001 0930 2361Department of Geology, Lund University, Lund, Sweden
| | - Johan Lindgren
- grid.4514.40000 0001 0930 2361Department of Geology, Lund University, Lund, Sweden
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6
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Anderson LA. Biomolecular histology as a novel proxy for ancient DNA and protein sequence preservation. Ecol Evol 2022; 12:e9518. [PMCID: PMC9743065 DOI: 10.1002/ece3.9518] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/04/2022] [Revised: 10/03/2022] [Accepted: 10/17/2022] [Indexed: 12/14/2022] Open
Abstract
Researchers' ability to accurately screen fossil and subfossil specimens for preservation of DNA and protein sequences remains limited. Thermal exposure and geologic age are usable proxies for sequence preservation on a broad scale but are of nominal use for specimens of similar depositional environments. Cell and tissue biomolecular histology is thus proposed as a novel proxy for determining sequence preservation potential of ancient specimens with improved accuracy. Biomolecular histology as a proxy is hypothesized to elucidate why fossils/subfossils of some depositional environments preserve sequences while others do not and to facilitate selection of ancient specimens for use in molecular studies.
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Affiliation(s)
- Landon A. Anderson
- Department of BiologyNorth Carolina State UniversityRaleighNorth CarolinaUSA
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7
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Drvenica IT, Stančić AZ, Maslovarić IS, Trivanović DI, Ilić VL. Extracellular Hemoglobin: Modulation of Cellular Functions and Pathophysiological Effects. Biomolecules 2022; 12:1708. [PMID: 36421721 PMCID: PMC9688122 DOI: 10.3390/biom12111708] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/29/2022] [Revised: 11/08/2022] [Accepted: 11/15/2022] [Indexed: 08/05/2023] Open
Abstract
Hemoglobin is essential for maintaining cellular bioenergetic homeostasis through its ability to bind and transport oxygen to the tissues. Besides its ability to transport oxygen, hemoglobin within erythrocytes plays an important role in cellular signaling and modulation of the inflammatory response either directly by binding gas molecules (NO, CO, and CO2) or indirectly by acting as their source. Once hemoglobin reaches the extracellular environment, it acquires several secondary functions affecting surrounding cells and tissues. By modulating the cell functions, this macromolecule becomes involved in the etiology and pathophysiology of various diseases. The up-to-date results disclose the impact of extracellular hemoglobin on (i) redox status, (ii) inflammatory state of cells, (iii) proliferation and chemotaxis, (iv) mitochondrial dynamic, (v) chemoresistance and (vi) differentiation. This review pays special attention to applied biomedical research and the use of non-vertebrate and vertebrate extracellular hemoglobin as a promising candidate for hemoglobin-based oxygen carriers, as well as cell culture medium additive. Although recent experimental settings have some limitations, they provide additional insight into the modulatory activity of extracellular hemoglobin in various cellular microenvironments, such as stem or tumor cells niches.
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Affiliation(s)
- Ivana T. Drvenica
- Group for Immunology, Institute for Medical Research, National Institute of Republic of Serbia, University of Belgrade, 11129 Belgrade, Serbia
| | - Ana Z. Stančić
- Group for Immunology, Institute for Medical Research, National Institute of Republic of Serbia, University of Belgrade, 11129 Belgrade, Serbia
| | - Irina S. Maslovarić
- Group for Immunology, Institute for Medical Research, National Institute of Republic of Serbia, University of Belgrade, 11129 Belgrade, Serbia
| | - Drenka I. Trivanović
- Group for Hematology and Stem Cells, Institute for Medical Research, National Institute of Republic of Serbia, University of Belgrade, 11129 Belgrade, Serbia
| | - Vesna Lj. Ilić
- Group for Immunology, Institute for Medical Research, National Institute of Republic of Serbia, University of Belgrade, 11129 Belgrade, Serbia
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8
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Taphonomic and Diagenetic Pathways to Protein Preservation, Part II: The Case of Brachylophosaurus canadensis Specimen MOR 2598. BIOLOGY 2022; 11:biology11081177. [PMID: 36009804 PMCID: PMC9404959 DOI: 10.3390/biology11081177] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 06/14/2022] [Revised: 07/31/2022] [Accepted: 08/03/2022] [Indexed: 11/25/2022]
Abstract
Simple Summary Reports of the recovery of proteins and other molecules from fossils have become so common over the last two decades that some paleontologists now focus almost entirely on studying how biologic molecules can persist in fossils. In this study, we explored the fossilization history of a specimen of the hadrosaurid dinosaur Brachylophosaurus which was previously shown to preserve original cells, tissues, and structural proteins. Trace element analyses of the tibia of this specimen revealed that after its bones were buried in a brackish estuarine channel, they fossilized under wet conditions which shifted in redox state multiple times. The successful recovery of proteins from this specimen, despite this complex history of chemical alterations, shows that the processes which bind and stabilize biologic molecules shortly after death provide them remarkable physical and chemical resiliency. By uniting our results with those of similar studies on other dinosaur fossils known to also preserve original proteins, we also conclude that exposure to oxidizing conditions in the initial ~48 h postmortem likely promotes molecular stabilization reactions, and the retention of early-diagenetic trace element signatures may be a useful proxy for molecular recovery potential. Abstract Recent recoveries of peptide sequences from two Cretaceous dinosaur bones require paleontologists to rethink traditional notions about how fossilization occurs. As part of this shifting paradigm, several research groups have recently begun attempting to characterize biomolecular decay and stabilization pathways in diverse paleoenvironmental and diagenetic settings. To advance these efforts, we assessed the taphonomic and geochemical history of Brachylophosaurus canadensis specimen MOR 2598, the left femur of which was previously found to retain endogenous cells, tissues, and structural proteins. Combined stratigraphic and trace element data show that after brief fluvial transport, this articulated hind limb was buried in a sandy, likely-brackish, estuarine channel. During early diagenesis, percolating groundwaters stagnated within the bones, forming reducing internal microenvironments. Recent exposure and weathering also caused the surficial leaching of trace elements from the specimen. Despite these shifting redox regimes, proteins within the bones were able to survive through diagenesis, attesting to their remarkable resiliency over geologic time. Synthesizing our findings with other recent studies reveals that oxidizing conditions in the initial ~48 h postmortem likely promote molecular stabilization reactions and that the retention of early-diagenetic trace element signatures may be a useful proxy for molecular recovery potential.
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Soft Tissue and Biomolecular Preservation in Vertebrate Fossils from Glauconitic, Shallow Marine Sediments of the Hornerstown Formation, Edelman Fossil Park, New Jersey. BIOLOGY 2022; 11:biology11081161. [PMID: 36009787 PMCID: PMC9405258 DOI: 10.3390/biology11081161] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 06/18/2022] [Revised: 07/18/2022] [Accepted: 07/22/2022] [Indexed: 11/17/2022]
Abstract
Endogenous biomolecules and soft tissues are known to persist in the fossil record. To date, these discoveries derive from a limited number of preservational environments, (e.g., fluvial channels and floodplains), and fossils from less common depositional environments have been largely unexplored. We conducted paleomolecular analyses of shallow marine vertebrate fossils from the Cretaceous–Paleogene Hornerstown Formation, an 80–90% glauconitic greensand from Jean and Ric Edelman Fossil Park in Mantua Township, NJ. Twelve samples were demineralized and found to yield products morphologically consistent with vertebrate osteocytes, blood vessels, and bone matrix. Specimens from these deposits that are dark in color exhibit excellent histological preservation and yielded a greater recovery of cells and soft tissues, whereas lighter-colored specimens exhibit poor histology and few to no cells/soft tissues. Additionally, a well-preserved femur of the marine crocodilian Thoracosaurus was found to have retained endogenous collagen I by immunofluorescence and enzyme-linked immunosorbent assays. Our results thus not only corroborate previous findings that soft tissue and biomolecular recovery from fossils preserved in marine environments are possible but also expand the range of depositional environments documented to preserve endogenous biomolecules, thus broadening the suite of geologic strata that may be fruitful to examine in future paleomolecular studies.
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Soft-Tissue, Rare Earth Element, and Molecular Analyses of Dreadnoughtus schrani, an Exceptionally Complete Titanosaur from Argentina. BIOLOGY 2022; 11:biology11081158. [PMID: 36009785 PMCID: PMC9404821 DOI: 10.3390/biology11081158] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 06/30/2022] [Revised: 07/27/2022] [Accepted: 07/31/2022] [Indexed: 11/22/2022]
Abstract
Evidence that organic material preserves in deep time (>1 Ma) has been reported using a wide variety of analytical techniques. However, the comprehensive geochemical data that could aid in building robust hypotheses for how soft-tissues persist over millions of years are lacking from most paleomolecular reports. Here, we analyze the molecular preservation and taphonomic history of the Dreadnougtus schrani holotype (MPM-PV 1156) at both macroscopic and microscopic levels. We review the stratigraphy, depositional setting, and physical taphonomy of the D. schrani skeletal assemblage, and extensively characterize the preservation and taphonomic history of the humerus at a micro-scale via: (1) histological analysis (structural integrity) and X-ray diffraction (exogenous mineral content); (2) laser ablation-inductively coupled plasma mass spectrometry (analyses of rare earth element content throughout cortex); (3) demineralization and optical microscopy (soft-tissue microstructures); (4) in situ and in-solution immunological assays (presence of endogenous protein). Our data show the D. schrani holotype preserves soft-tissue microstructures and remnants of endogenous bone protein. Further, it was exposed to LREE-enriched groundwaters and weakly-oxidizing conditions after burial, but experienced negligible further chemical alteration after early-diagenetic fossilization. These findings support previous hypotheses that fossils that display low trace element uptake are favorable targets for paleomolecular analyses.
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Tahoun M, Engeser M, Namasivayam V, Sander PM, Müller CE. Chemistry and Analysis of Organic Compounds in Dinosaurs. BIOLOGY 2022; 11:670. [PMID: 35625398 PMCID: PMC9138232 DOI: 10.3390/biology11050670] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 03/20/2022] [Revised: 04/12/2022] [Accepted: 04/22/2022] [Indexed: 11/17/2022]
Abstract
This review provides an overview of organic compounds detected in non-avian dinosaur fossils to date. This was enabled by the development of sensitive analytical techniques. Non-destructive methods and procedures restricted to the sample surface, e.g., light and electron microscopy, infrared (IR) and Raman spectroscopy, as well as more invasive approaches including liquid chromatography coupled to tandem mass spectrometry (LC-MS/MS), time-of-flight secondary ion mass spectrometry, and immunological methods were employed. Organic compounds detected in samples of dinosaur fossils include pigments (heme, biliverdin, protoporphyrin IX, melanin), and proteins, such as collagens and keratins. The origin and nature of the observed protein signals is, however, in some cases, controversially discussed. Molecular taphonomy approaches can support the development of suitable analytical methods to confirm reported findings and to identify further organic compounds in dinosaur and other fossils in the future. The chemical properties of the various organic compounds detected in dinosaurs, and the techniques utilized for the identification and analysis of each of the compounds will be discussed.
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Affiliation(s)
- Mariam Tahoun
- PharmaCenter Bonn, Pharmaceutical Institute, Pharmaceutical & Medicinal Chemistry, University of Bonn, D-53121 Bonn, Germany; (M.T.); (V.N.)
| | - Marianne Engeser
- Kekulé Institute for Organic Chemistry and Biochemistry, University of Bonn, D-53121 Bonn, Germany;
| | - Vigneshwaran Namasivayam
- PharmaCenter Bonn, Pharmaceutical Institute, Pharmaceutical & Medicinal Chemistry, University of Bonn, D-53121 Bonn, Germany; (M.T.); (V.N.)
| | - Paul Martin Sander
- Institute of Geosciences, Section Paleontology, University of Bonn, D-53113 Bonn, Germany;
| | - Christa E. Müller
- PharmaCenter Bonn, Pharmaceutical Institute, Pharmaceutical & Medicinal Chemistry, University of Bonn, D-53121 Bonn, Germany; (M.T.); (V.N.)
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12
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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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13
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Zheng X, Bailleul AM, Li Z, Wang X, Zhou Z. Nuclear preservation in the cartilage of the Jehol dinosaur Caudipteryx. Commun Biol 2021; 4:1125. [PMID: 34561538 PMCID: PMC8463611 DOI: 10.1038/s42003-021-02627-8] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/21/2021] [Accepted: 08/31/2021] [Indexed: 11/23/2022] Open
Abstract
Previous findings on dinosaur cartilage material from the Late Cretaceous of Montana suggested that cartilage is a vertebrate tissue with unique characteristics that favor nuclear preservation. Here, we analyze additional dinosaur cartilage in Caudipteryx (STM4-3) from the Early Cretaceous Jehol biota of Northeast China. The cartilage fragment is highly diagenetically altered when observed in ground-sections but shows exquisite preservation after demineralization. It reveals transparent, alumino-silicified chondrocytes and brown, ironized chondrocytes. The histochemical stain Hematoxylin and Eosin (that stains the nucleus and cytoplasm in extant cells) was applied to both the demineralized cartilage of Caudipteryx and that of a chicken. The two specimens reacted identically, and one dinosaur chondrocyte revealed a nucleus with fossilized threads of chromatin. This is the second example of fossilized chromatin threads in a vertebrate material. These data show that some of the original nuclear biochemistry is preserved in this dinosaur cartilage material and further support the hypothesis that cartilage is very prone to nuclear fossilization and a perfect candidate to further understand DNA preservation in deep time.
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Affiliation(s)
- Xiaoting Zheng
- Institute of Geology and Paleontology, Linyi University, Linyi City, Shandong, 276005, China
- Shandong Tianyu Museum of Nature, Pingyi, Shandong, 273300, China
| | - Alida M Bailleul
- Key Laboratory of Vertebrate Evolution and Human Origins, Institute of Vertebrate Paleontology and Paleoanthropology, 142 Xizhimenwai dajie, Beijing, 100044, China.
- CAS Center for Excellence in Life and Paleoenvironment, Beijing, 100044, China.
| | - Zhiheng Li
- Key Laboratory of Vertebrate Evolution and Human Origins, Institute of Vertebrate Paleontology and Paleoanthropology, 142 Xizhimenwai dajie, Beijing, 100044, China
- CAS Center for Excellence in Life and Paleoenvironment, Beijing, 100044, China
| | - Xiaoli Wang
- Institute of Geology and Paleontology, Linyi University, Linyi City, Shandong, 276005, China
- Shandong Tianyu Museum of Nature, Pingyi, Shandong, 273300, China
| | - Zhonghe Zhou
- Key Laboratory of Vertebrate Evolution and Human Origins, Institute of Vertebrate Paleontology and Paleoanthropology, 142 Xizhimenwai dajie, Beijing, 100044, China
- CAS Center for Excellence in Life and Paleoenvironment, Beijing, 100044, China
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14
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Cadena EA. In situ SEM/EDS compositional characterization of osteocytes and blood vessels in fossil and extant turtles on untreated bone surfaces; different preservational pathways microns away. PeerJ 2020; 8:e9833. [PMID: 32913685 PMCID: PMC7456530 DOI: 10.7717/peerj.9833] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/03/2020] [Accepted: 08/07/2020] [Indexed: 11/20/2022] Open
Abstract
Osteocytes and blood vessels are the main cellular and tissue components of the bone tissue of vertebrates. Evidence of these soft-tissue microstructures has been widely documented in the fossil record of Mesozoic and Cenozoic turtles. However, all these studies have characterized morphologically and elementally these microstructures via isolation from the fossilized bone matrix where they were preserved or in ground sections, which could raise skepticism about the results due to potential cross-contamination or reagents effects. Fossil turtle bones from three different localities with distinct preservation environments and geological settings, including Mongolemys elegans from the Late Cretaceous of Mongolia, Allaeochelys crassesculpta from the Eocene of Germany, and a podocnemidid indet. from the Miocene of Colombia are studied here. Bone from two extant turtle species, Lepidochelys olivacea, and Podocnemis lewyana, as well as a commercial chicken Gallus gallus were used for comparisons. Scanning Electron Microscopy-Energy Dispersive Spectroscopy analyses performed directly on untreated fresh surfaces show that osteocytes-like in the fossil turtle bone are mostly composed of iron and manganese. In contrast, the in situ blood vessels-like of the fossil turtles, as well as those from the extant taxa are rich in elements typically organic in origin (carbon and nitrogen), which are absent to minimally present in the surrounding bone or rock matrix; this suggests a possible endogenous composition for these fossil structures. Also, the results presented here show that although originally both (osteocytes and blood vessels) are organic soft components of bone as evidenced in the extant turtles and chicken, they can experience completely different preservational pathways only microns away from each other in the same fossil bone.
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Affiliation(s)
- Edwin-Alberto Cadena
- Facultad de Ciencias Naturales, Grupo de Investigación Paleontología Neotropical Tradicional y Molecular (PaleoNeo), Universidad del Rosario, Bogotá, Colombia
- Smithsonian Tropical Research Institute, Panama City, Panama
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15
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Bailleul AM, O'Connor J, Li Z, Wu Q, Zhao T, Martinez Monleon MA, Wang M, Zheng X. Confirmation of ovarian follicles in an enantiornithine (Aves) from the Jehol biota using soft tissue analyses. Commun Biol 2020; 3:399. [PMID: 32724075 PMCID: PMC7387556 DOI: 10.1038/s42003-020-01131-9] [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: 02/11/2020] [Accepted: 07/07/2020] [Indexed: 11/30/2022] Open
Abstract
The remains of ovarian follicles reported in nine specimens of basal birds represents one of the most remarkable examples of soft-tissue preservation in the Early Cretaceous Jehol Biota. This discovery was immediately contested and the structures alternatively interpreted as ingested seeds. Fragments of the purported follicles preserved in an enantiornithine (STM10-12) were extracted and subjected to multiple high-resolution analyses. The structures in STM10-12 possess the histological and histochemical characteristics of smooth muscles fibers intertwined together with collagen fibers, resembling the contractile structure in the perifollicular membrane (PFM) of living birds. Fossilized blood vessels, very abundant in extant PFMs, are also preserved. Energy Dispersive Spectroscopy shows the preserved tissues primarily underwent alumino-silicification, with minor mineralization via iron oxides. No evidence of plant tissue was found. These results confirm the original interpretation as follicles within the left ovary, supporting the interpretation that the right ovary was functionally lost early in avian evolution. Bailleul et al. employ histology, histochemistry and Energy Dispersive Spectroscopy to confirm the presence of disputed ovarian follicles in a specimen of fossil Cretaceous bird. These findings have implications for the evolution of the avian breeding system seen in birds today.
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Affiliation(s)
- Alida M Bailleul
- Key Laboratory of Vertebrate Evolution and Human Origins, Institute of Vertebrate Paleontology and Paleoanthropology, Chinese Academy of Sciences, 100044, Beijing, China. .,CAS Center for Excellence in Life and Paleoenvironment, 100044, Beijing, China.
| | - Jingmai O'Connor
- Key Laboratory of Vertebrate Evolution and Human Origins, Institute of Vertebrate Paleontology and Paleoanthropology, Chinese Academy of Sciences, 100044, Beijing, China.,CAS Center for Excellence in Life and Paleoenvironment, 100044, Beijing, China
| | - Zhiheng Li
- Key Laboratory of Vertebrate Evolution and Human Origins, Institute of Vertebrate Paleontology and Paleoanthropology, Chinese Academy of Sciences, 100044, Beijing, China.,CAS Center for Excellence in Life and Paleoenvironment, 100044, Beijing, China
| | - Qian Wu
- Key Laboratory of Vertebrate Evolution and Human Origins, Institute of Vertebrate Paleontology and Paleoanthropology, Chinese Academy of Sciences, 100044, Beijing, China.,CAS Center for Excellence in Life and Paleoenvironment, 100044, Beijing, China
| | - Tao Zhao
- State Key Laboratory of Palaeobiology and Stratigraphy, Nanjing Institute of Geology and Paleontology, Chinese Academy of Sciences, 210008, Nanjing, China
| | | | - Min Wang
- Key Laboratory of Vertebrate Evolution and Human Origins, Institute of Vertebrate Paleontology and Paleoanthropology, Chinese Academy of Sciences, 100044, Beijing, China.,CAS Center for Excellence in Life and Paleoenvironment, 100044, Beijing, China
| | - Xiaoting Zheng
- Institute of Geology and Paleontology, Linyi University, 276005, Linyi City, Shandong, China.,Shandong Tianyu Museum of Nature, 273300, Linyi City, Shandong, China
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16
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Alfonso-Rojas A, Cadena EA. Exceptionally preserved 'skin' in an Early Cretaceous fish from Colombia. PeerJ 2020; 8:e9479. [PMID: 32714661 PMCID: PMC7353916 DOI: 10.7717/peerj.9479] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/04/2020] [Accepted: 06/14/2020] [Indexed: 01/13/2023] Open
Abstract
Studies of soft tissue, cells and original biomolecular constituents preserved in fossil vertebrates have increased greatly in recent years. Here we report preservation of 'skin' with chemical and molecular characterization from a three-dimensionally preserved caudal portion of an aspidorhynchid Cretaceous fish from the equatorial Barremian of Colombia, increasing the number of localities for which exceptional preservation is known. We applied several analytical techniques including SEM-EDS, FTIR and ToF-SIMS to characterize the micromorphology and molecular and elemental composition of this fossil. Here, we show that the fossilized 'skin' exhibits similarities with those from extant fish, including the wrinkles after suffering compression stress and flexibility, as well as architectural and tissue aspects of the two main layers (epidermis and dermis). This similarity extends also to the molecular level, with the demonstrated preservation of potential residues of original proteins not consistent with a bacterial source. Our results show a potential preservation mechanism where scales may have acted as an external barrier and together with an internal phosphate layer resulting from the degradation of the dermis itself creating an encapsulated environment for the integument.
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Affiliation(s)
- Andrés Alfonso-Rojas
- Facultad de Ciencias Naturales, Grupo de Investigación Paleontología Neotropical Tradicional y Molecular (PaleoNeo), Universidad del Rosario, Bogotá, Colombia
| | - Edwin-Alberto Cadena
- Facultad de Ciencias Naturales, Grupo de Investigación Paleontología Neotropical Tradicional y Molecular (PaleoNeo), Universidad del Rosario, Bogotá, Colombia
- Smithsonian Tropical Research Institute, Panama City, Panama
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17
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Liang R, Lau MCY, Saitta ET, Garvin ZK, Onstott TC. Genome-centric resolution of novel microbial lineages in an excavated Centrosaurus dinosaur fossil bone from the Late Cretaceous of North America. ENVIRONMENTAL MICROBIOME 2020; 15:8. [PMID: 33902738 PMCID: PMC8067395 DOI: 10.1186/s40793-020-00355-w] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 02/23/2020] [Accepted: 02/27/2020] [Indexed: 06/12/2023]
Abstract
BACKGROUND Exceptional preservation of endogenous organics such as collagens and blood vessels has been frequently reported in Mesozoic dinosaur fossils. The persistence of these soft tissues in Mesozoic fossil bones has been challenged because of the susceptibility of proteins to degradation and because bone porosity allows microorganisms to colonize the inner microenvironments through geological time. Although protein lability has been studied extensively, the genomic diversity of microbiomes in dinosaur fossil bones and their potential roles in bone taphonomy remain underexplored. Genome-resolved metagenomics was performed, therefore, on the microbiomes recovered from a Late Cretaceous Centrosaurus bone and its encompassing mudstone in order to provide insight into the genomic potential for microbial alteration of fossil bone. RESULTS Co-assembly and binning of metagenomic reads resulted in a total of 46 high-quality metagenome-assembled genomes (MAGs) affiliated to six bacterial phyla (Actinobacteria, Proteobacteria, Nitrospira, Acidobacteria, Gemmatimonadetes and Chloroflexi) and 1 archaeal phylum (Thaumarchaeota). The majority of the MAGs represented uncultivated, novel microbial lineages from class to species levels based on phylogenetics, phylogenomics and average amino acid identity. Several MAGs from the classes Nitriliruptoria, Deltaproteobacteria and Betaproteobacteria were highly enriched in the bone relative to the adjacent mudstone. Annotation of the MAGs revealed that the distinct putative metabolic functions of different taxonomic groups were linked to carbon, nitrogen, sulfur and iron metabolism. Metaproteomics revealed gene expression from many of the MAGs, but no endogenous collagen peptides were identified in the bone that could have been derived from the dinosaur. Estimated in situ replication rates among the bacterial MAGs suggested that most of the microbial populations in the bone might have been actively growing but at a slow rate. CONCLUSIONS Our results indicate that excavated dinosaur bones are habitats for microorganisms including novel microbial lineages. The distinctive microhabitats and geochemistry of fossil bone interiors compared to that of the external sediment enrich a microbial biomass comprised of various novel taxa that harbor multiple gene sets related to interconnected biogeochemical processes. Therefore, the presence of these microbiomes in Mesozoic dinosaur fossils urges extra caution to be taken in the science of paleontology when hunting for endogenous biomolecules preserved from deep time.
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Affiliation(s)
- Renxing Liang
- Department of Geosciences, Princeton University, B88, Guyot Hall, Princeton University, Princeton, NJ, 08544, USA.
| | - Maggie C Y Lau
- Department of Geosciences, Princeton University, B88, Guyot Hall, Princeton University, Princeton, NJ, 08544, USA
- Present address: Institute of Deep-Sea Science and Engineering, Chinese Academy of Sciences, Sanya, China
| | - Evan T Saitta
- Integrative Research Center, Section of Earth Sciences, Field Museum of Natural History, Chicago, USA
| | - Zachary K Garvin
- Department of Geosciences, Princeton University, B88, Guyot Hall, Princeton University, Princeton, NJ, 08544, USA
| | - Tullis C Onstott
- Department of Geosciences, Princeton University, B88, Guyot Hall, Princeton University, Princeton, NJ, 08544, USA
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18
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Bailleul AM, Zheng W, Horner JR, Hall BK, Holliday CM, Schweitzer MH. Evidence of proteins, chromosomes and chemical markers of DNA in exceptionally preserved dinosaur cartilage. Natl Sci Rev 2020; 7:815-822. [PMID: 34692099 PMCID: PMC8289162 DOI: 10.1093/nsr/nwz206] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/11/2019] [Revised: 01/09/2020] [Accepted: 01/10/2020] [Indexed: 01/13/2023] Open
Abstract
A histological ground-section from a duck-billed dinosaur nestling (Hypacrosaurus stebingeri) revealed microstructures morphologically consistent with nuclei and chromosomes in cells within calcified cartilage. We hypothesized that this exceptional cellular preservation extended to the molecular level and had molecular features in common with extant avian cartilage. Histochemical and immunological evidence supports in situ preservation of extracellular matrix components found in extant cartilage, including glycosaminoglycans and collagen type II. Furthermore, isolated Hypacrosaurus chondrocytes react positively with two DNA intercalating stains. Specific DNA staining is only observed inside the isolated cells, suggesting endogenous nuclear material survived fossilization. Our data support the hypothesis that calcified cartilage is preserved at the molecular level in this Mesozoic material, and suggest that remnants of once-living chondrocytes, including their DNA, may preserve for millions of years.
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Affiliation(s)
- Alida M Bailleul
- Key Laboratory of Vertebrate Evolution and Human Origins, Institute of Vertebrate Paleontology and Paleoanthropology, Chinese Academy of Sciences, Beijing 100044, China
- CAS Center for Excellence in Life and Paleoenvironment, Beijing 100044, China
| | - Wenxia Zheng
- Department of Biological Sciences, North Carolina State University, Raleigh, NC 27695, USA
| | - John R Horner
- Honors Program, Chapman University, Orange, CA 92866, USA
| | - Brian K Hall
- Department of Biology, Dalhousie University, Halifax, B3H 4R2, Canada
| | - Casey M Holliday
- Department of Pathology and Anatomical Sciences, University of Missouri, Columbia, MO 65211, USA
| | - Mary H Schweitzer
- Department of Biological Sciences, North Carolina State University, Raleigh, NC 27695, USA
- North Carolina Museum of Natural Sciences, Raleigh, NC 27601, USA
- Department of Geology, University of Lund, 22362, Sweden
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19
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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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20
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Boatman EM, Goodwin MB, Holman HYN, Fakra S, Zheng W, Gronsky R, Schweitzer MH. Mechanisms of soft tissue and protein preservation in Tyrannosaurus rex. Sci Rep 2019; 9:15678. [PMID: 31666554 PMCID: PMC6821828 DOI: 10.1038/s41598-019-51680-1] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/02/2018] [Accepted: 09/29/2019] [Indexed: 01/08/2023] Open
Abstract
The idea that original soft tissue structures and the native structural proteins comprising them can persist across geological time is controversial, in part because rigorous and testable mechanisms that can occur under natural conditions, resulting in such preservation, have not been well defined. Here, we evaluate two non-enzymatic structural protein crosslinking mechanisms, Fenton chemistry and glycation, for their possible contribution to the preservation of blood vessel structures recovered from the cortical bone of a Tyrannosaurus rex (USNM 555000 [formerly, MOR 555]). We demonstrate the endogeneity of the fossil vessel tissues, as well as the presence of type I collagen in the outermost vessel layers, using imaging, diffraction, spectroscopy, and immunohistochemistry. Then, we use data derived from synchrotron FTIR studies of the T. rex vessels to analyse their crosslink character, with comparison against two non-enzymatic Fenton chemistry- and glycation-treated extant chicken samples. We also provide supporting X-ray microprobe analyses of the chemical state of these fossil tissues to support our conclusion that non-enzymatic crosslinking pathways likely contributed to stabilizing, and thus preserving, these T. rex vessels. Finally, we propose that these stabilizing crosslinks could play a crucial role in the preservation of other microvascular tissues in skeletal elements from the Mesozoic.
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Affiliation(s)
- Elizabeth M Boatman
- Department of Engineering, Wake Forest University, Winston Salem, NC, 27101, USA.
| | - Mark B Goodwin
- Museum of Paleontology, University of California, Berkeley, CA, 94720, USA
| | - Hoi-Ying N Holman
- Advanced Light Source, Lawrence Berkeley National Laboratory, Berkeley, CA, 94720, USA
| | - Sirine Fakra
- Advanced Light Source, Lawrence Berkeley National Laboratory, Berkeley, CA, 94720, USA
| | - Wenxia Zheng
- Department of Biological Sciences, North Carolina State University, Raleigh, NC, 27695, USA
| | - Ronald Gronsky
- Department of Materials Science and Engineering, University of California, Berkeley, CA, 94720, USA
| | - Mary H Schweitzer
- Department of Biological Sciences, North Carolina State University, Raleigh, NC, 27695, USA.,Department of Geology, Lund University, Lund, Sweden.,North Carolina Museum of Natural Sciences, Raleigh, NC, 27601, USA.,Museum of the Rockies, Montana State University, Bozeman, MT, 59715, USA
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21
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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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22
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Bailleul AM, O’Connor J, Schweitzer MH. Dinosaur paleohistology: review, trends and new avenues of investigation. PeerJ 2019; 7:e7764. [PMID: 31579624 PMCID: PMC6768056 DOI: 10.7717/peerj.7764] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/07/2019] [Accepted: 08/26/2019] [Indexed: 12/12/2022] Open
Abstract
In the mid-19th century, the discovery that bone microstructure in fossils could be preserved with fidelity provided a new avenue for understanding the evolution, function, and physiology of long extinct organisms. This resulted in the establishment of paleohistology as a subdiscipline of vertebrate paleontology, which has contributed greatly to our current understanding of dinosaurs as living organisms. Dinosaurs are part of a larger group of reptiles, the Archosauria, of which there are only two surviving lineages, crocodilians and birds. The goal of this review is to document progress in the field of archosaur paleohistology, focusing in particular on the Dinosauria. We briefly review the "growth age" of dinosaur histology, which has encompassed new and varied directions since its emergence in the 1950s, resulting in a shift in the scientific perception of non-avian dinosaurs from "sluggish" reptiles to fast-growing animals with relatively high metabolic rates. However, fundamental changes in growth occurred within the sister clade Aves, and we discuss this major evolutionary transition as elucidated by histology. We then review recent innovations in the field, demonstrating how paleohistology has changed and expanded to address a diversity of non-growth related questions. For example, dinosaur skull histology has elucidated the formation of curious cranial tissues (e.g., "metaplastic" tissues), and helped to clarify the evolution and function of oral adaptations, such as the dental batteries of duck-billed dinosaurs. Lastly, we discuss the development of novel techniques with which to investigate not only the skeletal tissues of dinosaurs, but also less-studied soft-tissues, through molecular paleontology and paleohistochemistry-recently developed branches of paleohistology-and the future potential of these methods to further explore fossilized tissues. We suggest that the combination of histological and molecular methods holds great potential for examining the preserved tissues of dinosaurs, basal birds, and their extant relatives. This review demonstrates the importance of traditional bone paleohistology, but also highlights the need for innovation and new analytical directions to improve and broaden the utility of paleohistology, in the pursuit of more diverse, highly specific, and sensitive methods with which to further investigate important paleontological questions.
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Affiliation(s)
- Alida M. Bailleul
- Key Laboratory of Vertebrate Evolution and Human Origins of the Chinese Academy of Sciences, Institute of Vertebrate Paleontology and Paleoanthropology, Beijing, China
- CAS Center for Excellence in Life and Paleoenvironment, Beijing, China
| | - Jingmai O’Connor
- Key Laboratory of Vertebrate Evolution and Human Origins of the Chinese Academy of Sciences, Institute of Vertebrate Paleontology and Paleoanthropology, Beijing, China
- CAS Center for Excellence in Life and Paleoenvironment, Beijing, China
| | - Mary H. Schweitzer
- Department of Biology, North Carolina State University, Raleigh, NC, USA
- North Carolina Museum of Natural Science, Raleigh, NC, USA
- Department of Geology, Lund University, Lund, Sweden
- Museum of the Rockies, Montana State University, Bozeman, MT, USA
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23
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Schweitzer MH, Schroeter ER, Cleland TP, Zheng W. Paleoproteomics of Mesozoic Dinosaurs and Other Mesozoic Fossils. Proteomics 2019; 19:e1800251. [PMID: 31172628 DOI: 10.1002/pmic.201800251] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/11/2018] [Revised: 05/07/2019] [Indexed: 12/20/2022]
Abstract
Molecular studies have contributed greatly to our understanding of evolutionary processes that act upon virtually every aspect of living organisms. However, these studies are limited with regard to extinct organisms, particularly those from the Mesozoic because fossils pose unique challenges to molecular workflows, and because prevailing wisdom suggests no endogenous molecular components can persist into deep time. Here, the power and potential of a molecular approach to Mesozoic fossils is discussed. Molecular methods that have been applied to Mesozoic fossils-including iconic, non-avian dinosaurs- and the challenges inherent in such analyses, are compared and evaluated. Taphonomic processes resulting in the transition of living organisms from the biosphere into the fossil record are reviewed, and the possible effects of taphonomic alteration on downstream analyses that can be problematic for very old material (e.g., molecular modifications, limitations of on comparative databases) are addressed. Molecular studies applied to ancient remains are placed in historical context, and past and current studies are evaluated with respect to producing phylogenetically and/or evolutionarily significant data. Finally, some criteria for assessing the presence of endogenous biomolecules in very ancient fossil remains are suggested as a starting framework for such studies.
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Affiliation(s)
- Mary Higby Schweitzer
- Department of Biological Sciences, North Carolina State University, Raleigh, 27695, NC.,North Carolina Museum of Natural Sciences, Raleigh, NC.,Museum of the Rockies, Montana State University, Bozeman, MT.,Department of Geology, Lund University, Sölvegatan 12, SE-223 62, Lund, Sweden
| | - Elena R Schroeter
- Department of Biological Sciences, North Carolina State University, Raleigh, 27695, NC
| | - Timothy P Cleland
- Museum Conservation Institute, Smithsonian Institution, Suitland, 20746, MD
| | - Wenxia Zheng
- Department of Biological Sciences, North Carolina State University, Raleigh, 27695, NC
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24
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Saitta ET, Liang R, Lau MCY, Brown CM, Longrich NR, Kaye TG, Novak BJ, Salzberg SL, Norell MA, Abbott GD, Dickinson MR, Vinther J, Bull ID, Brooker RA, Martin P, Donohoe P, Knowles TDJ, Penkman KEH, Onstott T. Cretaceous dinosaur bone contains recent organic material and provides an environment conducive to microbial communities. eLife 2019; 8:e46205. [PMID: 31210129 PMCID: PMC6581507 DOI: 10.7554/elife.46205] [Citation(s) in RCA: 26] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/19/2019] [Accepted: 05/12/2019] [Indexed: 12/12/2022] Open
Abstract
Fossils were thought to lack original organic molecules, but chemical analyses show that some can survive. Dinosaur bone has been proposed to preserve collagen, osteocytes, and blood vessels. However, proteins and labile lipids are diagenetically unstable, and bone is a porous open system, allowing microbial/molecular flux. These 'soft tissues' have been reinterpreted as biofilms. Organic preservation versus contamination of dinosaur bone was examined by freshly excavating, with aseptic protocols, fossils and sedimentary matrix, and chemically/biologically analyzing them. Fossil 'soft tissues' differed from collagen chemically and structurally; while degradation would be expected, the patterns observed did not support this. 16S rRNA amplicon sequencing revealed that dinosaur bone hosted an abundant microbial community different from lesser abundant communities of surrounding sediment. Subsurface dinosaur bone is a relatively fertile habitat, attracting microbes that likely utilize inorganic nutrients and complicate identification of original organic material. There exists potential post-burial taphonomic roles for subsurface microorganisms.
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Affiliation(s)
- Evan T Saitta
- Integrative Research Center, Section of Earth SciencesField Museum of Natural HistoryChicagoUnited States
| | - Renxing Liang
- Department of GeosciencesPrinceton UniversityPrincetonUnited States
| | - Maggie CY Lau
- Department of GeosciencesPrinceton UniversityPrincetonUnited States
- Institute of Deep-Sea Science and EngineeringChinese Academy of SciencesSanyaChina
| | - Caleb M Brown
- Royal Tyrrell Museum of PalaeontologyDrumhellerCanada
| | - Nicholas R Longrich
- Department of Biology and BiochemistryUniversity of BathBathUnited Kingdom
- Milner Centre for EvolutionUniversity of BathBathUnited Kingdom
| | - Thomas G Kaye
- Foundation for Scientific AdvancementSierra VistaUnited States
| | - Ben J Novak
- Revive and RestoreSan FranciscoUnited States
| | - Steven L Salzberg
- Department of Biomedical Engineering, Center for Computational Biology, McKusick-Nathans Institute of Genetic MedicineJohns Hopkins UniversityBaltimoreUnited States
- Department of Computer Science, Center for Computational Biology, McKusick-Nathans Institute of Genetic MedicineJohns Hopkins UniversityBaltimoreUnited States
- Department of Biostatistics, Center for Computational Biology, McKusick-Nathans Institute of Genetic MedicineJohns Hopkins UniversityBaltimoreUnited States
| | - Mark A Norell
- Division of PaleontologyAmerican Museum of Natural HistoryNew YorkUnited States
| | - Geoffrey D Abbott
- School of Natural and Environmental SciencesNewcastle UniversityNewcastle upon TyneUnited Kingdom
| | | | - Jakob Vinther
- School of Earth SciencesUniversity of BristolBristolUnited Kingdom
- School of Biological SciencesUniversity of BristolBristolUnited Kingdom
| | - Ian D Bull
- School of ChemistryUniversity of BristolBristolUnited Kingdom
| | | | - Peter Martin
- School of PhysicsUniversity of BristolBristolUnited Kingdom
| | - Paul Donohoe
- School of Natural and Environmental SciencesNewcastle UniversityNewcastle upon TyneUnited Kingdom
| | - Timothy DJ Knowles
- School of ChemistryUniversity of BristolBristolUnited Kingdom
- School of ArtsUniversity of BristolBristolUnited Kingdom
| | | | - Tullis Onstott
- Department of GeosciencesPrinceton UniversityPrincetonUnited States
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25
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Abstract
Ancient protein analysis is a rapidly developing field of research. Proteins ranging in age from the Quaternary to Jurassic are being used to answer questions about phylogeny, evolution, and extinction. However, these analyses are sometimes contentious, and focus primarily on large vertebrates in sedimentary fossilisation environments; there are few studies of protein preservation in fossils in amber. Here we show exceptionally slow racemisation rates during thermal degradation experiments of resin enclosed feathers, relative to previous thermal degradation experiments of ostrich eggshell, coral skeleton, and limpet shell. We also recover amino acids from two specimens of fossil feathers in amber. The amino acid compositions are broadly similar to those of degraded feathers, but concentrations are very low, suggesting that much of the original protein has been degraded and lost. High levels of racemisation in more apolar, slowly racemising amino acids suggest that some of the amino acids were ancient and therefore original. Our findings indicate that the unique fossilisation environment inside amber shows potential for the recovery of ancient amino acids and proteins.
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Dry-bonding to dentin using alternative conditioners based on iron-containing solutions or nitric acid. J Mech Behav Biomed Mater 2019; 94:238-248. [PMID: 30927591 DOI: 10.1016/j.jmbbm.2019.03.015] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/16/2018] [Revised: 02/06/2019] [Accepted: 03/17/2019] [Indexed: 11/21/2022]
Abstract
OBJECTIVES To evaluate the effect of experimental conditioners (10-3 solution - 10-3, 6.8% ferric oxalate - FOX, and 1.4% nitric acid - NI) on dentin elastic modulus, flexural strength, bond strength, failure mode, and adhesive interface morphology of two etch-and-rinse adhesives (XP Bond, Dentsply or One-Step, Bisco) applied on etched dry dentin. METHODS Sound human third molars were used for the microtensile bond strength test (n = 8), performed at 24 h and after one year of water storage. Failure modes were evaluated by scanning electron microscopy. Dentin bonding interface was analyzed by confocal laser scanning microscopy (n = 3). Adhesive systems were applied on phosphoric acid-etched, wet (positive control) and dry (negative control) dentin, and on etched and dry dentin previously treated with 10-3 (15s), FOX (60s), or NI (15s). Bovine dentin bars (n = 15) were immersed into the conditioning solutions and subjected to a three-point bending test. RESULTS XP Bond + 10-3 or NI resulted in lower bond strength than phosphoric acid. One-Step + 10-3 or NI resulted in bond strengths equivalent to the positive control. Experimental conditioners presented no bond strength reduction after one year, regardless of the bonding agent tested. One-Step resulted in more adhesive failures than XP Bond at 24 h, and mixed failures increased after storage. All experimental conditioners promoted hybridization and resin tags formation, except FOX. Dentin elastic modulus was not affected by the conditioners, whereas flexural strength was significantly reduced by FOX. CONCLUSIONS Adequate and stable dentin bonds were achieved when the bonding agents were applied on 10-3 or NI-treated dentin. None of the experimental conditioners reduced dentin elastic modulus, but dentin flexural strength was significantly reduced by FOX-conditioning.
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Schweitzer MH, Zheng W, Moyer AE, Sjövall P, Lindgren J. Preservation potential of keratin in deep time. PLoS One 2018; 13:e0206569. [PMID: 30485294 PMCID: PMC6261410 DOI: 10.1371/journal.pone.0206569] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/02/2017] [Accepted: 10/16/2018] [Indexed: 11/18/2022] Open
Abstract
Multiple fossil discoveries and taphonomic experiments have established the durability of keratin. The utility and specificity of antibodies to identify keratin peptides has also been established, both in extant feathers under varying treatment conditions, and in feathers from extinct organisms. Here, we show localization of feather-keratin antibodies to control and heat-treated feathers, testifying to the repeatability of initial data supporting the preservation potential of keratin. We then show new data at higher resolution that demonstrates the specific response of these antibodies to the feather matrix, we support the presence of protein in heat-treated feathers using ToF-SIMS, and we apply these methods to a fossil feather preserved in the unusual environment of sinter hot springs. We stress the importance of employing realistic conditions such as sediment burial when designing experiments intended as proxies for taphonomic processes occurring in the fossil record. Our data support the hypothesis that keratin, particularly the β-keratin that comprises feathers, has potential to preserve in fossil remains.
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Affiliation(s)
- Mary Higby Schweitzer
- Department of Biological Sciences, North Carolina State University, Raleigh, North Carolina, United States of America
- North Carolina Museum of Natural Sciences, Raleigh, North Carolina, United States of America
- Department of Geology, Lund University, Lund, Sweden
| | - Wenxia Zheng
- Department of Biological Sciences, North Carolina State University, Raleigh, North Carolina, United States of America
| | - Alison E. Moyer
- Department of Biology, Drexel University, Philadelphia, Pennsylvania, United States of America
| | - Peter Sjövall
- RISE Research Institutes of Sweden, Chemistry and Materials, Borås, Sweden
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28
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Wiemann J, Fabbri M, Yang TR, Stein K, Sander PM, Norell MA, Briggs DEG. Fossilization transforms vertebrate hard tissue proteins into N-heterocyclic polymers. Nat Commun 2018; 9:4741. [PMID: 30413693 PMCID: PMC6226439 DOI: 10.1038/s41467-018-07013-3] [Citation(s) in RCA: 66] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/10/2018] [Accepted: 10/10/2018] [Indexed: 02/06/2023] Open
Abstract
Vertebrate hard tissues consist of mineral crystallites within a proteinaceous scaffold that normally degrades post-mortem. Here we show, however, that decalcification of Mesozoic hard tissues preserved in oxidative settings releases brownish stained extracellular matrix, cells, blood vessels, and nerve projections. Raman Microspectroscopy shows that these fossil soft tissues are a product of diagenetic transformation to Advanced Glycoxidation and Lipoxidation End Products, a class of N-heterocyclic polymers generated via oxidative crosslinking of proteinaceous scaffolds. Hard tissues in reducing environments, in contrast, lack soft tissue preservation. Comparison of fossil soft tissues with modern and experimentally matured samples reveals how proteinaceous tissues undergo diagenesis and explains biases in their preservation in the rock record. This provides a target, focused on oxidative depositional environments, for finding cellular-to-subcellular soft tissue morphology in fossils and validates its use in phylogenetic and other evolutionary studies.
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Affiliation(s)
- Jasmina Wiemann
- Department of Geology & Geophysics, Yale University, 210 Whitney Avenue, New Haven, CT, 06511, USA.
| | - Matteo Fabbri
- Department of Geology & Geophysics, Yale University, 210 Whitney Avenue, New Haven, CT, 06511, USA
| | - Tzu-Ruei Yang
- Steinmann Institute for Geology, Mineralogy, and Paleontology, University of Bonn, Nussallee 8, 53115, Bonn, Germany
| | - Koen Stein
- Earth System Sciences AMGC, Vrije Universiteit Brussel, Pleinlaan 2, 1050, Brussels, Belgium
| | - P Martin Sander
- Steinmann Institute for Geology, Mineralogy, and Paleontology, University of Bonn, Nussallee 8, 53115, Bonn, Germany
- Dinosaur Institute, Natural History Museum of Los Angeles County, 900 Exposition Boulevard, Los Angeles, CA, 90007, USA
| | - Mark A Norell
- Division of Vertebrate Paleontology, American Museum of Natural History, Central Park West at 79th Street, New York, NY, 10024-5192, USA
| | - Derek E G Briggs
- Department of Geology & Geophysics, Yale University, 210 Whitney Avenue, New Haven, CT, 06511, USA
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Marsh AD, Rowe TB. Anatomy and systematics of the sauropodomorph Sarahsaurus aurifontanalis from the Early Jurassic Kayenta Formation. PLoS One 2018; 13:e0204007. [PMID: 30304035 PMCID: PMC6179219 DOI: 10.1371/journal.pone.0204007] [Citation(s) in RCA: 26] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/04/2017] [Accepted: 09/01/2018] [Indexed: 12/13/2022] Open
Abstract
Sarahsaurus aurifontanalis, from the Kayenta Formation of Arizona, is one of only three sauropodomorph dinosaurs known from the Early Jurassic of North America. It joins Anchisaurus polyzelus, from the older Portland Formation of the Hartford Basin, and Seitaad reussi, from the younger Navajo Sandstone of Utah, in representing the oldest North American sauropodomorphs. If it is true that sauropodomorphs were absent from North America during the Late Triassic, the relationship among these three dinosaurs offers a test of the mechanisms that drove recovery in North American biodiversity following the end-Triassic extinction event. Here we provide the first thorough description of Sarahsaurus aurifontanalis based on completed preparation and computed tomographic imaging of the holotype and referred specimens. With new anatomical data, our phylogenetic analysis supports the conclusion that Sarahsaurus aurifontanalis is nested within the primarily Gondwanan clade Massospondylidae, while agreeing with previous analyses that the three North American sauropodomorphs do not themselves form an exclusive clade. A revised diagnosis and more thorough understanding of the anatomy of Sarahsaurus aurifontanalis support the view that independent dispersal events were at least partly responsible for the recovery in North American vertebrate diversity following a major extinction event.
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Affiliation(s)
- Adam D. Marsh
- The Jackson School of Geosciences, University of Texas at Austin, Austin, Texas, United States of America
- Division of Science and Resource Management, Petrified Forest National Park, Arizona, United States of America
| | - Timothy B. Rowe
- The Jackson School of Geosciences, University of Texas at Austin, Austin, Texas, United States of America
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30
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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: 45] [Impact Index Per Article: 7.5] [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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31
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Xing L, O'Connor JK, McKellar RC, Chiappe LM, Bai M, Tseng K, Zhang J, Yang H, Fang J, Li G. A flattened enantiornithine in mid-Cretaceous Burmese amber: morphology and preservation. Sci Bull (Beijing) 2018; 63:235-243. [PMID: 36659012 DOI: 10.1016/j.scib.2018.01.019] [Citation(s) in RCA: 22] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/11/2017] [Revised: 01/02/2018] [Accepted: 01/03/2018] [Indexed: 01/21/2023]
Abstract
Cretaceous amber from Myanmar (∼99 Ma Burmese amber) has become a valuable supplement to the traditional skeletal record of small theropod dinosaurs preserved in sedimentary rocks, particularly for coelurosaurs and enantiornithines. The specimens recovered from this deposit preserve skeletal material and soft tissues in unmatched detail. This provides opportunities to study three-dimensional preservation of soft tissues, microstructure, and pigmentation patterns that are seldom available elsewhere in the fossil record. Ultimately, this line of research provides insights into life stages that are difficult to preserve, the ecology and appearance of the groups involved, and the evolutionary-development of structures such as feathers. Here we describe the most recent discovery from Burmese amber, an articulated skeleton of an enantiornithine bird. This individual has been sectioned along the coronal plane, providing a unique view inside multiple body regions. Osteological observations and plumage patterns support placement within the Enantiornithes, and suggest that the animal may have been a juvenile at the time of death. The specimen has a complex taphonomic history that includes exposure at the surface of a resin flow prior to encapsulation, and may include scavenging by some of the insects trapped within the same amber piece. The chemical composition observed along surface exposures and shallowly buried regions of the body indicate that the specimen has not undergone significant exchange with its surroundings. High iron concentrations are present in regions that preserve soft tissues as carbon films, and calcium distribution corresponds to regions where bones breach the surface of the amber.
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Affiliation(s)
- Lida Xing
- State Key Laboratory of Biogeology and Environmental Geology, China University of Geosciences, Beijing 100083, China; School of the Earth Sciences and Resources, China University of Geosciences, Beijing 100083, China
| | - Jingmai K O'Connor
- Key Laboratory of Vertebrate Evolution and Human Origins of the Chinese Academy of Sciences, Institute of Vertebrate Paleontology and Paleoanthropology, Beijing 100044, China
| | - Ryan C McKellar
- Royal Saskatchewan Museum, Regina, Saskatchewan S4P 4W7, Canada; Biology Department, University of Regina, Regina, Saskatchewan S4S 0A2, Canada; Department of Ecology and Evolutionary Biology, University of Kansas, Lawrence 66045, USA.
| | - Luis M Chiappe
- Dinosaur Institute, Natural History Museum of Los Angeles County, Los Angeles 90007, USA
| | - Ming Bai
- Key Laboratory of Zoological Systematics and Evolution, Institute of Zoology, Chinese Academy of Sciences, Beijing 100101, China
| | - Kuowei Tseng
- Department of Exercise and Health Science, University of Taipei, Taipei 11153, China
| | - Jie Zhang
- Institute of High Energy Physics, Chinese Academy of Sciences, Beijing 100049, China
| | - Haidong Yang
- Key Laboratory of Zoological Systematics and Evolution, Institute of Zoology, Chinese Academy of Sciences, Beijing 100101, China
| | - Jun Fang
- School of the Earth Sciences and Resources, China University of Geosciences, Beijing 100083, China
| | - Gang Li
- Institute of High Energy Physics, Chinese Academy of Sciences, Beijing 100049, China.
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32
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Moyer AE, Zheng W, Schweitzer MH. Microscopic and immunohistochemical analyses of the claw of the nesting dinosaur, Citipati osmolskae. Proc Biol Sci 2017; 283:rspb.2016.1997. [PMID: 28120795 DOI: 10.1098/rspb.2016.1997] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/09/2016] [Accepted: 10/19/2016] [Indexed: 02/02/2023] Open
Abstract
One of the most well-recognized Cretaceous fossils is Citipati osmolskae (MPC-D 100/979), an oviraptorid dinosaur discovered in brooding position on a nest of unhatched eggs. The original description refers to a thin lens of white material extending from a manus ungual, which was proposed to represent original keratinous claw sheath that, in life, would have covered it. Here, we test the hypothesis that this exceptional morphological preservation extends to the molecular level. The fossil sheath was compared with that of extant birds, revealing similar morphology and microstructural organization. In living birds, the claw sheath consists primarily of two structural proteins; alpha-keratin, expressed in all vertebrates, and beta-keratin, found only in reptiles and birds (sauropsids). We employed antibodies raised against avian feathers, which comprise almost entirely of beta-keratin, to demonstrate that fossil tissues respond with the same specificity, though less intensity, as those from living birds. Furthermore, we show that calcium chelation greatly increased antibody reactivity, suggesting a role for calcium in the preservation of this fossil material.
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Affiliation(s)
- Alison E Moyer
- Department of Biological Sciences, North Carolina State University, Raleigh, NC 27695, USA .,Department of Biology, Drexel University, Philadelphia, PA 19104, USA
| | - Wenxia Zheng
- Department of Biological Sciences, North Carolina State University, Raleigh, NC 27695, USA
| | - Mary H Schweitzer
- Department of Biological Sciences, North Carolina State University, Raleigh, NC 27695, USA.,North Carolina Museum of Natural Sciences, Raleigh, NC 27601, USA
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33
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Palaeobiology of red and white blood cell-like structures, collagen and cholesterol in an ichthyosaur bone. Sci Rep 2017; 7:13776. [PMID: 29061985 PMCID: PMC5653768 DOI: 10.1038/s41598-017-13873-4] [Citation(s) in RCA: 25] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/16/2017] [Accepted: 10/03/2017] [Indexed: 11/24/2022] Open
Abstract
Carbonate concretions are known to contain well-preserved fossils and soft tissues. Recently, biomolecules (e.g. cholesterol) and molecular fossils (biomarkers) were also discovered in a 380 million-year-old concretion, revealing their importance in exceptional preservation of biosignatures. Here, we used a range of microanalytical techniques, biomarkers and compound specific isotope analyses to report the presence of red and white blood cell-like structures as well as platelet-like structures, collagen and cholesterol in an ichthyosaur bone encapsulated in a carbonate concretion from the Early Jurassic (~182.7 Ma). The red blood cell-like structures are four to five times smaller than those identified in modern organisms. Transmission electron microscopy (TEM) analysis revealed that the red blood cell-like structures are organic in composition. We propose that the small size of the blood cell-like structures results from an evolutionary adaptation to the prolonged low oxygen atmospheric levels prevailing during the 70 Ma when ichthyosaurs thrived. The δ13C of the ichthyosaur bone cholesterol indicates that it largely derives from a higher level in the food chain and is consistent with a fish and cephalopod diet. The combined findings above demonstrate that carbonate concretions create isolated environments that promote exceptional preservation of fragile tissues and biomolecules.
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34
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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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35
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Effect of conditioning solutions containing ferric chloride on dentin bond strength and collagen degradation. Dent Mater 2017; 33:1093-1102. [DOI: 10.1016/j.dental.2017.07.004] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/22/2017] [Revised: 07/07/2017] [Accepted: 07/08/2017] [Indexed: 11/18/2022]
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36
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Iron minerals within specific microfossil morphospecies of the 1.88 Ga Gunflint Formation. Nat Commun 2017; 8:14890. [PMID: 28332570 PMCID: PMC5376642 DOI: 10.1038/ncomms14890] [Citation(s) in RCA: 49] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/14/2016] [Accepted: 02/10/2017] [Indexed: 01/19/2023] Open
Abstract
Problematic microfossils dominate the palaeontological record between the Great Oxidation Event 2.4 billion years ago (Ga) and the last Palaeoproterozoic iron formations, deposited 500–600 million years later. These fossils are often associated with iron-rich sedimentary rocks, but their affinities, metabolism, and, hence, their contributions to Earth surface oxidation and Fe deposition remain unknown. Here we show that specific microfossil populations of the 1.88 Ga Gunflint Iron Formation contain Fe-silicate and Fe-carbonate nanocrystal concentrations in cell interiors. Fe minerals are absent in/on all organically preserved cell walls. These features are consistent with in vivo intracellular Fe biomineralization, with subsequent in situ recrystallization, but contrast with known patterns of post-mortem Fe mineralization. The Gunflint populations that display relatively large cells (thick-walled spheres, filament-forming rods) and intra-microfossil Fe minerals are consistent with oxygenic photosynthesizers but not with other Fe-mineralizing microorganisms studied so far. Fe biomineralization may have protected oxygenic photosynthesizers against Fe2+ toxicity during the Palaeoproterozoic. Fossil microorganisms older than 1.7 billion years are challenging to interpret due to their size, simple shapes, and alteration. Here, in 1.88 billion year old microfossils, the authors show a pattern of cellular preservation and internal iron nanominerals consistent with oxygenic photosynthetic bacteria.
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37
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Unusual intraosseous fossilized soft tissues from the Middle Triassic Nothosaurus bone. Naturwissenschaften 2017; 104:25. [DOI: 10.1007/s00114-017-1451-y] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/05/2016] [Revised: 02/20/2017] [Accepted: 02/21/2017] [Indexed: 10/20/2022]
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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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Lee YC, Chiang CC, Huang PY, Chung CY, Huang TD, Wang CC, Chen CI, Chang RS, Liao CH, Reisz RR. Evidence of preserved collagen in an Early Jurassic sauropodomorph dinosaur revealed by synchrotron FTIR microspectroscopy. Nat Commun 2017; 8:14220. [PMID: 28140389 PMCID: PMC5290320 DOI: 10.1038/ncomms14220] [Citation(s) in RCA: 57] [Impact Index Per Article: 8.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/13/2015] [Accepted: 12/09/2016] [Indexed: 12/29/2022] Open
Abstract
Fossilized organic remains are important sources of information because they provide a unique form of biological and evolutionary information, and have the long-term potential for genomic explorations. Here we report evidence of protein preservation in a terrestrial vertebrate found inside the vascular canals of a rib of a 195-million-year-old sauropodomorph dinosaur, where blood vessels and nerves would normally have been present in the living organism. The in situ synchrotron radiation-based Fourier transform infrared (SR-FTIR) spectra exhibit the characteristic infrared absorption bands for amide A and B, amide I, II and III of collagen. Aggregated haematite particles (α-Fe2O3) about 6∼8 μm in diameter are also identified inside the vascular canals using confocal Raman microscopy, where the organic remains were preserved. We propose that these particles likely had a crucial role in the preservation of the proteins, and may be remnants partially contributed from haemoglobin and other iron-rich proteins from the original blood.
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Affiliation(s)
- Yao-Chang Lee
- National Synchrotron Radiation Research Center, Hsinchu 30076, Taiwan
- Department of Optics and Photonics, National Central University, Chung-Li 32001, Taiwan
| | | | - Pei-Yu Huang
- National Synchrotron Radiation Research Center, Hsinchu 30076, Taiwan
| | - Chao-Yu Chung
- Department of Applied Chemistry, National Chiao Tung University, Hsinchu 30010, Taiwan
| | - Timothy D. Huang
- Department of Optics and Photonics, National Central University, Chung-Li 32001, Taiwan
- Dinosaur Evolution Research Center of Jilin University, Changchun, Jilin 130012, China
- College of Life Sciences, National Chung Hsing University, Taichung 400, Taiwan
| | - Chun-Chieh Wang
- National Synchrotron Radiation Research Center, Hsinchu 30076, Taiwan
| | - Ching-Iue Chen
- National Synchrotron Radiation Research Center, Hsinchu 30076, Taiwan
| | - Rong-Seng Chang
- Department of Optics and Photonics, National Central University, Chung-Li 32001, Taiwan
| | | | - Robert R. Reisz
- Department of Optics and Photonics, National Central University, Chung-Li 32001, Taiwan
- Dinosaur Evolution Research Center of Jilin University, Changchun, Jilin 130012, China
- College of Life Sciences, National Chung Hsing University, Taichung 400, Taiwan
- Department of Biology, University of Toronto Mississauga, Mississauga, Ontario, Canada L5L 1C6
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40
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Xing L, McKellar RC, Xu X, Li G, Bai M, Persons WS, Miyashita T, Benton MJ, Zhang J, Wolfe AP, Yi Q, Tseng K, Ran H, Currie PJ. A Feathered Dinosaur Tail with Primitive Plumage Trapped in Mid-Cretaceous Amber. Curr Biol 2016; 26:3352-3360. [PMID: 27939315 DOI: 10.1016/j.cub.2016.10.008] [Citation(s) in RCA: 65] [Impact Index Per Article: 8.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/10/2016] [Revised: 09/07/2016] [Accepted: 10/05/2016] [Indexed: 10/20/2022]
Abstract
In the two decades since the discovery of feathered dinosaurs [1-3], the range of plumage known from non-avialan theropods has expanded significantly, confirming several features predicted by developmentally informed models of feather evolution [4-10]. However, three-dimensional feather morphology and evolutionary patterns remain difficult to interpret, due to compression in sedimentary rocks [9, 11]. Recent discoveries in Cretaceous amber from Canada, France, Japan, Lebanon, Myanmar, and the United States [12-18] reveal much finer levels of structural detail, but taxonomic placement is uncertain because plumage is rarely associated with identifiable skeletal material [14]. Here we describe the feathered tail of a non-avialan theropod preserved in mid-Cretaceous (∼99 Ma) amber from Kachin State, Myanmar [17], with plumage structure that directly informs the evolutionary developmental pathway of feathers. This specimen provides an opportunity to document pristine feathers in direct association with a putative juvenile coelurosaur, preserving fine morphological details, including the spatial arrangement of follicles and feathers on the body, and micrometer-scale features of the plumage. Many feathers exhibit a short, slender rachis with alternating barbs and a uniform series of contiguous barbules, supporting the developmental hypothesis that barbs already possessed barbules when they fused to form the rachis [19]. Beneath the feathers, carbonized soft tissues offer a glimpse of preservational potential and history for the inclusion; abundant Fe2+ suggests that vestiges of primary hemoglobin and ferritin remain trapped within the tail. The new finding highlights the unique preservation potential of amber for understanding the morphology and evolution of coelurosaurian integumentary structures.
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Affiliation(s)
- Lida Xing
- State Key Laboratory of Biogeology and Environmental Geology, China University of Geosciences, Beijing 100083, China; School of the Earth Sciences and Resources, China University of Geosciences, Beijing 100083, China.
| | - Ryan C McKellar
- Royal Saskatchewan Museum, Regina, Saskatchewan S4P 4W7, Canada; Biology Department, University of Regina, Regina, Saskatchewan S4S 0A2, Canada.
| | - Xing Xu
- Key Laboratory of Vertebrate Evolution and Human Origins, Institute of Vertebrate Paleontology and Paleoanthropology, Chinese Academy of Sciences, Beijing 100044, China
| | - Gang Li
- Beijing Synchrotron Radiation Facility, Institute of High Energy Physics, Chinese Academy of Science, Beijing 100049, China
| | - Ming Bai
- Key Laboratory of Zoological Systematics and Evolution, Institute of Zoology, Chinese Academy of Sciences, Beijing 100101, China
| | - W Scott Persons
- Department of Biological Sciences, University of Alberta, Edmonton, Alberta T6G 2E9, Canada
| | - Tetsuto Miyashita
- Department of Biological Sciences, University of Alberta, Edmonton, Alberta T6G 2E9, Canada
| | - Michael J Benton
- School of Earth Sciences, University of Bristol, Bristol BS8 1RJ, UK
| | - Jianping Zhang
- School of the Earth Sciences and Resources, China University of Geosciences, Beijing 100083, China
| | - Alexander P Wolfe
- Department of Biological Sciences, University of Alberta, Edmonton, Alberta T6G 2E9, Canada
| | - Qiru Yi
- Beijing Synchrotron Radiation Facility, Institute of High Energy Physics, Chinese Academy of Science, Beijing 100049, China
| | - Kuowei Tseng
- Department of Exercise and Health Science, University of Taipei, Taipei 11153, China; Department of Geology, Chinese Culture University, Taipei 11114, China
| | - Hao Ran
- Key Laboratory of Ecology of Rare and Endangered Species and Environmental Protection, Ministry of Education, Guilin 541004, China
| | - Philip J Currie
- Department of Biological Sciences, University of Alberta, Edmonton, Alberta T6G 2E9, Canada
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41
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Abstract
Some fragments of ancient protein are less prone to degradation because they bind strongly to the surfaces of minerals.
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Affiliation(s)
- Adam F Wallace
- Department of Geological Sciences, University of Delaware, Newark, United States
| | - James D Schiffbauer
- Department of Geological Sciences, University of Missouri, Columbia, United States
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42
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Spectroscopic Studies on Organic Matter from Triassic Reptile Bones, Upper Silesia, Poland. PLoS One 2016; 11:e0151143. [PMID: 26977600 PMCID: PMC4792425 DOI: 10.1371/journal.pone.0151143] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/08/2015] [Accepted: 02/24/2016] [Indexed: 11/19/2022] Open
Abstract
Fossil biomolecules from an endogenous source were previously identified in Cretaceous to Pleistocene fossilized bones, the evidence coming from molecular analyses. These findings, however, were called into question and an alternative hypothesis of the invasion of the bone by bacterial biofilm was proposed. Herewith we report a new finding of morphologically preserved blood-vessel-like structures enclosing organic molecules preserved in iron-oxide-mineralized vessel walls from the cortical region of nothosaurid and tanystropheid (aquatic and terrestrial diapsid reptiles) bones. These findings are from the Early/Middle Triassic boundary (Upper Roetian/Lowermost Muschelkalk) strata of Upper Silesia, Poland. Multiple spectroscopic analyses (FTIR, ToF-SIMS, and XPS) of the extracted "blood vessels" showed the presence of organic compounds, including fragments of various amino acids such as hydroxyproline and hydroxylysine as well as amides, that may suggest the presence of collagen protein residues. Because these amino acids are absent from most proteins other than collagen, we infer that the proteinaceous molecules may originate from endogenous collagen. The preservation of molecular signals of proteins within the "blood vessels" was most likely made possible through the process of early diagenetic iron oxide mineralization. This discovery provides the oldest evidence of in situ preservation of complex organic molecules in vertebrate remains in a marine environment.
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Schweitzer MH, Moyer AE, Zheng W. Testing the Hypothesis of Biofilm as a Source for Soft Tissue and Cell-Like Structures Preserved in Dinosaur Bone. PLoS One 2016; 11:e0150238. [PMID: 26926069 PMCID: PMC4771714 DOI: 10.1371/journal.pone.0150238] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/27/2015] [Accepted: 02/11/2016] [Indexed: 12/04/2022] Open
Abstract
Recovery of still-soft tissue structures, including blood vessels and osteocytes, from dinosaur bone after demineralization was reported in 2005 and in subsequent publications. Despite multiple lines of evidence supporting an endogenous source, it was proposed that these structures arose from contamination from biofilm-forming organisms. To test the hypothesis that soft tissue structures result from microbial invasion of the fossil bone, we used two different biofilm-forming microorganisms to inoculate modern bone fragments from which organic components had been removed. We show fundamental morphological, chemical and textural differences between the resultant biofilm structures and those derived from dinosaur bone. The data do not support the hypothesis that biofilm-forming microorganisms are the source of these structures.
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Affiliation(s)
- Mary Higby Schweitzer
- Department of Biological Science, North Carolina State University, Raleigh, North Carolina, United States of America
- North Carolina Museum of Natural Sciences, Raleigh, North Carolina, United States of America
| | - Alison E. Moyer
- Department of Biological Science, North Carolina State University, Raleigh, North Carolina, United States of America
| | - Wenxia Zheng
- Department of Biological Science, North Carolina State University, Raleigh, North Carolina, United States of America
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Schroeter ER, Cleland TP. Glutamine deamidation: an indicator of antiquity, or preservational quality? RAPID COMMUNICATIONS IN MASS SPECTROMETRY : RCM 2016; 30:251-255. [PMID: 26689157 DOI: 10.1002/rcm.7445] [Citation(s) in RCA: 41] [Impact Index Per Article: 5.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/02/2015] [Revised: 10/26/2015] [Accepted: 10/27/2015] [Indexed: 06/05/2023]
Abstract
RATIONALE Much credence has been given in the paleoproteomic community to glutamine deamidation as a proxy for the age of proteins derived from fossil and subfossil material, and this modification has been invoked as a means for determining the endogeneity of molecules recovered from very old fossil specimens. METHODS We re-evaluated the relationship between glutamine deamidation and geologic time by examining previously published data from five recent mass spectrometry studies of archeaological fossils. Deamidation values recovered for fossils were graphed against their reported chronologic age using WebPlotDigitizer. RESULTS The experimental data that has been produced from fossil material to date show that the extent of glutamine deamidation does not correspond to the absolute age of the specimens being examined, but rather show extreme variation between specimens of similar age and taxonomic affinity. CONCLUSIONS Because deamidation rates and levels can be greatly affected by numerous chemical and environmental factors, we propose that glutamine deamidation is better suited as an indicator of preservational quality and/or environmental conditions than a mark of the endogeneity or authenticity of ancient proteins.
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Affiliation(s)
- Elena R Schroeter
- Department of Biological Sciences, North Carolina State University, Raleigh, NC, 27695, USA
| | - Timothy P Cleland
- Department of Biomedical Engineering, Rensselaer Polytechnic Institute, Troy, NY, 12182, USA
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45
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Cadena E. Microscopical and elemental FESEM and Phenom ProX-SEM-EDS analysis of osteocyte- and blood vessel-like microstructures obtained from fossil vertebrates of the Eocene Messel Pit, Germany. PeerJ 2016; 4:e1618. [PMID: 26819855 PMCID: PMC4727973 DOI: 10.7717/peerj.1618] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/01/2015] [Accepted: 01/02/2016] [Indexed: 11/20/2022] Open
Abstract
The Eocene (∾48 Ma) Messel Pit in Germany is a UNESCO World Heritage Site because of its exceptionally preserved fossils, including vertebrates, invertebrates, and plants. Messel fossil vertebrates are typically characterized by their articulated state, and in some cases the skin, hair, feathers, scales and stomach contents are also preserved. Despite the exceptional macroscopic preservation of Messel fossil vertebrates, the microstructural aspect of these fossils has been poorly explored. In particular, soft tissue structures such as hair or feathers have not been chemically analyzed, nor have bone microstructures. I report here the preservation and recovery of osteocyte-like and blood vessel-like microstructures from the bone of Messel Pit specimens, including the turtles Allaeochelys crassesculpta and Neochelys franzeni, the crocodile Diplocynodon darwini, and the pangolin Eomanis krebsi. I used a Field Emission Scanning Electron Microscope (FESEM) and a Phenom ProX desktop scanning electron microscope (LOT-QuantumDesign) equipped with a thermionic CeB6 source and a high sensitivity multi-mode backscatter electron (BSE) for microscopical and elemental characterization of these bone microstructures. Osteocyte-like and blood vessel-like microstructures are constituted by a thin layer (∾50 nm thickness), external and internal mottled texture with slightly marked striations. Circular to linear marks are common on the external surface of the osteocyte-like microstructures and are interpreted as microbial troughs. Iron (Fe) is the most abundant element found in the osteocyte-like and blood vessel-like microstructures, but not in the bone matrix or collagen fibril-like microstructures. The occurrence of well-preserved soft-tissue elements (at least their physical form) establishes a promising background for future studies on preservation of biomolecules (proteins or DNA) in Messel Pit fossils.
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Affiliation(s)
- Edwin Cadena
- Paleoherpetology, Senckenberg Research Institute , Frankfurt am Main , Germany
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46
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Cleland TP, Schroeter ER, Zamdborg L, Zheng W, Lee JE, Tran JC, Bern M, Duncan MB, Lebleu VS, Ahlf DR, Thomas PM, Kalluri R, Kelleher NL, Schweitzer MH. Mass Spectrometry and Antibody-Based Characterization of Blood Vessels from Brachylophosaurus canadensis. J Proteome Res 2015; 14:5252-62. [PMID: 26595531 DOI: 10.1021/acs.jproteome.5b00675] [Citation(s) in RCA: 48] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
Structures similar to blood vessels in location, morphology, flexibility, and transparency have been recovered after demineralization of multiple dinosaur cortical bone fragments from multiple specimens, some of which are as old as 80 Ma. These structures were hypothesized to be either endogenous to the bone (i.e., of vascular origin) or the result of biofilm colonizing the empty osteonal network after degradation of original organic components. Here, we test the hypothesis that these structures are endogenous and thus retain proteins in common with extant archosaur blood vessels that can be detected with high-resolution mass spectrometry and confirmed by immunofluorescence. Two lines of evidence support this hypothesis. First, peptide sequencing of Brachylophosaurus canadensis blood vessel extracts is consistent with peptides comprising extant archosaurian blood vessels and is not consistent with a bacterial, cellular slime mold, or fungal origin. Second, proteins identified by mass spectrometry can be localized to the tissues using antibodies specific to these proteins, validating their identity. Data are available via ProteomeXchange with identifier PXD001738.
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Affiliation(s)
| | | | - Leonid Zamdborg
- Department of Chemistry, University of Illinois , Urbana, Illinois 61801, United States
| | | | - Ji Eun Lee
- Department of Chemistry, University of Illinois , Urbana, Illinois 61801, United States.,Center for Theragnosis, Biomedical Research Institute, Korea Institute of Science and Technology , Hwarang-ro 14-gil 5, Seongbuk-gu, Seoul 136-791, Republic of Korea
| | - John C Tran
- Departments of Chemistry, Molecular Biosciences and the Proteomics Center of Excellence, Northwestern University , Evanston, Illinois 60208, United States
| | - Marshall Bern
- Protein Metrics , San Carlos, California 94070, United States
| | - Michael B Duncan
- Division of Matrix Biology, Beth Israel Deaconess Medical Center , Boston, Massachusetts 02115, United States.,Department of Medicine, Harvard Medical School , Boston, Massachusetts 02115, United States
| | - Valerie S Lebleu
- Division of Matrix Biology, Beth Israel Deaconess Medical Center , Boston, Massachusetts 02115, United States.,Department of Medicine, Harvard Medical School , Boston, Massachusetts 02115, United States.,Department of Cancer Biology, Metastasis Research Center, University of Texas MD Anderson Cancer Center , Houston, Texas 77054, United States
| | - Dorothy R Ahlf
- Departments of Chemistry, Molecular Biosciences and the Proteomics Center of Excellence, Northwestern University , Evanston, Illinois 60208, United States
| | - Paul M Thomas
- Departments of Chemistry, Molecular Biosciences and the Proteomics Center of Excellence, Northwestern University , Evanston, Illinois 60208, United States
| | - Raghu Kalluri
- Division of Matrix Biology, Beth Israel Deaconess Medical Center , Boston, Massachusetts 02115, United States.,Department of Medicine, Harvard Medical School , Boston, Massachusetts 02115, United States.,Department of Cancer Biology, Metastasis Research Center, University of Texas MD Anderson Cancer Center , Houston, Texas 77054, United States.,Department of Biological Chemistry and Molecular Pharmacology and Harvard-MIT Division of Health Sciences and Technology, Harvard University , Cambridge, Massachusetts 02139, United States
| | - Neil L Kelleher
- Departments of Chemistry, Molecular Biosciences and the Proteomics Center of Excellence, Northwestern University , Evanston, Illinois 60208, United States
| | - Mary H Schweitzer
- North Carolina Museum of Natural Sciences , Raleigh, North Carolina 27601, United States
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47
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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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48
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Bertazzo S, Maidment SCR, Kallepitis C, Fearn S, Stevens MM, Xie HN. Fibres and cellular structures preserved in 75-million-year-old dinosaur specimens. Nat Commun 2015; 6:7352. [PMID: 26056764 PMCID: PMC4468865 DOI: 10.1038/ncomms8352] [Citation(s) in RCA: 59] [Impact Index Per Article: 6.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/25/2015] [Accepted: 04/30/2015] [Indexed: 02/05/2023] Open
Abstract
Exceptionally preserved organic remains are known throughout the vertebrate fossil record, and recently, evidence has emerged that such soft tissue might contain original components. We examined samples from eight Cretaceous dinosaur bones using nano-analytical techniques; the bones are not exceptionally preserved and show no external indication of soft tissue. In one sample, we observe structures consistent with endogenous collagen fibre remains displaying ∼ 67 nm banding, indicating the possible preservation of the original quaternary structure. Using ToF-SIMS, we identify amino-acid fragments typical of collagen fibrils. Furthermore, we observe structures consistent with putative erythrocyte remains that exhibit mass spectra similar to emu whole blood. Using advanced material characterization approaches, we find that these putative biological structures can be well preserved over geological timescales, and their preservation is more common than previously thought. The preservation of protein over geological timescales offers the opportunity to investigate relationships, physiology and behaviour of long extinct animals.
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Affiliation(s)
- Sergio Bertazzo
- Department of Materials, Imperial College London, South Kensington Campus, London SW7 2AZ, UK
- Present address: Department of Medical Physics and Biomedical Engineering, University College London, Malet Place Engineering Building, London WC1E 6BT, UK
| | - Susannah C. R. Maidment
- Department of Earth Science and Engineering, Imperial College London, South Kensington Campus, London SW7 2AZ, UK
| | - Charalambos Kallepitis
- Department of Materials, Imperial College London, South Kensington Campus, London SW7 2AZ, UK
- Department of Bioengineering, Imperial College London, South Kensington Campus, London SW7 2AZ, UK
- Institute for Biomedical Engineering, Imperial College London, South Kensington Campus, London SW7 2AZ, UK
| | - Sarah Fearn
- Department of Materials, Imperial College London, South Kensington Campus, London SW7 2AZ, UK
| | - Molly M. Stevens
- Department of Materials, Imperial College London, South Kensington Campus, London SW7 2AZ, UK
- Department of Bioengineering, Imperial College London, South Kensington Campus, London SW7 2AZ, UK
- Institute for Biomedical Engineering, Imperial College London, South Kensington Campus, London SW7 2AZ, UK
| | - Hai-nan Xie
- Department of Materials, Imperial College London, South Kensington Campus, London SW7 2AZ, UK
- Department of Bioengineering, Imperial College London, South Kensington Campus, London SW7 2AZ, UK
- Institute for Biomedical Engineering, Imperial College London, South Kensington Campus, London SW7 2AZ, UK
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