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de Sousa DV, Maia PVS, Eltink E, de Moura Guimarães L. Biomolecules in Pleistocene fossils from tropical cave indicate fossil biofilm. Sci Rep 2024; 14:21071. [PMID: 39256439 DOI: 10.1038/s41598-024-71313-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/09/2024] [Accepted: 08/27/2024] [Indexed: 09/12/2024] Open
Abstract
Finding biomolecules in fossils is a challenging task due to their degradation over time from physical, chemical, and biological factors. The primary hypothesis for explaining the presence of biomolecules in fossilized bones tissues suggests their survival in the fossilization process. In contrast, some of these biomolecules could either derive from bacteria biofilm, thus without a direct relationship with the fossil record or could be an artifact from measurement procedures. Raman spectroscopy studies across various fossil ages and environments have detected multiple bands ranging from 1200 to 1800 cm-1 associative of organic compounds. However, the significance of these bands remains elusive. Our research aims to address this issue through a deep Raman spectroscopy investigation on Pleistocene teeth from Tayassu and Smilodon populator. These fossils were obtained from a well-preserved stratigraphic succession in Toca de Cima do Pilão cave, near the National Park of Serra da Capivara in semiarid Brazil. We propose two hypotheses to explain the presence of organic compounds related to 1200 to 1800 cm-1 Raman spectral range in fossil tissues: (i) these bands are biological signatures of preserved fossil biomolecules, or (ii) they are exogenous biological signatures associated with the bacterial biofilm formation during post-depositional processes. Our results align with the latter hypothesis, followed by biofilm degradation. However, the specific mechanisms involved in the natural biofilm degradation in fossil records remain unexplored in this study. In our case, the formation of biofilm on fossil bones is attributed to the oligotrophic conditions of the cave sediment matrix. We present a comprehensive model to elucidate the existence of biofilm on fossilized tissues, emphasizing the pivotal role of post-depositional processes, especially water action, in the cave environment. As the fossils were discovered in a cave setting, post-depositional processes significantly contribute to the formation of the biofilm matrix. Although our study provides insights into biofilm formation, further research is needed to delve into the specific mechanisms driving natural biofilm degradation in fossils.
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Affiliation(s)
- Daniel Vieira de Sousa
- Colegiado de Geografia, Universidade Federal do Vale do São Francisco, Senhor do Bonfim, Petrolina, 48970-000, Brazil.
| | | | - Estevan Eltink
- Colegiado de Ecologia, Universidade Federal do Vale do São Francisco, Senhor do Bonfim, Petrolina, 48970-000, Brazil
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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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Wu Q, Chen H, Li Z, Jiang S, Wang X, Zhou Z. The morphology and histology of the pectoral girdle of Hamipterus (Pterosauria), from the Early Cretaceous of Northwest China. Anat Rec (Hoboken) 2023. [PMID: 36787121 DOI: 10.1002/ar.25167] [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: 11/29/2022] [Revised: 01/05/2023] [Accepted: 01/10/2023] [Indexed: 02/15/2023]
Abstract
As one of the mysteries volant vertebrates, pterosaurs were completely extinct in the K-Pg extinction event, which hampered our understanding of their flight. Recent studies on pterosaur flight usually use birds as analogies, since their shoulder girdle share many features. However, it was also proposed that these two groups may differ in some critical flight mechanisms, such as the primary muscles for the upstroke of the wings. Here, we describe and characterize the detail features of the pectoral girdle morphology and histology in Hamipterus from the Early Cretaceous of Northwest China for the first time. Our research reveals that the scapula and coracoid of Hamipterus form a synostosis joint, representing a distinct pectoral girdle adaption during pterosaur flight evolution, different from that of birds. The residual of the articular cartilage of the glenoid fossa supports the potential for cartilage tissue preservation in this location. The morphology of the acrocoracoid process of Hamipterus indicates it may work as a pulley for M. supracoracoideus as the main power of flight upstroke resembles that of birds. But the saddle type of the shoulder joint of the pterosaur may limit the rotation of the humerus head, suggesting a particular mechanism to control the angle of attack unlike birds. The presence of both the similarity and differences between the flight apparatus of pterosaurs and birds are highlighted in our research, which may be related to the flight mechanism and forelimb functional adaption. The distinctive feature of the flight apparatus of pterosaur should be treated with caution in future research, to better understand the life of this unique extinct volant vertebrate.
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Affiliation(s)
- Qian Wu
- University of the Chinese Academy of Sciences, Beijing, China
- Key Laboratory of Vertebrate Evolution and Human Origins, Institute of Vertebrate Paleontology and Paleoanthropology, Chinese Academy of Sciences, Beijing, China
- CAS Center for Excellence in Life and Paleoenvironment, Beijing, China
| | - He Chen
- School of Ecology, Sun Yat-sen University, Shenzhen, China
| | - Zhiheng Li
- Key Laboratory of Vertebrate Evolution and Human Origins, Institute of Vertebrate Paleontology and Paleoanthropology, Chinese Academy of Sciences, Beijing, China
- CAS Center for Excellence in Life and Paleoenvironment, Beijing, China
| | - Shunxing Jiang
- Key Laboratory of Vertebrate Evolution and Human Origins, Institute of Vertebrate Paleontology and Paleoanthropology, Chinese Academy of Sciences, Beijing, China
- CAS Center for Excellence in Life and Paleoenvironment, Beijing, China
| | - Xiaolin Wang
- University of the Chinese Academy of Sciences, Beijing, China
- Key Laboratory of Vertebrate Evolution and Human Origins, Institute of Vertebrate Paleontology and Paleoanthropology, Chinese Academy of Sciences, Beijing, China
- CAS Center for Excellence in Life and Paleoenvironment, Beijing, China
| | - Zhonghe Zhou
- University of the Chinese Academy of Sciences, Beijing, China
- Key Laboratory of Vertebrate Evolution and Human Origins, Institute of Vertebrate Paleontology and Paleoanthropology, Chinese Academy of Sciences, Beijing, China
- CAS Center for Excellence in Life and Paleoenvironment, Beijing, China
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4
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Anderson LA. Biomolecular histology as a novel proxy for ancient DNA and protein sequence preservation. Ecol Evol 2022; 12:e9518. [PMID: 36518622 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 Biology North Carolina State University Raleigh North Carolina USA
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5
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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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7
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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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8
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Korneisel DE, Nesbitt SJ, Werning S, Xiao S. Putative fossil blood cells reinterpreted as diagenetic structures. PeerJ 2022; 9:e12651. [PMID: 35003935 PMCID: PMC8684720 DOI: 10.7717/peerj.12651] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/12/2021] [Accepted: 11/28/2021] [Indexed: 01/08/2023] Open
Abstract
Red to red-orange spheres in the vascular canals of fossil bone thin sections have been repeatedly reported using light microscopy. Some of these have been interpreted as the fossilized remains of blood cells or, alternatively, pyrite framboids. Here, we assess claims of blood cell preservation within bones of the therizinosauroid theropod Beipiaosaurus inexpectus from the Jehol Lagerstätte. Using Raman spectroscopy, Energy Dispersive X-ray Spectrometry, and Time of Flight Secondary Ion Mass Spectroscopy, we found evidence of high taphonomic alteration of the bone. We also found that the vascular canals in the bone, once purported to contain fossil red blood cell, are filled with a mix of clay minerals and carbonaceous compounds. The spheres could not be analyzed in isolation, but we did not find any evidence of pyrite or heme compounds in the vessels, surrounding bone, or matrix. However, we did observe similar spheres under light microscopy in petrified wood found in proximity to the dinosaur. Consequently, we conclude that the red spheres are most likely diagenetic structures replicated by the clay minerals present throughout the vascular canals.
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Affiliation(s)
- Dana E Korneisel
- Department of Geosciences, Virginia Polytechnic Institute and State University (Virginia Tech), Blacksburg, VA, United States of America
| | - Sterling J Nesbitt
- Department of Geosciences, Virginia Polytechnic Institute and State University (Virginia Tech), Blacksburg, VA, United States of America
| | - Sarah Werning
- Department of Anatomy, Des Moines University, Des Moines, IA, United States of America
| | - Shuhai Xiao
- Department of Geosciences, Virginia Polytechnic Institute and State University (Virginia Tech), Blacksburg, VA, United States of America
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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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10
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Inkret J, Podovšovnik E, Zupanc T, Haring G, Pajnič IZ. Intra-bone nuclear DNA variability in Second World War metatarsal and metacarpal bones. Int J Legal Med 2021; 135:1245-1256. [PMID: 33624158 DOI: 10.1007/s00414-021-02528-9] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/18/2020] [Accepted: 02/03/2021] [Indexed: 11/30/2022]
Abstract
DNA analysis of Second World War skeletal remains is challenging because of the limited yield of DNA that is usually recovered. Recent forensic research has focused on determining which skeletal elements are superior in their preservation of DNA, and little focus has been placed on measuring intra-bone variability. Metatarsals and metacarpals outperformed all the other bones in DNA yield when analyzing all representative skeletal elements of three Second World War victims, and intra-bone variability was not studied. Soft-tissue remnants were found to contribute to higher DNA yield in trabecular bone tissue. Because metatarsals and metacarpals are composed of trabecular epiphyses and a dense diaphysis, the goal of this study was to explore intra-bone variability in DNA content by measuring nuclear DNA quantity and quality using the PowerQuant System (Promega). A total of 193 bones from a single Second World War mass grave were examined. From each bone, DNA was extracted from the compact diaphysis and from both spongy epiphyses combined. This study confirms higher DNA quantity in epiphyses than diaphyses among all the bones analyzed, and more DNA was obtained from metacarpal epiphyses than from metatarsal epiphyses. Therefore, whenever the possibility for sampling both metacarpals and metatarsals from skeletal remains exists, collecting metacarpals is recommended. In cases in which the hands are missing, metatarsals should be sampled. In any case, epiphyses are a richer source of DNA than diaphyses.
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Affiliation(s)
- Jezerka Inkret
- Institute of Forensic Medicine, Faculty of Medicine, University of Ljubljana, Korytkova 2, 1000, Ljubljana, Slovenia
| | - Eva Podovšovnik
- Faculty of Tourism Studies - Turistica, University of Primorska, Portorož, Slovenia
| | - Tomaž Zupanc
- Institute of Forensic Medicine, Faculty of Medicine, University of Ljubljana, Korytkova 2, 1000, Ljubljana, Slovenia
| | - Gregor Haring
- Institute of Forensic Medicine, Faculty of Medicine, University of Ljubljana, Korytkova 2, 1000, Ljubljana, Slovenia
| | - Irena Zupanič Pajnič
- Institute of Forensic Medicine, Faculty of Medicine, University of Ljubljana, Korytkova 2, 1000, Ljubljana, Slovenia.
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11
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Molecular tests support the viability of rare earth elements as proxies for fossil biomolecule preservation. Sci Rep 2020; 10:15566. [PMID: 32968129 PMCID: PMC7511940 DOI: 10.1038/s41598-020-72648-6] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/10/2020] [Accepted: 08/13/2020] [Indexed: 11/22/2022] Open
Abstract
The rare earth element (REE) composition of a fossil bone reflects its chemical alteration during diagenesis. Consequently, fossils presenting low REE concentrations and/or REE profiles indicative of simple diffusion, signifying minimal alteration, have been proposed as ideal candidates for paleomolecular investigation. We directly tested this prediction by conducting multiple biomolecular assays on a well-preserved fibula of the dinosaur Edmontosaurus from the Cretaceous Hell Creek Formation previously found to exhibit low REE concentrations and steeply-declining REE profiles. Gel electrophoresis identified the presence of organic material in this specimen, and subsequent immunofluorescence and enzyme-linked immunosorbant assays identified preservation of epitopes of the structural protein collagen I. Our results thereby support the utility of REE profiles as proxies for soft tissue and biomolecular preservation in fossil bones. Based on considerations of trace element taphonomy, we also draw predictions as to the biomolecular recovery potential of additional REE profile types exhibited by fossil bones.
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12
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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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13
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Righetti PG, Zilberstein G, Zilberstein S. EVA Technology and Proteomics: A Two-Pronged Attack on Cultural Heritage. J Proteome Res 2020; 19:2914-2925. [PMID: 32442381 DOI: 10.1021/acs.jproteome.0c00080] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
A novel way for exploring the world's cultural heritage in the absence of damage or contamination (such as removing pigments in paintings or chipping away pieces of bones) of the items under investigation is here reported, called the EVA technique. It is based on films of ethylene vinyl acetate (EVA) impregnated with strong anion and cation exchangers, admixed with hydrophobic resins, C8 and C18. When in contact with any surface these films can harvest nanomoles of macromolecules (proteins and DNA) as well as metabolites, which can then be identified by standard instrumentation. Some important applications are reported, such as the findings of the renal pathology and assumption of morphine in the original manuscript of Master I Margarita by Bulgakov, the presence of TBC bacterium in Chekhov's shirt and in a letter by Orwell, the Y. pestis and anthrax bacteria in the death registries of Milan's lazaretto in the 1630 plague bout, as well as ample traces of five metals in Kepler's manuscripts, suggesting his potential practice of alchemy. Also, in the pages of the Memoirs of Casanova, although the gonorrhea bacterium could not be found, spots of HgS could be measured, suggesting its use for curing the disease. A family of EVA films is described, enlarging its use to dedicated applications, such as the capture of drugs of abuse in the pages of famous writers and even in the paintings of fauvists. It is hoped that the present methodology could open the doors of museums, state archives, and private collections for detecting biological traces left by artists, literates, and men of culture in their masterpieces.
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Affiliation(s)
- Pier Giorgio Righetti
- Department of Chemistry, Materials and Chemical Engineering "'Giulio Natta"', Politecnico di Milano, Via Mancinelli 7, Milano 20131, Italy
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Wöss C, Unterberger SH, Degenhart G, Akolkar A, Traxl R, Kuhn V, Schirmer M, Pallua AK, Tappert R, Pallua JD. Comparison of structure and composition of a fossil Champsosaurus vertebra with modern Crocodylidae vertebrae: A multi-instrumental approach. J Mech Behav Biomed Mater 2020; 104:103668. [PMID: 32174426 DOI: 10.1016/j.jmbbm.2020.103668] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/04/2019] [Revised: 01/29/2020] [Accepted: 02/01/2020] [Indexed: 11/30/2022]
Abstract
Information on the adaptation of bone structures during evolution is rare since histological data are limited. Micro- and nano-computed tomography of a fossilized vertebra from Champsosaurus sp., which has an estimated age of 70-73 million years, revealed lower porosity and higher bone density compared to modern Crocodylidae vertebrae. Mid-infrared reflectance and energy dispersive X-ray mapping excluded a petrification process, and demonstrated a typical carbonate apatite distribution, confirming histology in light- and electron microscopy of the preserved vertebra. As a consequence of this evolutionary process, the two vertebrae of modern Crocodylidae show reduced overall stiffness in the finite element analysis simulation compared to the fossilized Champsosaurus sp. vertebra, with predominant stiffness along the longitudinal z-axes.
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Affiliation(s)
- C Wöss
- Institute of Legal Medicine, Medical University of Innsbruck, Müllerstraße 44, 6020, Innsbruck, Austria
| | - S H Unterberger
- Unit for Material Technology, University of Innsbruck, Technikerstraße 13, 6020, Innsbruck, Austria
| | - G Degenhart
- Department of Radiology, Medical University of Innsbruck, Anichstraße 35, 6020, Innsbruck, Austria
| | - A Akolkar
- Illwerke vkw Professorship for Energy Efficiency, Vorarlberg University of Applied Sciences, Hochschulstraße 1, 6850, Dornbirn, Austria; Josef Ressel Center for Applied Computational Science in Energy, Finance, and Logistics, Hochschulstraße 1, 6850, Dornbirn, Austria
| | - R Traxl
- Unit for Material Technology, University of Innsbruck, Technikerstraße 13, 6020, Innsbruck, Austria
| | - V Kuhn
- Department of Traumatology, Medical University of Innsbruck, Anichstraße 35, 6020, Innsbruck, Austria
| | - M Schirmer
- Department of Internal Medicine, Clinic II, Medical University of Innsbruck, Anichstrasse 35, 6020, Innsbruck, Austria
| | - A K Pallua
- Former Institute for Computed Tomography-Neuro CT, Medical University of Innsbruck, Anichstraße 35, 6020, Innsbruck, Austria
| | - R Tappert
- Hyperspectral Intelligence Inc., Box 851, Gibsons, British Columbia, V0N 1V0, Canada
| | - J D Pallua
- Institute of Legal Medicine, Medical University of Innsbruck, Müllerstraße 44, 6020, Innsbruck, Austria; Institute of Pathology, Neuropathology and Molecular Pathology, Medical University of Innsbruck, Müllerstraße 44, 6020, Innsbruck, Austria.
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15
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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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16
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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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17
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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] [Key Words] [MESH Headings] [Grants] [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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18
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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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19
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Schroeter ER, Blackburn K, Goshe MB, Schweitzer MH. Proteomic method to extract, concentrate, digest and enrich peptides from fossils with coloured (humic) substances for mass spectrometry analyses. ROYAL SOCIETY OPEN SCIENCE 2019; 6:181433. [PMID: 31598217 PMCID: PMC6731700 DOI: 10.1098/rsos.181433] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 08/30/2018] [Accepted: 07/23/2019] [Indexed: 06/10/2023]
Abstract
Humic substances are breakdown products of decaying organic matter that co-extract with proteins from fossils. These substances are difficult to separate from proteins in solution and interfere with analyses of fossil proteomes. We introduce a method combining multiple recent advances in extraction protocols to both concentrate proteins from fossil specimens with high humic content and remove humics, producing clean samples easily analysed by mass spectrometry (MS). This method includes: (i) a non-demineralizing extraction buffer that eliminates protein loss during the demineralization step in routine methods; (ii) filter-aided sample preparation (FASP) of peptides, which concentrates and digests extracts in one filter, allowing the separation of large humics after digestion; (iii) centrifugal stage tipping, which further clarifies and concentrates samples in a uniform process performed simultaneously on multiple samples. We apply this method to a moa fossil (approx. 800-1000 years) dark with humic content, generating colourless samples and enabling the detection of more proteins with greater sequence coverage than previous MS analyses on this same specimen. This workflow allows analyses of low-abundance proteins in fossils containing humics and thus may widen the range of extinct organisms and regions of their proteomes we can explore with MS.
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Affiliation(s)
- Elena R. Schroeter
- Department of Biological Sciences, North Carolina State University, Raleigh, NC 27513, USA
| | - Kevin Blackburn
- Department of Molecular and Structural Biochemistry, North Carolina State University, Raleigh, NC 27513, USA
| | - Michael B. Goshe
- Department of Molecular and Structural Biochemistry, North Carolina State University, Raleigh, NC 27513, USA
| | - Mary H. Schweitzer
- Department of Biological Sciences, North Carolina State University, Raleigh, NC 27513, USA
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20
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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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21
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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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Shah FA, Ruscsák K, Palmquist A. 50 years of scanning electron microscopy of bone-a comprehensive overview of the important discoveries made and insights gained into bone material properties in health, disease, and taphonomy. Bone Res 2019; 7:15. [PMID: 31123620 PMCID: PMC6531483 DOI: 10.1038/s41413-019-0053-z] [Citation(s) in RCA: 43] [Impact Index Per Article: 8.6] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/03/2019] [Revised: 04/09/2019] [Accepted: 04/11/2019] [Indexed: 02/06/2023] Open
Abstract
Bone is an architecturally complex system that constantly undergoes structural and functional optimisation through renewal and repair. The scanning electron microscope (SEM) is among the most frequently used instruments for examining bone. It offers the key advantage of very high spatial resolution coupled with a large depth of field and wide field of view. Interactions between incident electrons and atoms on the sample surface generate backscattered electrons, secondary electrons, and various other signals including X-rays that relay compositional and topographical information. Through selective removal or preservation of specific tissue components (organic, inorganic, cellular, vascular), their individual contribution(s) to the overall functional competence can be elucidated. With few restrictions on sample geometry and a variety of applicable sample-processing routes, a given sample may be conveniently adapted for multiple analytical methods. While a conventional SEM operates at high vacuum conditions that demand clean, dry, and electrically conductive samples, non-conductive materials (e.g., bone) can be imaged without significant modification from the natural state using an environmental scanning electron microscope. This review highlights important insights gained into bone microstructure and pathophysiology, bone response to implanted biomaterials, elemental analysis, SEM in paleoarchaeology, 3D imaging using focused ion beam techniques, correlative microscopy and in situ experiments. The capacity to image seamlessly across multiple length scales within the meso-micro-nano-continuum, the SEM lends itself to many unique and diverse applications, which attest to the versatility and user-friendly nature of this instrument for studying bone. Significant technological developments are anticipated for analysing bone using the SEM.
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Affiliation(s)
- Furqan A. Shah
- Department of Biomaterials, Sahlgrenska Academy, University of Gothenburg, Gothenburg, Sweden
| | - Krisztina Ruscsák
- Department of Biomaterials, Sahlgrenska Academy, University of Gothenburg, Gothenburg, Sweden
| | - Anders Palmquist
- Department of Biomaterials, Sahlgrenska Academy, University of Gothenburg, Gothenburg, Sweden
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23
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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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24
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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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25
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Héctor R, Omar EN, González M, Mario C. Ultrastructural preservation of tissues and their reaction to the infection with trichinella in the El Plomo mummy: Muscle fiber ultrastructure and trichinosis/mummy of the Cerro El Plomo. Microsc Res Tech 2017; 80:898-903. [DOI: 10.1002/jemt.22879] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/06/2017] [Accepted: 04/04/2017] [Indexed: 11/08/2022]
Affiliation(s)
- Rodríguez Héctor
- Facultad de Medicina; Universidad de Chile. Chile; Independencia 1027 Santiago Chile
| | - Espinoza-Navarro Omar
- Departamento de Biología; Universidad de Tarapacá; General Velázquez 1775 Arica Chile
| | - Mercedes González
- Instituto de Estudios Científicos de Momias de Madrid. España; Urbanización Las Rosas; N° 37 Madrid España
| | - Castro Mario
- DIBAM. Chile; Recoleta Domínica 683 Santiago Chile
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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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Cleland TP, Schroeter ER, Schweitzer MH. Biologically and diagenetically derived peptide modifications in moa collagens. Proc Biol Sci 2016; 282:20150015. [PMID: 25972464 DOI: 10.1098/rspb.2015.0015] [Citation(s) in RCA: 59] [Impact Index Per Article: 7.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
Abstract
The modifications that occur on proteins in natural environments over time are not well studied, yet characterizing them is vital to correctly interpret sequence data recovered from fossils. The recently extinct moa (Dinornithidae) is an excellent candidate for investigating the preservation of proteins, their post-translational modifications (PTMs) and diagenetic alterations during degradation. Moa protein extracts were analysed using mass spectrometry, and peptides from collagen I, collagen II and collagen V were identified. We also identified biologically derived PTMs (i.e. methylation, di-methylation, alkylation, hydroxylation, fucosylation) on amino acids at locations consistent with extant proteins. In addition to these in vivo modifications, we detected novel modifications that are probably diagenetically derived. These include loss of hydroxylation/glutamic semialdehyde, carboxymethyllysine and peptide backbone cleavage, as well as previously noted deamidation. Moa collagen sequences and modifications provide a baseline by which to evaluate proteomic studies of other fossils, and a framework for defining the molecular relationship of moa to other closely related taxa.
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Affiliation(s)
- Timothy P Cleland
- Department of Biomedical Engineering, Rensselaer Polytechnic Institute, Troy, NY 12182, USA
| | - Elena R Schroeter
- 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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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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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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31
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Tomescu AMF, Klymiuk AA, Matsunaga KKS, Bippus AC, Shelton GWK. Microbes and the Fossil Record: Selected Topics in Paleomicrobiology. THEIR WORLD: A DIVERSITY OF MICROBIAL ENVIRONMENTS 2016. [DOI: 10.1007/978-3-319-28071-4_3] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
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32
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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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33
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Cappella A, Bertoglio B, Castoldi E, Maderna E, Di Giancamillo A, Domeneghini C, Andreola S, Cattaneo C. The taphonomy of blood components in decomposing bone and its relevance to physical anthropology. AMERICAN JOURNAL OF PHYSICAL ANTHROPOLOGY 2015; 158:636-45. [DOI: 10.1002/ajpa.22830] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/21/2015] [Revised: 07/17/2015] [Accepted: 07/23/2015] [Indexed: 11/07/2022]
Affiliation(s)
- Annalisa Cappella
- Dipartimento Di Scienze Biomediche per La Salute, LABANOF, Laboratorio Di Antropologia E Odontologia Forense, Sezione Di Medicina Legale; Università Degli Studi Di Milano; Milan 20133 Italy
| | - Barbara Bertoglio
- Dipartimento Di Scienze Biomediche per La Salute, LABANOF, Laboratorio Di Antropologia E Odontologia Forense, Sezione Di Medicina Legale; Università Degli Studi Di Milano; Milan 20133 Italy
- Fellow of the Genetics; Molecular and Cellular Biology Ph.D. program of the University of Pavia
| | - Elisa Castoldi
- Dipartimento Di Scienze Biomediche per La Salute, LABANOF, Laboratorio Di Antropologia E Odontologia Forense, Sezione Di Medicina Legale; Università Degli Studi Di Milano; Milan 20133 Italy
| | - Emanuela Maderna
- Dipartimento Di Scienze Biomediche per La Salute, LABANOF, Laboratorio Di Antropologia E Odontologia Forense, Sezione Di Medicina Legale; Università Degli Studi Di Milano; Milan 20133 Italy
| | - Alessia Di Giancamillo
- Department of Health, Animal Science and Food Safety; Università Degli Studi Di Milano; Milan 20133 Italy
| | - Cinzia Domeneghini
- Department of Health, Animal Science and Food Safety; Università Degli Studi Di Milano; Milan 20133 Italy
| | - Salvatore Andreola
- Dipartimento Di Scienze Biomediche per La Salute, LABANOF, Laboratorio Di Antropologia E Odontologia Forense, Sezione Di Medicina Legale; Università Degli Studi Di Milano; Milan 20133 Italy
| | - Cristina Cattaneo
- Dipartimento Di Scienze Biomediche per La Salute, LABANOF, Laboratorio Di Antropologia E Odontologia Forense, Sezione Di Medicina Legale; Università Degli Studi Di Milano; Milan 20133 Italy
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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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35
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Gaul JS, Winter E, Grossschmidt K. Ancient pathogens in museal dry bone specimens: analysis of paleocytology and aDNA. Wien Med Wochenschr 2015; 165:133-9. [PMID: 25994097 DOI: 10.1007/s10354-015-0357-6] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/20/2014] [Accepted: 04/16/2015] [Indexed: 11/29/2022]
Abstract
Bone samples investigated in this study derive from the pathologic-anatomical collection of the Natural History Museum of Vienna. In order to explore the survival of treponemes and treponemal ancient DNA in museal dry bone specimens, we analyzed three individuals known to have been infected with Treponema pallidum pallidum. No reproducible evidence of surviving pathogen's ancient DNA (aDNA) was obtained, despite the highly sensitive extraction and amplification techniques (TPP15 and arp). Additionally, decalcification fluid of bone sections was smear stained with May-Gruenwald-Giemsa. The slides were examined using direct light microscope and dark field illumination. Remnants of spirochetal structures were detectable in every smear. Our results demonstrate that aDNA is unlikely to survive, but spirochetal remains are stainable and thus detectable.
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Affiliation(s)
- Johanna Sophia Gaul
- Department of Anthropology, University of Vienna, Althanstrasse 14, 1090, Vienna, Austria,
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36
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Coulson-Thomas YM, Norton AL, Coulson-Thomas VJ, Florencio-Silva R, Ali N, Elmrghni S, Gil CD, Sasso GRS, Dixon RA, Nader HB. DNA and bone structure preservation in medieval human skeletons. Forensic Sci Int 2015; 251:186-94. [PMID: 25912776 DOI: 10.1016/j.forsciint.2015.04.005] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/13/2014] [Revised: 01/29/2015] [Accepted: 04/03/2015] [Indexed: 10/23/2022]
Abstract
Morphological and ultrastructural data from archaeological human bones are scarce, particularly data that have been correlated with information on the preservation of molecules such as DNA. Here we examine the bone structure of macroscopically well-preserved medieval human skeletons by transmission electron microscopy and immunohistochemistry, and the quantity and quality of DNA extracted from these skeletons. DNA technology has been increasingly used for analyzing physical evidence in archaeological forensics; however, the isolation of ancient DNA is difficult since it is highly degraded, extraction yields are low and the co-extraction of PCR inhibitors is a problem. We adapted and optimised a method that is frequently used for isolating DNA from modern samples, Chelex(®) 100 (Bio-Rad) extraction, for isolating DNA from archaeological human bones and teeth. The isolated DNA was analysed by real-time PCR using primers targeting the sex determining region on the Y chromosome (SRY) and STR typing using the AmpFlSTR(®) Identifiler PCR Amplification kit. Our results clearly show the preservation of bone matrix in medieval bones and the presence of intact osteocytes with well preserved encapsulated nuclei. In addition, we show how effective Chelex(®) 100 is for isolating ancient DNA from archaeological bones and teeth. This optimised method is suitable for STR typing using kits aimed specifically at degraded and difficult DNA templates since amplicons of up to 250bp were successfully amplified.
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Affiliation(s)
- Yvette M Coulson-Thomas
- Department of Biochemistry, Universidade Federal de São Paulo, Rua Três de Maio 100, São Paulo, 04044-020, Brazil; School of Life Sciences, University of Lincoln, Brayford Pool, Lincoln, LN6 7TS, UK.
| | | | - Vivien J Coulson-Thomas
- Department of Biochemistry, Universidade Federal de São Paulo, Rua Três de Maio 100, São Paulo, 04044-020, Brazil; John van Geest Centre for Brain Repair, University of Cambridge, Forvie Site, Robinson Way, Cambridge, CB2 0PY, UK
| | - Rinaldo Florencio-Silva
- Department of Morphology and Genetics, Universidade Federal de São Paulo, Rua Botucatu 740, São Paulo, 04023-900, Brazil
| | - Nadir Ali
- School of Life Sciences, University of Lincoln, Brayford Pool, Lincoln, LN6 7TS, UK
| | - Samir Elmrghni
- School of Life Sciences, University of Lincoln, Brayford Pool, Lincoln, LN6 7TS, UK
| | - Cristiane D Gil
- Department of Morphology and Genetics, Universidade Federal de São Paulo, Rua Botucatu 740, São Paulo, 04023-900, Brazil
| | - Gisela R S Sasso
- Department of Morphology and Genetics, Universidade Federal de São Paulo, Rua Botucatu 740, São Paulo, 04023-900, Brazil
| | - Ronald A Dixon
- School of Life Sciences, University of Lincoln, Brayford Pool, Lincoln, LN6 7TS, UK
| | - Helena B Nader
- Department of Biochemistry, Universidade Federal de São Paulo, Rua Três de Maio 100, São Paulo, 04044-020, Brazil
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Blood or spores? A cautionary note on interpreting cellular debris on human skeletal remains. Int J Legal Med 2015; 129:919-26. [PMID: 25563601 DOI: 10.1007/s00414-014-1140-8] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/19/2014] [Accepted: 12/19/2014] [Indexed: 10/24/2022]
Abstract
The identification of red blood cells on both skeletal human remains and decomposed corpses is of remarkable importance in forensic sciences, irrespective of its diagnostic value; their presence is often perplexing and difficult to interpret especially when in the context of decomposition and taphonomical variables. Some clinical research has focused on the morphological changes of red blood cells over time by scanning electron microscopy (SEM), but no research has investigated whether botanical structures can be confused for red blood cells. Since some literature has recently presumed the detection of erythrocyte-like cells on skeletal remains (even ancient) as surely erythrocytes, and most have never taken into consideration the chance of an origin different from blood, such as botanical, the present study aims at verifying the possibility of confusion between erythrocytes and botanical cells by applying SEM analysis and at highlighting the pitfalls in this particular issue through a test submitted to pathologists and natural scientists asked to discriminate between red blood cells and different vegetal structures (60 images obtained by SEM analysis). The results showed that although there are diagnostic features useful in identifying red blood cells from botanical structures, some spores resulted very similar to decaying red blood cells, which calls for attention and great caution when studying decomposed human remains.
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38
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A Pelomedusoid Turtle from the Paleocene–Eocene of Colombia Exhibiting Preservation of Blood Vessels and Osteocytes. J HERPETOL 2014. [DOI: 10.1670/13-046] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
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39
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Setzer TJ. Malaria detection in the field of paleopathology: a meta-analysis of the state of the art. Acta Trop 2014; 140:97-104. [PMID: 25149357 DOI: 10.1016/j.actatropica.2014.08.010] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/22/2014] [Revised: 08/06/2014] [Accepted: 08/09/2014] [Indexed: 01/10/2023]
Abstract
An integrative literature review was conducted to identify the current state of the art regarding malaria research in human remains and to identify novel methods to test for malaria infections in archaeological samples. This review was comprised of two surveys. The first survey established methods used currently to detect malaria in human remains from archaeological contexts. The second survey identified diagnostic approaches in the field of medicine. Techniques in medicine that could have applications with samples from archaeological contexts, such as preserved soft tissue and skeletal remains, are presented.
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Prondvai E, Stein KHW, de Ricqlès A, Cubo J. Development-based revision of bone tissue classification: the importance of semantics for science. Biol J Linn Soc Lond 2014. [DOI: 10.1111/bij.12323] [Citation(s) in RCA: 68] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/29/2022]
Affiliation(s)
- Edina Prondvai
- MTA-ELTE Lendület Dinosaur Research Group; Eötvös Loránd University; Pázmány Péter s. 1/c, 1117 Budapest Hungary
| | - Koen H. W. Stein
- Museum für Naturkunde Berlin; Leibniz Institute for Evolution and Biodiversity Science; Invalidenstrasse 43 10115 Berlin Germany
| | - Armand de Ricqlès
- UPMC; UMR 7193, ISTeP; Sorbonne Universités; Univ Paris 06 4 Place Jussieu BC 19 F-75005 Paris France
- CNRS; UMR 7193, ISTeP; 4 place Jussieu BC 19 F-75005 Paris France
| | - Jorge Cubo
- UPMC; UMR 7193, ISTeP; Sorbonne Universités; Univ Paris 06 4 Place Jussieu BC 19 F-75005 Paris France
- CNRS; UMR 7193, ISTeP; 4 place Jussieu BC 19 F-75005 Paris France
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Schweitzer MH, Zheng W, Cleland TP, Goodwin MB, Boatman E, Theil E, Marcus MA, Fakra SC. A role for iron and oxygen chemistry in preserving soft tissues, cells and molecules from deep time. Proc Biol Sci 2014; 281:20132741. [PMID: 24285202 PMCID: PMC3866414 DOI: 10.1098/rspb.2013.2741] [Citation(s) in RCA: 57] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/21/2013] [Accepted: 10/29/2013] [Indexed: 01/15/2023] Open
Abstract
The persistence of original soft tissues in Mesozoic fossil bone is not explained by current chemical degradation models. We identified iron particles (goethite-αFeO(OH)) associated with soft tissues recovered from two Mesozoic dinosaurs, using transmission electron microscopy, electron energy loss spectroscopy, micro-X-ray diffraction and Fe micro-X-ray absorption near-edge structure. Iron chelators increased fossil tissue immunoreactivity to multiple antibodies dramatically, suggesting a role for iron in both preserving and masking proteins in fossil tissues. Haemoglobin (HB) increased tissue stability more than 200-fold, from approximately 3 days to more than two years at room temperature (25°C) in an ostrich blood vessel model developed to test post-mortem 'tissue fixation' by cross-linking or peroxidation. HB-induced solution hypoxia coupled with iron chelation enhances preservation as follows: HB + O2 > HB - O2 > -O2 >> +O2. The well-known O2/haeme interactions in the chemistry of life, such as respiration and bioenergetics, are complemented by O2/haeme interactions in the preservation of fossil soft tissues.
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Affiliation(s)
- Mary H. Schweitzer
- Marine, Earth, and Atmospheric Sciences, North Carolina State University, Campus Box 8208, Raleigh, NC 27695, USA
- North Carolina Museum of Natural Sciences, 11 West Jones Street, Raleigh, NC 27601, USA
| | - Wenxia Zheng
- Marine, Earth, and Atmospheric Sciences, North Carolina State University, Campus Box 8208, Raleigh, NC 27695, USA
| | - Timothy P. Cleland
- Marine, Earth, and Atmospheric Sciences, North Carolina State University, Campus Box 8208, Raleigh, NC 27695, USA
| | - Mark B. Goodwin
- Museum of Paleontology, University of California, Berkeley, CA 94720, USA
| | - Elizabeth Boatman
- Department of Material Sciences and Engineering, University of California, Berkeley, CA 94720, USA
| | - Elizabeth Theil
- CHORI (Children's Hospital Oakland Research Institute), 5700 Martin Luther King, Jr. Way, Oakland, CA 94609, USA
- Department of Molecular and Structural Biochemistry, North Carolina State University, Raleigh, NC 27695-7622, USA
| | - Matthew A. Marcus
- Advanced Light Source, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA
| | - Sirine C. Fakra
- Advanced Light Source, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA
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Smejkal GB, Poinar GO, Righetti PG. Will amber inclusions provide the first glimpse of a Mesozoic proteome? Expert Rev Proteomics 2014; 6:1-4. [DOI: 10.1586/14789450.6.1.1] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
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43
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Smejkal GB, Schweitzer MH. Will current technologies enable dinosaur proteomics? Expert Rev Proteomics 2014; 4:695-9. [DOI: 10.1586/14789450.4.6.695] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
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Pang K, Tang Q, Schiffbauer JD, Yao J, Yuan X, Wan B, Chen L, Ou Z, Xiao S. The nature and origin of nucleus-like intracellular inclusions in Paleoproterozoic eukaryote microfossils. GEOBIOLOGY 2013; 11:499-510. [PMID: 24033870 DOI: 10.1111/gbi.12053] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/04/2013] [Accepted: 07/23/2013] [Indexed: 05/19/2023]
Abstract
The well-known debate on the nature and origin of intracellular inclusions (ICIs) in silicified microfossils from the early Neoproterozoic Bitter Springs Formation has recently been revived by reports of possible fossilized nuclei in phosphatized animal embryo-like fossils from the Ediacaran Doushantuo Formation of South China. The revisitation of this discussion prompted a critical and comprehensive investigation of ICIs in some of the oldest indisputable eukaryote microfossils-the ornamented acritarchs Dictyosphaera delicata and Shuiyousphaeridium macroreticulatum from the Paleoproterozoic Ruyang Group of North China-using a suite of characterization approaches: scanning electron microscopy (SEM), transmission electron microscopy (TEM), and focused ion beam scanning electron microscopy (FIB-SEM). Although the Ruyang acritarchs must have had nuclei when alive, our data suggest that their ICIs represent neither fossilized nuclei nor taphonomically condensed cytoplasm. We instead propose that these ICIs likely represent biologically contracted and consolidated eukaryotic protoplasts (the combination of the nucleus, surrounding cytoplasm, and plasma membrane). As opposed to degradational contraction of prokaryotic cells within a mucoidal sheath-a model proposed to explain the Bitter Springs ICIs-our model implies that protoplast condensation in the Ruyang acritarchs was an in vivo biologically programmed response to adverse conditions in preparation for encystment. While the discovery of bona fide nuclei in Paleoproterozoic acritarchs would be a substantial landmark in our understanding of eukaryote evolution, the various processes (such as degradational and biological condensation of protoplasts) capable of producing nuclei-mimicking structures require that interpretation of ICIs as fossilized nuclei be based on comprehensive investigations.
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Affiliation(s)
- K Pang
- State Key Laboratory of Paleobiology and Stratigraphy, Nanjing Institute of Geology and Paleontology, Chinese Academy of Sciences, Nanjing, China; Department of Geosciences, Virginia Polytechnic Institute and State University, Blacksburg, VA, USA
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Setzer TJ, Sundell IB, Dibbley SK, Les C. Technical note: a histological technique for detecting the cryptic preservation of erythrocytes and soft tissue in ancient human skeletonized remains. AMERICAN JOURNAL OF PHYSICAL ANTHROPOLOGY 2013; 152:566-8. [PMID: 24122740 DOI: 10.1002/ajpa.22375] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/05/2013] [Accepted: 08/30/2013] [Indexed: 11/10/2022]
Abstract
Bone samples from a Middle Bronze Age (ca., 1600-1300 BC) site were prepared for histological analysis. Preliminary results suggested that components of bone marrow remained preserved. To verify these findings and optimize the sample preparation procedure, we conducted experiments varying the type of acid used to decalcify the bones for histology preparation, as well as the exposure time to the demineralizing agents and thickness of sections taken from the samples for slide preparation. Subsequent examination of the slides revealed the presence of well-preserved erythrocytes and other cellular structures consistent with bone marrow. Our results demonstrate that the traditional methods used to prepare bone samples for histology may be adjusted to improve the quality of the soft tissue architecture and cellular morphology for histological observation.
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Affiliation(s)
- Teddi J Setzer
- Department of Anthropology, Wayne State University, Detroit, MI, 48201
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Armitage MH, Anderson KL. Soft sheets of fibrillar bone from a fossil of the supraorbital horn of the dinosaur Triceratops horridus. Acta Histochem 2013; 115:603-8. [PMID: 23414624 DOI: 10.1016/j.acthis.2013.01.001] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/09/2012] [Revised: 12/28/2012] [Accepted: 01/03/2013] [Indexed: 11/28/2022]
Abstract
Soft fibrillar bone tissues were obtained from a supraorbital horn of Triceratops horridus collected at the Hell Creek Formation in Montana, USA. Soft material was present in pre and post-decalcified bone. Horn material yielded numerous small sheets of lamellar bone matrix. This matrix possessed visible microstructures consistent with lamellar bone osteocytes. Some sheets of soft tissue had multiple layers of intact tissues with osteocyte-like structures featuring filipodial-like interconnections and secondary branching. Both oblate and stellate types of osteocyte-like cells were present in sheets of soft tissues and exhibited organelle-like microstructures. SEM analysis yielded osteocyte-like cells featuring filipodial extensions of 18-20μm in length. Filipodial extensions were delicate and showed no evidence of any permineralization or crystallization artifact and therefore were interpreted to be soft. This is the first report of sheets of soft tissues from Triceratops horn bearing layers of osteocytes, and extends the range and type of dinosaur specimens known to contain non-fossilized material in bone matrix.
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Affiliation(s)
- Mark Hollis Armitage
- Department of Biology, California State University, 18111 Nordhoff Street, Northridge, CA 91330-8303, USA.
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Schweitzer MH, Zheng W, Cleland TP, Bern M. Molecular analyses of dinosaur osteocytes support the presence of endogenous molecules. Bone 2013; 52:414-23. [PMID: 23085295 DOI: 10.1016/j.bone.2012.10.010] [Citation(s) in RCA: 69] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 08/24/2012] [Revised: 10/05/2012] [Accepted: 10/06/2012] [Indexed: 11/15/2022]
Abstract
The discovery of soft, transparent microstructures in dinosaur bone consistent in morphology with osteocytes was controversial. We hypothesize that, if original, these microstructures will have molecular features in common with extant osteocytes. We present immunological and mass spectrometry evidence for preservation of proteins comprising extant osteocytes (Actin, Tubulin, PHEX, Histone H4) in osteocytes recovered from two non-avian dinosaurs. Furthermore, antibodies to DNA show localized binding to these microstructures, which also react positively with DNA intercalating stains propidium iodide (PI) and 4',6'-diamidino-2-phenylindole dihydrochloride (DAPI). Each antibody binds dinosaur cells in patterns similar to extant cells. These data are the first to support preservation of multiple proteins and to present multiple lines of evidence for material consistent with DNA in dinosaurs, supporting the hypothesis that these structures were part of the once living animals. We propose mechanisms for preservation of cells and component molecules, and discuss implications for dinosaurian cellular biology.
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Affiliation(s)
- Mary Higby Schweitzer
- Department of Marine, Earth and Atmospheric Sciences, North Carolina State University, Raleigh, NC 27695, USA.
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Cadena EA, Schweitzer MH. Variation in osteocytes morphology vs bone type in turtle shell and their exceptional preservation from the Jurassic to the present. Bone 2012; 51:614-20. [PMID: 22584008 DOI: 10.1016/j.bone.2012.05.002] [Citation(s) in RCA: 22] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 01/19/2012] [Revised: 05/03/2012] [Accepted: 05/04/2012] [Indexed: 01/11/2023]
Abstract
Here we describe variations in osteocytes derived from each of the three bone layers that comprise the turtle shell. We examine osteocytes in bone from four extant turtle species to form a morphological 'baseline', and then compare these with morphologies of osteocytes preserved in Cenozoic and Mesozoic fossils. Two different morphotypes of osteocytes are recognized: flattened-oblate osteocytes (FO osteocytes), which are particularly abundant in the internal cortex and lamellae of secondary osteons in cancellous bone, and stellate osteocytes (SO osteocytes), principally present in the interstitial lamellae between secondary osteons and external cortex. We show that the morphology of osteocytes in each of the three bone layers is conserved through ontogeny. We also demonstrate that these morphological variations are phylogenetically independent, as well as independent of the bone origin (intramembranous or endochondral). Preservation of microstructures consistent with osteocytes in the morphology in Cenozoic and Mesozoic fossil turtle bones appears to be common, and occurs in diverse diagenetic environments including marine, freshwater, and terrestrial deposits. These data have potential to illuminate aspects of turtle biology and evolution previously unapproachable, such as estimates of genome size of extinct species, differences in metabolic rates among different bones from a single individual, and potential function of osteocytes as capsules for preservation of ancient biomolecules.
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Affiliation(s)
- Edwin A Cadena
- Marine Earth and Atmospheric Sciences Department, North Carolina State University, Raleigh, NC 27695, USA.
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Cleland TP, Voegele K, Schweitzer MH. Empirical evaluation of bone extraction protocols. PLoS One 2012; 7:e31443. [PMID: 22348088 PMCID: PMC3279360 DOI: 10.1371/journal.pone.0031443] [Citation(s) in RCA: 46] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/09/2011] [Accepted: 01/09/2012] [Indexed: 11/30/2022] Open
Abstract
The application of high-resolution analytical techniques to characterize ancient bone proteins requires clean, efficient extraction to obtain high quality data. Here, we evaluated many different protocols from the literature on ostrich cortical bone and moa cortical bone to evaluate their yield and relative purity using the identification of antibody-antigen complexes on enzyme-linked immunosorbent assay and gel electrophoresis. Moa bone provided an ancient comparison for the effectiveness of bone extraction protocols tested on ostrich bone. For the immunological part of this study, we focused on collagen I, osteocalcin, and hemoglobin because collagen and osteocalcin are the most abundant proteins in the mineralized extracellular matrix and hemoglobin is common in the vasculature. Most of these procedures demineralize the bone first, and then the remaining organics are chemically extracted. We found that the use of hydrochloric acid, rather than ethylenediaminetetraacetic acid, for demineralization resulted in the cleanest extractions because the acid was easily removed. In contrast, the use of ethylenediaminetetraacetic acid resulted in smearing upon electrophoretic separation, possibly indicating these samples were not as pure. The denaturing agents sodium dodecyl sulfate, urea, and guanidine HCl have been used extensively for the solubilization of proteins in non-biomineralized tissue, but only the latter has been used on bone. We show that all three denaturing agents are effective for extracting bone proteins. One additional method tested uses ammonium bicarbonate as a solubilizing buffer that is more appropriate for post-extraction analyses (e.g., proteomics) by removing the need for desalting. We found that both guanidine HCl and ammonium bicarbonate were effective for extracting many bone proteins, resulting in similar electrophoretic patterns. With the increasing use of proteomics, a new generation of scientists are now interested in the study of proteins from not only extant bone but also from ancient bone.
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Affiliation(s)
- Timothy P Cleland
- Department of Marine, Earth, Atmospheric Sciences, North Carolina State University, Raleigh, North Carolina, United States of America.
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