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Enya K, Yamagishi A, Kobayashi K, Yoshimura Y, Tasker EJ. A Comparative Study of Methods for Detecting Extraterrestrial Life in Exploration Missions to Mars and the Solar System II: Targeted Characteristics, Detection Techniques, and Their Combination for Survey, Detection, and Analysis. ASTROBIOLOGY 2023; 23:1099-1117. [PMID: 37768711 PMCID: PMC10616949 DOI: 10.1089/ast.2022.0148] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/26/2022] [Accepted: 08/15/2023] [Indexed: 09/29/2023]
Abstract
We present a comparative study of the methods used in the search for extraterrestrial microorganism life, including a summary table where different life-detection techniques can be easily compared as an aid to mission and instrument design aimed at life detection. This is an extension of previous study, where detection techniques for a series of target characteristics and molecules that could constitute a positive life detection were evaluated. This comparison has been extended with a particular consideration to sources of false positives, the causes of negative detection, the results of detection techniques when presented regarding terrestrial life, and additional science objectives that could be achieved outside the primary aim of detecting life. These additions address both the scientific and programmatic side of exploration mission design, where a successful proposal must demonstrate probable outcomes and be able to return valuable results even if no life is found. The applicability of the life detection techniques is considered for Earth life, Earth-independent life (life emerging independently from that on Earth,) and Earth-kin life (sharing a common ancestor with life on Earth), and techniques effective in detecting Earth life should also be useful in the detection of Earth-kin life. However, their applicability is not guaranteed for Earth-independent life. As found in our previous study, there exists no realistic single detection method that can conclusively determine the discovery of extraterrestrial life, and no method is superior to all others. In this study, we further consider combinations of detection techniques and identify imaging as a valuable addition to molecule detection methods, even in cases where there is insufficient resolution to observe the detailed morphology of a microbial cell. The search for extraterrestrial life is further divided into a survey-and-detection and analysis-and-conclusion step. These steps benefit from different detection techniques, but imaging is necessary for both parts.
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Affiliation(s)
- Keigo Enya
- Department of Solar System Sciences, Institute of Space and Astronautical Science, Japan Aerospace Exploration Agency, Sagamihara, Japan
- Space and Astronautical Science, Graduate Institute for Advanced Studies, SOKENDAI, Hayama, Japan
| | - Akihiko Yamagishi
- Department of Applied Life Science, School of Life Science, Tokyo University of Pharmacy and Life Sciences, Tokyo, Japan
| | - Kensei Kobayashi
- Department of Chemistry, Yokohama National University, Yokohama, Japan
- Department of Earth and Planetary Science, Tokyo Institute of Technology, Tokyo, Japan
| | | | - Elizabeth J. Tasker
- Department of Solar System Sciences, Institute of Space and Astronautical Science, Japan Aerospace Exploration Agency, Sagamihara, Japan
- Space and Astronautical Science, Graduate Institute for Advanced Studies, SOKENDAI, Hayama, Japan
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2
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Anné J, Canoville A, Edwards NP, Schweitzer MH, Zanno LE. Independent Evidence for the Preservation of Endogenous Bone Biochemistry in a Specimen of Tyrannosaurus rex. BIOLOGY 2023; 12:biology12020264. [PMID: 36829540 PMCID: PMC9953530 DOI: 10.3390/biology12020264] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 12/29/2022] [Revised: 02/03/2023] [Accepted: 02/04/2023] [Indexed: 02/11/2023]
Abstract
Biomolecules preserved in deep time have potential to shed light on major evolutionary questions, driving the search for new and more rigorous methods to detect them. Despite the increasing body of evidence from a wide variety of new, high resolution/high sensitivity analytical techniques, this research is commonly met with skepticism, as the long standing dogma persists that such preservation in very deep time (>1 Ma) is unlikely. The Late Cretaceous dinosaur Tyrannosaurus rex (MOR 1125) has been shown, through multiple biochemical studies, to preserve original bone chemistry. Here, we provide additional, independent support that deep time bimolecular preservation is possible. We use synchrotron X-ray fluorescence imaging (XRF) and X-ray absorption spectroscopy (XAS) to investigate a section from the femur of this dinosaur, and demonstrate preservation of elements (S, Ca, and Zn) associated with bone remodeling and redeposition. We then compare these data to the bone of an extant dinosaur (bird), as well as a second non-avian dinosaur, Tenontosaurus tilletti (OMNH 34784) that did not preserve any sign of original biochemistry. Our data indicate that MOR 1125 bone cortices have similar bone elemental distributions to that of an extant bird, which supports preservation of original endogenous chemistry in this specimen.
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Affiliation(s)
- Jennifer Anné
- The Children’s Museum of Indianapolis, Indianapolis, IN 46208, USA
- Correspondence:
| | | | - Nicholas P. Edwards
- Stanford Synchrotron Radiation Light Source, SLAC National Accelerator Laboratory, Menlo Park, CA 94025, USA
| | - Mary H. Schweitzer
- Department of Biological Sciences, Campus Box 7617, North Carolina State University, Raleigh, NC 27695, USA
- Paleontology, North Carolina Museum of Natural Sciences, 11 W. Jones St., Raleigh, NC 27601, USA
- Department of Geology, Lund University, Sölvegatan 12, 223 62 Lund, Sweden
| | - Lindsay E. Zanno
- Department of Biological Sciences, Campus Box 7617, North Carolina State University, Raleigh, NC 27695, USA
- Paleontology, North Carolina Museum of Natural Sciences, 11 W. Jones St., Raleigh, NC 27601, USA
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3
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Taphonomic and Diagenetic Pathways to Protein Preservation, Part II: The Case of Brachylophosaurus canadensis Specimen MOR 2598. BIOLOGY 2022; 11:biology11081177. [PMID: 36009804 PMCID: PMC9404959 DOI: 10.3390/biology11081177] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 06/14/2022] [Revised: 07/31/2022] [Accepted: 08/03/2022] [Indexed: 11/25/2022]
Abstract
Simple Summary Reports of the recovery of proteins and other molecules from fossils have become so common over the last two decades that some paleontologists now focus almost entirely on studying how biologic molecules can persist in fossils. In this study, we explored the fossilization history of a specimen of the hadrosaurid dinosaur Brachylophosaurus which was previously shown to preserve original cells, tissues, and structural proteins. Trace element analyses of the tibia of this specimen revealed that after its bones were buried in a brackish estuarine channel, they fossilized under wet conditions which shifted in redox state multiple times. The successful recovery of proteins from this specimen, despite this complex history of chemical alterations, shows that the processes which bind and stabilize biologic molecules shortly after death provide them remarkable physical and chemical resiliency. By uniting our results with those of similar studies on other dinosaur fossils known to also preserve original proteins, we also conclude that exposure to oxidizing conditions in the initial ~48 h postmortem likely promotes molecular stabilization reactions, and the retention of early-diagenetic trace element signatures may be a useful proxy for molecular recovery potential. Abstract Recent recoveries of peptide sequences from two Cretaceous dinosaur bones require paleontologists to rethink traditional notions about how fossilization occurs. As part of this shifting paradigm, several research groups have recently begun attempting to characterize biomolecular decay and stabilization pathways in diverse paleoenvironmental and diagenetic settings. To advance these efforts, we assessed the taphonomic and geochemical history of Brachylophosaurus canadensis specimen MOR 2598, the left femur of which was previously found to retain endogenous cells, tissues, and structural proteins. Combined stratigraphic and trace element data show that after brief fluvial transport, this articulated hind limb was buried in a sandy, likely-brackish, estuarine channel. During early diagenesis, percolating groundwaters stagnated within the bones, forming reducing internal microenvironments. Recent exposure and weathering also caused the surficial leaching of trace elements from the specimen. Despite these shifting redox regimes, proteins within the bones were able to survive through diagenesis, attesting to their remarkable resiliency over geologic time. Synthesizing our findings with other recent studies reveals that oxidizing conditions in the initial ~48 h postmortem likely promote molecular stabilization reactions and that the retention of early-diagenetic trace element signatures may be a useful proxy for molecular recovery potential.
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Soft Tissue and Biomolecular Preservation in Vertebrate Fossils from Glauconitic, Shallow Marine Sediments of the Hornerstown Formation, Edelman Fossil Park, New Jersey. BIOLOGY 2022; 11:biology11081161. [PMID: 36009787 PMCID: PMC9405258 DOI: 10.3390/biology11081161] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 06/18/2022] [Revised: 07/18/2022] [Accepted: 07/22/2022] [Indexed: 11/17/2022]
Abstract
Endogenous biomolecules and soft tissues are known to persist in the fossil record. To date, these discoveries derive from a limited number of preservational environments, (e.g., fluvial channels and floodplains), and fossils from less common depositional environments have been largely unexplored. We conducted paleomolecular analyses of shallow marine vertebrate fossils from the Cretaceous–Paleogene Hornerstown Formation, an 80–90% glauconitic greensand from Jean and Ric Edelman Fossil Park in Mantua Township, NJ. Twelve samples were demineralized and found to yield products morphologically consistent with vertebrate osteocytes, blood vessels, and bone matrix. Specimens from these deposits that are dark in color exhibit excellent histological preservation and yielded a greater recovery of cells and soft tissues, whereas lighter-colored specimens exhibit poor histology and few to no cells/soft tissues. Additionally, a well-preserved femur of the marine crocodilian Thoracosaurus was found to have retained endogenous collagen I by immunofluorescence and enzyme-linked immunosorbent assays. Our results thus not only corroborate previous findings that soft tissue and biomolecular recovery from fossils preserved in marine environments are possible but also expand the range of depositional environments documented to preserve endogenous biomolecules, thus broadening the suite of geologic strata that may be fruitful to examine in future paleomolecular studies.
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5
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Proteins, possibly human, found in World War II concentration camp artifact. Sci Rep 2022; 12:12369. [PMID: 35858951 PMCID: PMC9300652 DOI: 10.1038/s41598-022-16192-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/25/2022] [Accepted: 07/06/2022] [Indexed: 11/23/2022] Open
Abstract
Museums displaying artifacts of the human struggle against oppression are often caught in their own internal struggle between presenting factual and unbiased descriptions of their collections, or relying on testament of survivors. Often this quandary is resolved in favor of what can be verified, not what is remembered. However, with improving instrumentation, methods and informatic approaches, science can help uncover evidence able to reconcile memory and facts. Following World War II, thousands of small, cement-like disks with numbers impressed on one side were found at concentration camps throughout Europe. Survivors claimed these disks were made of human cremains; museums erred on the side of caution—without documentation of the claims, was it justifiable to present them as fact? The ability to detect species relevant biological material in these disks could help resolve this question. Proteomic mass spectrometry of five disks revealed all contained proteins, including collagens and hemoglobins, suggesting they were made, at least in part, of animal remains. A new protein/informatics approach to species identification showed that while human was not always identified as the top contributor, human was the most likely explanation for one disk. To our knowledge, this is the first demonstration of protein recovery from cremains. Data are available via ProteomeXchange with identifier PXD035267.
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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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7
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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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8
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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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9
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Horn IR, Kenens Y, Palmblad NM, van der Plas-Duivesteijn SJ, Langeveld BW, Meijer HJM, Dalebout H, Marissen RJ, Fischer A, Vincent Florens FB, Niemann J, Rijsdijk KF, Schulp AS, Laros JFJ, Gravendeel B. Palaeoproteomics of bird bones for taxonomic classification. Zool J Linn Soc 2019. [DOI: 10.1093/zoolinnean/zlz012] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022]
Affiliation(s)
- Ivo R Horn
- University of Applied Sciences Leiden, Faculty of Science and Technology, Zernikedreef, CK, Leiden, The Netherlands
- Naturalis Biodiversity Center, Endless Forms Group, Darwinweg, CR Leiden, The Netherlands
| | - Yvo Kenens
- University of Applied Sciences Leiden, Faculty of Science and Technology, Zernikedreef, CK, Leiden, The Netherlands
| | - N Magnus Palmblad
- Center for Proteomics and Metabolomics, Leiden University Medical Center, Leiden, The Netherlands
| | | | - Bram W Langeveld
- Natural History Museum Rotterdam, Museumpark, Rotterdam, The Netherlands
| | - Hanneke J M Meijer
- Naturalis Biodiversity Center, Endless Forms Group, Darwinweg, CR Leiden, The Netherlands
- University Museum, Department of Natural History, University of Bergen, Bergen, Norway
| | - Hans Dalebout
- Center for Proteomics and Metabolomics, Leiden University Medical Center, Leiden, The Netherlands
| | - Rob J Marissen
- Center for Proteomics and Metabolomics, Leiden University Medical Center, Leiden, The Netherlands
| | - Anja Fischer
- University of Amsterdam, Faculty of Humanities, Amsterdam, The Netherlands
| | - F B Vincent Florens
- Tropical Island Biodiversity, Ecology and Conservation Pole of Research, University of Mauritius, Réduit, Mauritius
| | - Jonas Niemann
- Natural History Museum of Denmark, Copenhagen, Denmark
| | - Kenneth F Rijsdijk
- BIOMAC group, Institute for Biodiversity and Ecosystem Dynamics, University of Amsterdam, Faculty of Natural Sciences, Science Park, Amsterdam, The Netherlands
| | - Anne S Schulp
- Naturalis Biodiversity Center, Endless Forms Group, Darwinweg, CR Leiden, The Netherlands
| | | | - Barbara Gravendeel
- University of Applied Sciences Leiden, Faculty of Science and Technology, Zernikedreef, CK, Leiden, The Netherlands
- Naturalis Biodiversity Center, Endless Forms Group, Darwinweg, CR Leiden, The Netherlands
- Institute of Biology Leiden, Leiden University, Sylviusweg, BE Leiden, The Netherlands
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10
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Dry-bonding to dentin using alternative conditioners based on iron-containing solutions or nitric acid. J Mech Behav Biomed Mater 2019; 94:238-248. [PMID: 30927591 DOI: 10.1016/j.jmbbm.2019.03.015] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/16/2018] [Revised: 02/06/2019] [Accepted: 03/17/2019] [Indexed: 11/21/2022]
Abstract
OBJECTIVES To evaluate the effect of experimental conditioners (10-3 solution - 10-3, 6.8% ferric oxalate - FOX, and 1.4% nitric acid - NI) on dentin elastic modulus, flexural strength, bond strength, failure mode, and adhesive interface morphology of two etch-and-rinse adhesives (XP Bond, Dentsply or One-Step, Bisco) applied on etched dry dentin. METHODS Sound human third molars were used for the microtensile bond strength test (n = 8), performed at 24 h and after one year of water storage. Failure modes were evaluated by scanning electron microscopy. Dentin bonding interface was analyzed by confocal laser scanning microscopy (n = 3). Adhesive systems were applied on phosphoric acid-etched, wet (positive control) and dry (negative control) dentin, and on etched and dry dentin previously treated with 10-3 (15s), FOX (60s), or NI (15s). Bovine dentin bars (n = 15) were immersed into the conditioning solutions and subjected to a three-point bending test. RESULTS XP Bond + 10-3 or NI resulted in lower bond strength than phosphoric acid. One-Step + 10-3 or NI resulted in bond strengths equivalent to the positive control. Experimental conditioners presented no bond strength reduction after one year, regardless of the bonding agent tested. One-Step resulted in more adhesive failures than XP Bond at 24 h, and mixed failures increased after storage. All experimental conditioners promoted hybridization and resin tags formation, except FOX. Dentin elastic modulus was not affected by the conditioners, whereas flexural strength was significantly reduced by FOX. CONCLUSIONS Adequate and stable dentin bonds were achieved when the bonding agents were applied on 10-3 or NI-treated dentin. None of the experimental conditioners reduced dentin elastic modulus, but dentin flexural strength was significantly reduced by FOX-conditioning.
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11
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Prieto-Bonete G, Pérez-Cárceles MD, Maurandi-López A, Pérez-Martínez C, Luna A. Association between protein profile and postmortem interval in human bone remains. J Proteomics 2018; 192:54-63. [PMID: 30145274 DOI: 10.1016/j.jprot.2018.08.008] [Citation(s) in RCA: 28] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/22/2017] [Revised: 06/08/2018] [Accepted: 08/07/2018] [Indexed: 12/15/2022]
Abstract
Proteomic techniques in bones forensic samples are increasingly, being applied. The main aim of forensic sciences is the estimation of postmortem interval. Most current techniques are useful for the first post-mortem stages. However, in the case of osseous remains, these techniques may be difficult to use due to the high level of decomposition of the sample. Our objective was to attempt to know whether there is a protein profile in human bone remains that would enable a late postmortem. interval ranging from 5 to 20 years postmortem to be estimated. A total of 40 femur bones from 40 different cadavers (data range 5-20 years) were use. Of the 275 total proteins, we excluded the circulating ones (n = 227), leaving a total of 48 proteins (29 structural and 19 functional) were found. A multiple correspondence analysis was applied on the 48 proteins. Finally selecting 32 proteins that allowed us to discriminate between the. two groups of postmortem interval. Analysis of the protein profile present in bone permits an approximation of the date of death within the studied interval, and could be used to complement other tests for estimating the postmortem interval.
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Affiliation(s)
| | | | - Antonio Maurandi-López
- Department of Didactics of Mathematical and Social Sciences, University of Murcia, Spain
| | | | - Aurelio Luna
- Department of Legal and Forensic Medicine, University of Murcia, Spain
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12
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Buckley M, Warwood S, van Dongen B, Kitchener AC, Manning PL. A fossil protein chimera; difficulties in discriminating dinosaur peptide sequences from modern cross-contamination. Proc Biol Sci 2017; 284:rspb.2017.0544. [PMID: 28566488 PMCID: PMC5454271 DOI: 10.1098/rspb.2017.0544] [Citation(s) in RCA: 57] [Impact Index Per Article: 8.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/14/2017] [Accepted: 05/02/2017] [Indexed: 02/05/2023] Open
Abstract
A decade ago, reports that organic-rich soft tissue survived from dinosaur fossils were apparently supported by proteomics-derived sequence information of exceptionally well-preserved bone. This initial claim to the sequencing of endogenous collagen peptides from an approximately 68 Myr Tyrannosaurus rex fossil was highly controversial, largely on the grounds of potential contamination from either bacterial biofilms or from laboratory practice. In a subsequent study, collagen peptide sequences from an approximately 78 Myr Brachylophosaurus canadensis fossil were reported that have remained largely unchallenged. However, the endogeneity of these sequences relies heavily on a single peptide sequence, apparently unique to both dinosaurs. Given the potential for cross-contamination from modern bone analysed by the same team, here we extract collagen from bone samples of three individuals of ostrich, Struthio camelus The resulting LC-MS/MS data were found to match all of the proposed sequences for both the original Tyrannosaurus and Brachylophosaurus studies. Regardless of the true nature of the dinosaur peptides, our finding highlights the difficulty of differentiating such sequences with confidence. Our results not only imply that cross-contamination cannot be ruled out, but that appropriate measures to test for endogeneity should be further evaluated.
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Affiliation(s)
- Michael Buckley
- Faculty of Science and Engineering, The University of Manchester, Manchester Institute of Biotechnology, Manchester M1 7DN, UK .,School of Earth and Environmental Sciences, Faculty of Science and Engineering, Interdisciplinary Centre for Ancient Life, The University of Manchester, Manchester, M13 9PL, UK
| | - Stacey Warwood
- Faculty of Biology, Medicine and Health, The University of Manchester, Michael Smith Building, Manchester M13 9PL, UK
| | - Bart van Dongen
- School of Earth and Environmental Sciences, Faculty of Science and Engineering, Interdisciplinary Centre for Ancient Life, The University of Manchester, Manchester, M13 9PL, UK
| | - Andrew C Kitchener
- Department of Natural Sciences, National Museums Scotland, Chambers Street, Edinburgh EH1 1JF, UK.,Institute of Geography, School of Geosciences, University of Edinburgh, Drummond Street, Edinburgh EH8 9XP, UK
| | - Phillip L Manning
- School of Earth and Environmental Sciences, Faculty of Science and Engineering, Interdisciplinary Centre for Ancient Life, The University of Manchester, Manchester, M13 9PL, UK.,Department of Geology and Environmental Geosciences, College of Charleston, 66 George Street, Charleston, SC 29424, USA
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13
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Cleland TP, Schroeter ER, Feranec RS, Vashishth D. Peptide sequences from the first Castoroides ohioensis skull and the utility of old museum collections for palaeoproteomics. Proc Biol Sci 2017; 283:rspb.2016.0593. [PMID: 27306052 DOI: 10.1098/rspb.2016.0593] [Citation(s) in RCA: 33] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/14/2016] [Accepted: 05/19/2016] [Indexed: 11/12/2022] Open
Abstract
Vertebrate fossils have been collected for hundreds of years and are stored in museum collections around the world. These remains provide a readily available resource to search for preserved proteins; however, the vast majority of palaeoproteomic studies have focused on relatively recently collected bones with a well-known handling history. Here, we characterize proteins from the nasal turbinates of the first Castoroides ohioensis skull ever discovered. Collected in 1845, this is the oldest museum-curated specimen characterized using palaeoproteomic tools. Our mass spectrometry analysis detected many collagen I peptides, a peptide from haemoglobin beta, and in vivo and diagenetic post-translational modifications. Additionally, the identified collagen I sequences provide enough resolution to place C. ohioensis within Rodentia. This study illustrates the utility of archived museum specimens for both the recovery of preserved proteins and phylogenetic analyses.
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Affiliation(s)
- Timothy P Cleland
- Department of Biomedical Engineering, Rensselaer Polytechnic Institute, Troy, NY 12180, USA
| | - Elena R Schroeter
- Department of Biological Sciences, North Carolina State University, Raleigh, NC 27695, USA
| | | | - Deepak Vashishth
- Department of Biomedical Engineering, Rensselaer Polytechnic Institute, Troy, NY 12180, USA
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14
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Zaucha J, Heddle JG. Resurrecting the Dead (Molecules). Comput Struct Biotechnol J 2017; 15:351-358. [PMID: 28652896 PMCID: PMC5472138 DOI: 10.1016/j.csbj.2017.05.002] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/15/2017] [Revised: 05/11/2017] [Accepted: 05/21/2017] [Indexed: 12/15/2022] Open
Abstract
Biological molecules, like organisms themselves, are subject to genetic drift and may even become "extinct". Molecules that are no longer extant in living systems are of high interest for several reasons including insight into how existing life forms evolved and the possibility that they may have new and useful properties no longer available in currently functioning molecules. Predicting the sequence/structure of such molecules and synthesizing them so that their properties can be tested is the basis of "molecular resurrection" and may lead not only to a deeper understanding of evolution, but also to the production of artificial proteins with novel properties and even to insight into how life itself began.
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Affiliation(s)
- Jan Zaucha
- Departament of Computer Science, University of Bristol, Life Sciences Building, 24 Tyndall Avenue, Bristol BS8 1TQ, United Kingdom
| | - Jonathan G. Heddle
- Bionanoscience and Biochemistry Laboratory, Jagiellonian University, Malopolska Centre of Biotechnology, Gronstajowa 7A, 30-387 Kraków, Poland
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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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16
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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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17
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Chemistry supports the identification of gender-specific reproductive tissue in Tyrannosaurus rex. Sci Rep 2016; 6:23099. [PMID: 26975806 PMCID: PMC4791554 DOI: 10.1038/srep23099] [Citation(s) in RCA: 30] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/17/2015] [Accepted: 03/01/2016] [Indexed: 11/09/2022] Open
Abstract
Medullary bone (MB), an estrogen-dependent reproductive tissue present in extant gravid birds, is texturally, histologically and compositionally distinct from other bone types. Phylogenetic proximity led to the proposal that MB would be present in non-avian dinosaurs, and recent studies have used microscopic, morphological, and regional homologies to identify this reproductive tissue in both theropod and ornithischian dinosaurs. Here, we capitalize on the unique chemical and histological fingerprint of MB in birds to characterize, at the molecular level, MB in the non-avian theropod Tyrannosaurus rex (MOR 1125), and show that the retention of original molecular components in fossils allows deeper physiological and evolutionary questions to be addressed.
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18
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Stewart NA, Molina GF, Mardegan Issa JP, Yates NA, Sosovicka M, Vieira AR, Line SRP, Montgomery J, Gerlach RF. The identification of peptides by nanoLC-MS/MS from human surface tooth enamel following a simple acid etch extraction. RSC Adv 2016. [DOI: 10.1039/c6ra05120k] [Citation(s) in RCA: 26] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022] Open
Abstract
Tooth enamel is the hardest, densest and most mineralized tissue in vertebrates.
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Affiliation(s)
| | - Gabriela Ferian Molina
- Department of Morphology
- Physiology, and Basic Pathology
- School of Dentistry of Ribeirão Preto
- University of São Paulo
- 14040-904 Ribeirão Preto
| | - João Paulo Mardegan Issa
- Department of Morphology
- Physiology, and Basic Pathology
- School of Dentistry of Ribeirão Preto
- University of São Paulo
- 14040-904 Ribeirão Preto
| | - Nathan Andrew Yates
- Department of Cell Biology
- University of Pittsburgh School of Medicine
- Pittsburgh
- USA
- Biomedical Mass Spectrometry Center
| | - Mark Sosovicka
- Department of Oral and Maxillofacial Surgery
- School of Dental Medicine
- University of Pittsburgh
- Pittsburgh
- USA
| | - Alexandre Rezende Vieira
- Department of Oral Biology
- School of Dental Medicine
- University of Pittsburgh. 3501 Terrace Street
- Pittsburgh
- USA
| | | | | | - Raquel Fernanda Gerlach
- Department of Morphology
- Physiology, and Basic Pathology
- School of Dentistry of Ribeirão Preto
- University of São Paulo
- 14040-904 Ribeirão Preto
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19
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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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20
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Dallongeville S, Garnier N, Rolando C, Tokarski C. Proteins in Art, Archaeology, and Paleontology: From Detection to Identification. Chem Rev 2015; 116:2-79. [PMID: 26709533 DOI: 10.1021/acs.chemrev.5b00037] [Citation(s) in RCA: 80] [Impact Index Per Article: 8.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
Affiliation(s)
- Sophie Dallongeville
- Miniaturisation pour la Synthèse, l'Analyse & la Protéomique (MSAP), USR CNRS 3290, Université de Lille 1 Sciences et Technologies , 59655 Villeneuve d'Ascq Cedex, France
| | - Nicolas Garnier
- SARL Laboratoire Nicolas Garnier , 63270 Vic le Comte, France
| | - Christian Rolando
- Miniaturisation pour la Synthèse, l'Analyse & la Protéomique (MSAP), USR CNRS 3290, Université de Lille 1 Sciences et Technologies , 59655 Villeneuve d'Ascq Cedex, France
| | - Caroline Tokarski
- Miniaturisation pour la Synthèse, l'Analyse & la Protéomique (MSAP), USR CNRS 3290, Université de Lille 1 Sciences et Technologies , 59655 Villeneuve d'Ascq Cedex, France
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21
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Quack M. On Biomolecular Homochirality as a Quasi-Fossil of the Evolution of Life. ADVANCES IN CHEMICAL PHYSICS 2014. [DOI: 10.1002/9781118959602.ch18] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
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Schweitzer MH, Schroeter ER, Goshe MB. Protein Molecular Data from Ancient (>1 million years old) Fossil Material: Pitfalls, Possibilities and Grand Challenges. Anal Chem 2014; 86:6731-40. [DOI: 10.1021/ac500803w] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
Affiliation(s)
- Mary Higby Schweitzer
- North
Carolina Museum of Natural Sciences, Raleigh, North Carolina 27601, United States
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23
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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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24
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Body fluid identification by mass spectrometry. Int J Legal Med 2013; 127:1065-77. [DOI: 10.1007/s00414-013-0848-1] [Citation(s) in RCA: 46] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/21/2012] [Accepted: 03/05/2013] [Indexed: 12/26/2022]
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25
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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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26
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Wang SY, Cappellini E, Zhang HY. Why collagens best survived in fossils? Clues from amino acid thermal stability. Biochem Biophys Res Commun 2012; 422:5-7. [PMID: 22564740 DOI: 10.1016/j.bbrc.2012.04.122] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/17/2012] [Accepted: 04/22/2012] [Indexed: 11/18/2022]
Affiliation(s)
- Shuang-Yin Wang
- National Key Laboratory of Crop Genetic Improvement, College of Life Science and Technology, Huazhong Agricultural University, Wuhan 430070, PR China
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27
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Yong E. Twisted structure preserved dinosaur proteins. Nature 2011. [DOI: 10.1038/news.2011.369] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
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