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Sharma G, Seth A, Giri RP, Hayen N, Murphy BM, Ghosh SK. Ionic Liquid-Induced Assembly of DNA at Air-Water Interface. LANGMUIR : THE ACS JOURNAL OF SURFACES AND COLLOIDS 2023; 39:16079-16089. [PMID: 37922422 DOI: 10.1021/acs.langmuir.3c02212] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/05/2023]
Abstract
DNA nanotechnology is the future of many products in the pharmaceutical and cosmetic industries. Self-assembly of this negatively charged biopolymer at surfaces and interfaces is an essential step to elaborate its field of applications. In this study, the ionic liquid (IL) monolayer-assisted self-assembly of DNA macromolecules at the air-water interface has been closely monitored by employing various quantitative techniques, namely, surface pressure-area (π-A) isotherms, surface potential, interfacial rheology, and X-ray reflectivity (XRR). The π-A isotherms reveal that the IL 1,3-didecyl 3-methyl imidazolium chloride induces DNA self-assembly at the interface, leading to a thick viscoelastic film. The interfacial rheology exhibits a notable rise in the viscoelastic modulus as the surface pressure increases. The values of storage and loss moduli measured as a function of strain frequency suggest a relaxation frequency that depends on the length of the macromolecule. The XRR measurements indicate a considerable increase in DNA layer thickness at the elevated surface pressures depending on the number of base pairs of the DNA. The results are considered in terms of the electrostatic and hydrophobic interactions, allowing a quantitative conclusion about the arrangement of DNA strands underneath the monolayer of the ILs at the air-water interface.
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Affiliation(s)
- Gunjan Sharma
- Department of Physics, School of Natural Sciences, Shiv Nadar Institution of Eminence, NH 91, Tehsil Dadri, G. B. Nagar, Uttar Pradesh, 201314, India
| | - Ajit Seth
- Department of Physics, School of Natural Sciences, Shiv Nadar Institution of Eminence, NH 91, Tehsil Dadri, G. B. Nagar, Uttar Pradesh, 201314, India
| | - Rajendra P Giri
- Institut für Experimentelle und Angewandte Physik, Christian-Albrechts-Universität Zu Kiel, 24098 Kiel, Germany
| | - Nicolas Hayen
- Institut für Experimentelle und Angewandte Physik, Christian-Albrechts-Universität Zu Kiel, 24098 Kiel, Germany
| | - Bridget M Murphy
- Institut für Experimentelle und Angewandte Physik, Christian-Albrechts-Universität Zu Kiel, 24098 Kiel, Germany
| | - Sajal K Ghosh
- Department of Physics, School of Natural Sciences, Shiv Nadar Institution of Eminence, NH 91, Tehsil Dadri, G. B. Nagar, Uttar Pradesh, 201314, India
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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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Zhao W, Whelton HL, Blong JC, Shillito LM, Jenkins DL, Bull ID. Volatile organic compounds (VOCs) as a rapid means for assessing the source of coprolites. iScience 2023; 26:106806. [PMID: 37255664 PMCID: PMC10225897 DOI: 10.1016/j.isci.2023.106806] [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: 11/09/2022] [Revised: 12/22/2022] [Accepted: 05/01/2023] [Indexed: 06/01/2023] Open
Abstract
The odor of rehydrated coprolites can be used as an informal means of fecal identification. To date, the analysis of volatiles emitted by coprolites from different sources has not been attempted, and the possibility of utilizing volatile organic compounds (VOCs) as fecal biomarkers unexplored. VOCs released by coprolites from the Paisley Caves, were analyzed using solid-phase microextraction (SPME), to assess the variance of results from different coprolites (carnivores, herbivores, or humans). Coprolites from carnivores can be clearly distinguished from those produced by herbivores and humans; these latter two are separated to a lesser degree. Eight discriminatory compounds differentiated between the coprolite sources, and their identities were verified using reference standards. Coprolites and their associated sediments could not be differentiated between using this method, suggesting leaching of VOCs into the burial matrix. This work provides an alternative, more rapid way to assess coprolite origin.
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Affiliation(s)
- Wanyue Zhao
- Organic Geochemistry Unit, School of Chemistry, University of Bristol, Cantock’s Close, Bristol BS8 1TS, UK
| | - Helen L. Whelton
- Organic Geochemistry Unit, School of Chemistry, University of Bristol, Cantock’s Close, Bristol BS8 1TS, UK
| | - John C. Blong
- Department of Anthropology, Washington State University, College Hall, Pullman, WA 99164-4910, USA
| | - Lisa-Marie Shillito
- School of History, Classics and Archaeology, Armstrong Building, Newcastle University, Newcastle upon Tyne NE1 7RU, UK
| | - Dennis L. Jenkins
- Museum of Natural and Cultural History, University of Oregon, Eugene, OR 97403, USA
| | - Ian D. Bull
- Organic Geochemistry Unit, School of Chemistry, University of Bristol, Cantock’s Close, Bristol BS8 1TS, UK
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Application of Forensic DNA Phenotyping for Prediction of Eye, Hair and Skin Colour in Highly Decomposed Bodies. Healthcare (Basel) 2023; 11:healthcare11050647. [PMID: 36900653 PMCID: PMC10000573 DOI: 10.3390/healthcare11050647] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/31/2023] [Revised: 02/18/2023] [Accepted: 02/21/2023] [Indexed: 02/25/2023] Open
Abstract
In the last few years, predicting externally visible characteristics (EVCs) by adopting informative DNA molecular markers has become a method in forensic genetics that has increased its value, giving rise to an interesting field called "Forensic DNA Phenotyping" (FDP). The most meaningful forensic applications of EVCs prediction are those in which, having only a DNA sample isolated from highly decomposed remains, it is essential to reconstruct the physical appearance of a person. Through this approach, we set out to evaluate 20 skeletal remains of Italian provenance in order to associate them with as many cases of missing persons as possible. To achieve the intended goal, in this work we applied the HIrisPlex-S multiplex system through the conventional short tandem repeats (STR) method to confirm the expected identity of subjects by evaluating phenotypic features. To investigate the reliability and accuracy of the DNA-based EVCs prediction, pictures of the cases were compared as they were available to researchers. Results showed an overall prediction accuracy greater than 90% for all three phenotypic features-iris, hair, and skin colour-at a probability threshold of 0.7. The experimental analysis showed inconclusive results in only two cases; this is probably due to the characteristics of subjects who had an intermediate eye and hair colour, for which the DNA-based system needs to improve the prediction accuracy.
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Patalano R, Hu J, Leng Q, Liu W, Wang H, Roberts P, Storozum M, Yang L, Yang H. Ancient Great Wall building materials reveal environmental changes associated with oases in northwestern China. Sci Rep 2022; 12:22517. [PMID: 36581698 PMCID: PMC9800585 DOI: 10.1038/s41598-022-27071-4] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/16/2022] [Accepted: 12/23/2022] [Indexed: 12/30/2022] Open
Abstract
Plant materials used in the construction of segments and beacon towers of the ancient Great Wall in northwestern China contain untapped potential for revealing local paleoclimatic and environmental conditions. For the first time, we characterize the molecular preservation and stable carbon and nitrogen isotope compositions of AMS-dated common reeds (Phragmites) collected from ancient Great Wall fascines in today's Gansu and Xinjiang using a combination of chromatographic techniques and isotope analyses. Our molecular data, along with Scanning Electron Microscopy, demonstrate excellent preservation of these ancient reeds, which were harvested from nearby habitats during periods of significant expansion of Imperial China when climate conditions sustained sizeable oases in the region. Stable isotope data capture differential rates of environmental change along the eastern margin of the Tarim Basin since the Han Dynasty (170 BC), implying that significant surface-water hydrological changes occurred only after the Song Dynasty (1160 AD) due to regional climate change. This study reveals the wealth of environmental and climate information obtainable from these site-specific organic building materials and establishes the foundation for further applications of advanced molecular, biochemical, and isotopic technologies to study these common and widely-distributed organic archaeological materials.
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Affiliation(s)
- Robert Patalano
- grid.4372.20000 0001 2105 1091Department of Archaeology, Max Planck Institute for Geoanthropology, 07745 Jena, Germany ,grid.411805.90000 0004 0464 7119Laboratory for Terrestrial Environments, Department of Biological and Biomedical Sciences, School of Health and Behavioral Sciences, Bryant University, Smithfield, 02917 USA
| | - Jing Hu
- grid.9227.e0000000119573309State Key Laboratory of Loess and Quaternary Geology, Institute of Earth Environment, Chinese Academy of Sciences, Xi’an, 710061 China
| | - Qin Leng
- grid.411805.90000 0004 0464 7119Laboratory for Terrestrial Environments, Department of Biological and Biomedical Sciences, School of Health and Behavioral Sciences, Bryant University, Smithfield, 02917 USA
| | - Weiguo Liu
- grid.9227.e0000000119573309State Key Laboratory of Loess and Quaternary Geology, Institute of Earth Environment, Chinese Academy of Sciences, Xi’an, 710061 China ,grid.410726.60000 0004 1797 8419University of Chinese Academy of Sciences, Beijing, 100049 China ,grid.458457.f0000 0004 1792 8067CAS Center for Excellence in Quaternary Science and Global Change, Xi’an, 710061 China
| | - Huanye Wang
- grid.9227.e0000000119573309State Key Laboratory of Loess and Quaternary Geology, Institute of Earth Environment, Chinese Academy of Sciences, Xi’an, 710061 China ,grid.458457.f0000 0004 1792 8067CAS Center for Excellence in Quaternary Science and Global Change, Xi’an, 710061 China
| | - Patrick Roberts
- grid.4372.20000 0001 2105 1091Department of Archaeology, Max Planck Institute for Geoanthropology, 07745 Jena, Germany ,grid.4372.20000 0001 2105 1091IsoTROPIC Research Group, Max Planck Institute for Geoanthropology, 07745 Jena, Germany ,grid.1003.20000 0000 9320 7537School of Social Science, The University of Queensland, Brisbane, Australia ,grid.11134.360000 0004 0636 6193Archaeological Studies Program, University of Philippines, Diliman, Quezon City, Philippines
| | - Michael Storozum
- grid.1006.70000 0001 0462 7212School of History, Classics and Archaeology, Newcastle University, Newcastle Upon Tyne, England UK
| | - Lin Yang
- grid.500608.b0000 0004 0386 7291National Museum of China, Beijing, 100006 China
| | - Hong Yang
- grid.411805.90000 0004 0464 7119Laboratory for Terrestrial Environments, Department of Biological and Biomedical Sciences, School of Health and Behavioral Sciences, Bryant University, Smithfield, 02917 USA
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D'Agostino A, Di Marco G, Marvelli S, Marchesini M, Rizzoli E, Rolfo MF, Canini A, Gismondi A. Neolithic dental calculi provide evidence for environmental proxies and consumption of wild edible fruits and herbs in central Apennines. Commun Biol 2022; 5:1384. [PMID: 36536113 PMCID: PMC9763411 DOI: 10.1038/s42003-022-04354-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/16/2022] [Accepted: 12/08/2022] [Indexed: 12/23/2022] Open
Abstract
Looking for a biological fingerprint relative to new aspects of the relationship between humans and natural environment during prehistoric times is challenging. Although many issues still need to be addressed in terms of authentication and identification, microparticles hidden in ancient dental calculus can provide interesting information for bridging this gap of knowledge. Here, we show evidence about the role of edible plants for the early Neolithic individuals in the central Apennines of the Italian peninsula and relative cultural landscape. Dental calculi from human and animal specimens exhumed at Grotta Mora Cavorso (Lazio), one of the largest prehistoric burial deposits, have returned an archaeobotanical record made up of several types of palaeoecological proxies. The organic fraction of this matrix was investigated by a multidisciplinary approach, whose novelty consisted in the application of next generation sequencing to ancient plant DNA fragments, specifically codifying for maturase K barcode gene. Panicoideae and Triticeae starches, together with genetic indicators of Rosaceae fruits, figs, and Lamiaceae herbs, suggested subsistence practices most likely still based on wild plant resources. On the other hand, pollen, and non-pollen palynomorphs allowed us to outline a general vegetational framework dominated by woodland patches alternated with meadows, where semi-permanent settlements could have been established.
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Affiliation(s)
- Alessia D'Agostino
- PhD Program in Evolutionary Biology and Ecology, Department of Biology, University of Rome Tor Vergata, Rome, Italy
- Laboratory of Botany, Department of Biology, University of Rome "Tor Vergata", Rome, Italy
| | - Gabriele Di Marco
- Laboratory of Botany, Department of Biology, University of Rome "Tor Vergata", Rome, Italy
| | - Silvia Marvelli
- Laboratorio di Palinologia e Archeobotanica-C.A.A. Giorgio Nicoli, San Giovanni in Persiceto, Bologna, Italy
| | - Marco Marchesini
- Laboratorio di Palinologia e Archeobotanica-C.A.A. Giorgio Nicoli, San Giovanni in Persiceto, Bologna, Italy
| | - Elisabetta Rizzoli
- Laboratorio di Palinologia e Archeobotanica-C.A.A. Giorgio Nicoli, San Giovanni in Persiceto, Bologna, Italy
| | - Mario Federico Rolfo
- Department of History, Culture and Society, University of Rome "Tor Vergata", Rome, Italy
| | - Antonella Canini
- Laboratory of Botany, Department of Biology, University of Rome "Tor Vergata", Rome, Italy
| | - Angelo Gismondi
- Laboratory of Botany, Department of Biology, University of Rome "Tor Vergata", Rome, Italy.
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Murakami N, Onggaruly A, Rakhimzhanova S, Standall EA, Talbot HM, Lucquin A, Suzuki M, Karimagambetov A, Nuskabay A, Nam SW, Craig OE, Shoda S. Lipid residues in ancient pastoralist pottery from Kazakhstan reveal regional differences in cooking practices. Front Ecol Evol 2022. [DOI: 10.3389/fevo.2022.1032637] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022] Open
Abstract
The Bronze Age—Iron Age transition in Central Asia (ca. 800 BCE) was a period of significant cultural change that was heavily influenced by greater population interaction and mobility. Indeed, scholars have increasingly emphasized the role that “food globalization in prehistory” has played in defining this period. In the mountain foothills of Kazakhstan, culinary traditions from across Eurasia were combined through the use of Southwest Asian wheat, barley, and livestock (cattle, sheep, and goats) with East Asian foxtail and broomcorn millets. The development of food cultures during this period has been investigated by archaeobotanical and isotopic analysis, yet lipid residues from pottery, which directly represent culinary practices, have not been adequately examined. In this study, lipid residue analysis was conducted on 72 pottery sherds, excavated from three burial mounds and one non-burial, ritual site located in Kazakhstan, dating to ca. 700–200 BCE. A particularly informative observation was the frequency of miliacin, a biomarker of broomcorn millet, detected in residues that corresponded well with previously published regional differences observed in carbon isotope ratios of human remains that indicate the consumption of C4 plants. This study also demonstrates continuity of Bronze Age dairying traditions into the Iron Age. Finally, this study sheds new light on the diversity of food cultures and mortuary practices in this region, which were not uniform across either space or time.
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Colleary C, O’Reilly S, Dolocan A, Toyoda JG, Chu RK, Tfaily MM, Hochella MF, Nesbitt SJ. Using Macro- and Microscale Preservation in Vertebrate Fossils as Predictors for Molecular Preservation in Fluvial Environments. BIOLOGY 2022; 11:biology11091304. [PMID: 36138783 PMCID: PMC9495945 DOI: 10.3390/biology11091304] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 06/30/2022] [Revised: 08/18/2022] [Accepted: 08/26/2022] [Indexed: 11/16/2022]
Abstract
Exceptionally preserved fossils retain soft tissues and often the biomolecules that were present in an animal during its life. The majority of terrestrial vertebrate fossils are not traditionally considered exceptionally preserved, with fossils falling on a spectrum ranging from very well-preserved to poorly preserved when considering completeness, morphology and the presence of microstructures. Within this variability of anatomical preservation, high-quality macro-scale preservation (e.g., articulated skeletons) may not be reflected in molecular-scale preservation (i.e., biomolecules). Excavation of the Hayden Quarry (HQ; Chinle Formation, Ghost Ranch, NM, USA) has resulted in the recovery of thousands of fossilized vertebrate specimens. This has contributed greatly to our knowledge of early dinosaur evolution and paleoenvironmental conditions during the Late Triassic Period (~212 Ma). The number of specimens, completeness of skeletons and fidelity of osteohistological microstructures preserved in the bone all demonstrate the remarkable quality of the fossils preserved at this locality. Because the Hayden Quarry is an excellent example of good preservation in a fluvial environment, we have tested different fossil types (i.e., bone, tooth, coprolite) to examine the molecular preservation and overall taphonomy of the HQ to determine how different scales of preservation vary within a single locality. We used multiple high-resolution mass spectrometry techniques (TOF-SIMS, GC-MS, FT-ICR MS) to compare the fossils to unaltered bone from extant vertebrates, experimentally matured bone, and younger dinosaurian skeletal material from other fluvial environments. FT-ICR MS provides detailed molecular information about complex mixtures, and TOF-SIMS has high elemental spatial sensitivity. Using these techniques, we did not find convincing evidence of a molecular signal that can be confidently interpreted as endogenous, indicating that very good macro- and microscale preservation are not necessarily good predictors of molecular preservation.
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Affiliation(s)
- Caitlin Colleary
- Department of Geosciences, Virginia Tech, Blacksburg, VA 24061, USA
- Cleveland Museum of Natural History, Cleveland, OH 44106, USA
- Correspondence:
| | - Shane O’Reilly
- Atlantic Technological University, ATU Sligo, Ash Lane, F91 YW50 Sligo, Ireland
| | - Andrei Dolocan
- Texas Materials Institute, University of Texas at Austin, Austin, TX 78712, USA
| | - Jason G. Toyoda
- Environmental Molecular Sciences Laboratory, Pacific Northwest National Laboratory, Richland, WA 99354, USA
| | - Rosalie K. Chu
- Environmental Molecular Sciences Laboratory, Pacific Northwest National Laboratory, Richland, WA 99354, USA
| | - Malak M. Tfaily
- Environmental Molecular Sciences Laboratory, Pacific Northwest National Laboratory, Richland, WA 99354, USA
- Department of Environmental Science, University of Arizona, Tucson, AZ 87519, USA
| | - Michael F. Hochella
- Department of Geosciences, Virginia Tech, Blacksburg, VA 24061, USA
- Earth Systems Science Division, Pacific Northwest National Laboratory, Richland, WA 99354, USA
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Taphonomic and Diagenetic Pathways to Protein Preservation, Part II: The Case of Brachylophosaurus canadensis Specimen MOR 2598. BIOLOGY 2022; 11:biology11081177. [PMID: 36009804 PMCID: PMC9404959 DOI: 10.3390/biology11081177] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 06/14/2022] [Revised: 07/31/2022] [Accepted: 08/03/2022] [Indexed: 11/25/2022]
Abstract
Simple Summary Reports of the recovery of proteins and other molecules from fossils have become so common over the last two decades that some paleontologists now focus almost entirely on studying how biologic molecules can persist in fossils. In this study, we explored the fossilization history of a specimen of the hadrosaurid dinosaur Brachylophosaurus which was previously shown to preserve original cells, tissues, and structural proteins. Trace element analyses of the tibia of this specimen revealed that after its bones were buried in a brackish estuarine channel, they fossilized under wet conditions which shifted in redox state multiple times. The successful recovery of proteins from this specimen, despite this complex history of chemical alterations, shows that the processes which bind and stabilize biologic molecules shortly after death provide them remarkable physical and chemical resiliency. By uniting our results with those of similar studies on other dinosaur fossils known to also preserve original proteins, we also conclude that exposure to oxidizing conditions in the initial ~48 h postmortem likely promotes molecular stabilization reactions, and the retention of early-diagenetic trace element signatures may be a useful proxy for molecular recovery potential. Abstract Recent recoveries of peptide sequences from two Cretaceous dinosaur bones require paleontologists to rethink traditional notions about how fossilization occurs. As part of this shifting paradigm, several research groups have recently begun attempting to characterize biomolecular decay and stabilization pathways in diverse paleoenvironmental and diagenetic settings. To advance these efforts, we assessed the taphonomic and geochemical history of Brachylophosaurus canadensis specimen MOR 2598, the left femur of which was previously found to retain endogenous cells, tissues, and structural proteins. Combined stratigraphic and trace element data show that after brief fluvial transport, this articulated hind limb was buried in a sandy, likely-brackish, estuarine channel. During early diagenesis, percolating groundwaters stagnated within the bones, forming reducing internal microenvironments. Recent exposure and weathering also caused the surficial leaching of trace elements from the specimen. Despite these shifting redox regimes, proteins within the bones were able to survive through diagenesis, attesting to their remarkable resiliency over geologic time. Synthesizing our findings with other recent studies reveals that oxidizing conditions in the initial ~48 h postmortem likely promote molecular stabilization reactions and that the retention of early-diagenetic trace element signatures may be a useful proxy for molecular recovery potential.
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Soft Tissue and Biomolecular Preservation in Vertebrate Fossils from Glauconitic, Shallow Marine Sediments of the Hornerstown Formation, Edelman Fossil Park, New Jersey. BIOLOGY 2022; 11:biology11081161. [PMID: 36009787 PMCID: PMC9405258 DOI: 10.3390/biology11081161] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 06/18/2022] [Revised: 07/18/2022] [Accepted: 07/22/2022] [Indexed: 11/17/2022]
Abstract
Endogenous biomolecules and soft tissues are known to persist in the fossil record. To date, these discoveries derive from a limited number of preservational environments, (e.g., fluvial channels and floodplains), and fossils from less common depositional environments have been largely unexplored. We conducted paleomolecular analyses of shallow marine vertebrate fossils from the Cretaceous–Paleogene Hornerstown Formation, an 80–90% glauconitic greensand from Jean and Ric Edelman Fossil Park in Mantua Township, NJ. Twelve samples were demineralized and found to yield products morphologically consistent with vertebrate osteocytes, blood vessels, and bone matrix. Specimens from these deposits that are dark in color exhibit excellent histological preservation and yielded a greater recovery of cells and soft tissues, whereas lighter-colored specimens exhibit poor histology and few to no cells/soft tissues. Additionally, a well-preserved femur of the marine crocodilian Thoracosaurus was found to have retained endogenous collagen I by immunofluorescence and enzyme-linked immunosorbent assays. Our results thus not only corroborate previous findings that soft tissue and biomolecular recovery from fossils preserved in marine environments are possible but also expand the range of depositional environments documented to preserve endogenous biomolecules, thus broadening the suite of geologic strata that may be fruitful to examine in future paleomolecular studies.
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Soft-Tissue, Rare Earth Element, and Molecular Analyses of Dreadnoughtus schrani, an Exceptionally Complete Titanosaur from Argentina. BIOLOGY 2022; 11:biology11081158. [PMID: 36009785 PMCID: PMC9404821 DOI: 10.3390/biology11081158] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 06/30/2022] [Revised: 07/27/2022] [Accepted: 07/31/2022] [Indexed: 11/22/2022]
Abstract
Evidence that organic material preserves in deep time (>1 Ma) has been reported using a wide variety of analytical techniques. However, the comprehensive geochemical data that could aid in building robust hypotheses for how soft-tissues persist over millions of years are lacking from most paleomolecular reports. Here, we analyze the molecular preservation and taphonomic history of the Dreadnougtus schrani holotype (MPM-PV 1156) at both macroscopic and microscopic levels. We review the stratigraphy, depositional setting, and physical taphonomy of the D. schrani skeletal assemblage, and extensively characterize the preservation and taphonomic history of the humerus at a micro-scale via: (1) histological analysis (structural integrity) and X-ray diffraction (exogenous mineral content); (2) laser ablation-inductively coupled plasma mass spectrometry (analyses of rare earth element content throughout cortex); (3) demineralization and optical microscopy (soft-tissue microstructures); (4) in situ and in-solution immunological assays (presence of endogenous protein). Our data show the D. schrani holotype preserves soft-tissue microstructures and remnants of endogenous bone protein. Further, it was exposed to LREE-enriched groundwaters and weakly-oxidizing conditions after burial, but experienced negligible further chemical alteration after early-diagenetic fossilization. These findings support previous hypotheses that fossils that display low trace element uptake are favorable targets for paleomolecular analyses.
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Collins S, Maestrini L, Ueland M, Stuart B. A preliminary investigation to determine the suitability of pigs as human analogues for post-mortem lipid analysis. TALANTA OPEN 2022. [DOI: 10.1016/j.talo.2022.100100] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/25/2022] Open
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Irto A, Micalizzi G, Bretti C, Chiaia V, Mondello L, Cardiano P. Lipids in Archaeological Pottery: A Review on Their Sampling and Extraction Techniques. Molecules 2022; 27:molecules27113451. [PMID: 35684389 PMCID: PMC9182108 DOI: 10.3390/molecules27113451] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/29/2022] [Revised: 05/21/2022] [Accepted: 05/25/2022] [Indexed: 11/21/2022] Open
Abstract
Several studies have been performed so far for the effective recovery, detection and quantification of specific compounds and their degradation products in archaeological materials. According to the literature, lipid molecules are the most durable and widespread biomarkers in ancient pottery. Artificial ageing studies to simulate lipid alterations over time have been reported. In this review, specific lipid archaeological biomarkers and well-established sampling and extraction methodologies are discussed. Although suitable analytical techniques have unraveled archaeological questions, some issues remain open such as the need to introduce innovative and miniaturized protocols to avoid extractions with organic solvents, which are often laborious and non-environmentally friendly.
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Affiliation(s)
- Anna Irto
- Department of Chemical, Biological, Pharmaceutical and Environmental Sciences, University of Messina, 98168 Messina, Italy; (C.B.); (V.C.); (L.M.); (P.C.)
- Correspondence: (A.I.); (G.M.)
| | - Giuseppe Micalizzi
- Department of Chemical, Biological, Pharmaceutical and Environmental Sciences, University of Messina, 98168 Messina, Italy; (C.B.); (V.C.); (L.M.); (P.C.)
- Correspondence: (A.I.); (G.M.)
| | - Clemente Bretti
- Department of Chemical, Biological, Pharmaceutical and Environmental Sciences, University of Messina, 98168 Messina, Italy; (C.B.); (V.C.); (L.M.); (P.C.)
| | - Valentina Chiaia
- Department of Chemical, Biological, Pharmaceutical and Environmental Sciences, University of Messina, 98168 Messina, Italy; (C.B.); (V.C.); (L.M.); (P.C.)
| | - Luigi Mondello
- Department of Chemical, Biological, Pharmaceutical and Environmental Sciences, University of Messina, 98168 Messina, Italy; (C.B.); (V.C.); (L.M.); (P.C.)
- Chromaleont s.r.l., c/o Department of Chemical, Biological, Pharmaceutical and Environmental Sciences, University of Messina, 98168 Messina, Italy
- Unit of Food Science and Nutrition, Department of Medicine, University Campus Bio-Medico of Rome, 00128 Rome, Italy
| | - Paola Cardiano
- Department of Chemical, Biological, Pharmaceutical and Environmental Sciences, University of Messina, 98168 Messina, Italy; (C.B.); (V.C.); (L.M.); (P.C.)
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14
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Agrawal R, Kumar A, Singh S, Sharma K. Recent advances and future perspectives of lignin biopolymers. JOURNAL OF POLYMER RESEARCH 2022. [DOI: 10.1007/s10965-022-03068-5] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/17/2022]
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15
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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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16
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Chirality in Organic and Mineral Systems: A Review of Reactivity and Alteration Processes Relevant to Prebiotic Chemistry and Life Detection Missions. Symmetry (Basel) 2022. [DOI: 10.3390/sym14030460] [Citation(s) in RCA: 10] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/01/2023] Open
Abstract
Chirality is a central feature in the evolution of biological systems, but the reason for biology’s strong preference for specific chiralities of amino acids, sugars, and other molecules remains a controversial and unanswered question in origins of life research. Biological polymers tend toward homochiral systems, which favor the incorporation of a single enantiomer (molecules with a specific chiral configuration) over the other. There have been numerous investigations into the processes that preferentially enrich one enantiomer to understand the evolution of an early, racemic, prebiotic organic world. Chirality can also be a property of minerals; their interaction with chiral organics is important for assessing how post-depositional alteration processes could affect the stereochemical configuration of simple and complex organic molecules. In this paper, we review the properties of organic compounds and minerals as well as the physical, chemical, and geological processes that affect organic and mineral chirality during the preservation and detection of organic compounds. We provide perspectives and discussions on the reactions and analytical techniques that can be performed in the laboratory, and comment on the state of knowledge of flight-capable technologies in current and future planetary missions, with a focus on organics analysis and life detection.
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17
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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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18
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Fernández-Remolar DC, Carrizo D, Harir M, Huang T, Amils R, Schmitt-Kopplin P, Sánchez-García L, Gomez-Ortiz D, Malmberg P. Unveiling microbial preservation under hyperacidic and oxidizing conditions in the Oligocene Rio Tinto deposit. Sci Rep 2021; 11:21543. [PMID: 34728655 PMCID: PMC8563943 DOI: 10.1038/s41598-021-00730-8] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/14/2021] [Accepted: 10/11/2021] [Indexed: 11/22/2022] Open
Abstract
The preservation of biosignatures on Mars is largely associated with extensive deposits of clays formed under mild early Noachian conditions (> 3.9 Ga). They were followed by widespread precipitation of acidic sulfates considered adverse for biomolecule preservation. In this paper, an exhaustive mass spectrometry investigation of ferric subsurface materials in the Rio Tinto gossan deposit (~ 25 Ma) provides evidence of well-preserved molecular biosignatures under oxidative and acidic conditions. Time of flight secondary ion mass spectrometry (ToF–SIMS) analysis shows a direct association between physical-templating biological structures and molecular biosignatures. This relation implies that the quality of molecular preservation is exceptional and provides information on microbial life formerly operating in the shallow regions of the Rio Tinto subsurface. Consequently, low-pH oxidative environments on Mars could also record molecular information about ancient life in the same way as the Noachian clay-rich deposits.
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Affiliation(s)
- David C Fernández-Remolar
- CEA, CNRS, IBS, Metalloproteins Unit, Université Grenoble Alpes, 38000, Grenoble, France. .,State Key Laboratory of Lunar and Planetary Sciences, Macau University of Science and Technology, Macau, 999078, PR China. .,CNSA Macau Center for Space Exploration and Science, Macau, 999078, PR China.
| | | | - Mourad Harir
- Research Unit Analytical Biogeochemistry, Helmholtz Zentrum München, Neuherberg, Germany
| | - Ting Huang
- State Key Laboratory of Lunar and Planetary Sciences, Macau University of Science and Technology, Macau, China
| | - Ricardo Amils
- Centro de Astrobiología (INTA-CSIC), Madrid, Spain.,Centro de Biología Molecular Severo Ochoa, Universidad Autónoma de Madrid, Madrid, Spain
| | - Philippe Schmitt-Kopplin
- Research Unit Analytical Biogeochemistry, Helmholtz Zentrum München, Neuherberg, Germany.,Chair of Analytical Food Chemistry, Technical University Munich, 85354, Freising-Weihenstephan, Germany
| | | | - David Gomez-Ortiz
- ESCET-Área de Geología, Universidad Rey Juan Carlos, 28933, Móstoles, Madrid, Spain
| | - Per Malmberg
- Chemistry and Chemical Engineering, Chalmers University of Technology, Kemivägen 10, 412 96, Gothenburg, Sweden
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19
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Davis SN, Clarke JA. Estimating the distribution of carotenoid coloration in skin and integumentary structures of birds and extinct dinosaurs. Evolution 2021; 76:42-57. [PMID: 34719783 DOI: 10.1111/evo.14393] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/23/2021] [Revised: 09/22/2021] [Accepted: 09/24/2021] [Indexed: 11/27/2022]
Abstract
Carotenoids are pigments responsible for most bright yellow, red, and orange hues in birds. Their distribution has been investigated in avian plumage, but the evolution of their expression in skin and other integumentary structures has not been approached in detail. Here, we investigate the expression of carotenoid-consistent coloration across tissue types in all extant, nonpasserine species (n = 4022) and archelosaur outgroups in a phylogenetic framework. We collect dietary data for a subset of birds and investigate how dietary carotenoid intake may relate to carotenoid expression in various tissues. We find that carotenoid-consistent expression in skin or nonplumage keratin has a 50% probability of being present in the most recent common ancestor of Archosauria. Skin expression has a similar probability at the base of the avian crown clade, but plumage expression is unambiguously absent in that ancestor and shows hundreds of independent gains within nonpasserine neognaths, consistent with previous studies. Although our data do not support a strict sequence of tissue expression in nonpasserine birds, we find support that expression of carotenoid-consistent color in nonplumage integument structures might evolve in a correlated manner and feathers are rarely the only region of expression. Taxa with diets high in carotenoid content also show expression in more body regions and tissue types. Our results may inform targeted assays for carotenoids in tissues other than feathers, and expectations of these pigments in nonavian dinosaurs. In extinct groups, bare-skin regions and the rhamphotheca, especially in species with diets rich in plants, may express these pigments, which are not expected in feathers or feather homologues.
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Affiliation(s)
- Sarah N Davis
- Department of Geological Sciences, Jackson School of Geosciences, The University of Texas at Austin, Austin, Texas, 78712
| | - Julia A Clarke
- Department of Geological Sciences, Jackson School of Geosciences, The University of Texas at Austin, Austin, Texas, 78712.,Department of Integrative Biology, The University of Texas at Austin, Austin, Texas, 78712
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20
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Duchêne S, Ho SYW, Carmichael AG, Holmes EC, Poinar H. The Recovery, Interpretation and Use of Ancient Pathogen Genomes. Curr Biol 2021; 30:R1215-R1231. [PMID: 33022266 PMCID: PMC7534838 DOI: 10.1016/j.cub.2020.08.081] [Citation(s) in RCA: 22] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022]
Abstract
The ability to sequence genomes from ancient biological material has provided a rich source of information for evolutionary biology and engaged considerable public interest. Although most studies of ancient genomes have focused on vertebrates, particularly archaic humans, newer technologies allow the capture of microbial pathogens and microbiomes from ancient and historical human and non-human remains. This coming of age has been made possible by techniques that allow the preferential capture and amplification of discrete genomes from a background of predominantly host and environmental DNA. There are now near-complete ancient genome sequences for three pathogens of considerable historical interest — pre-modern bubonic plague (Yersinia pestis), smallpox (Variola virus) and cholera (Vibrio cholerae) — and for three equally important endemic human disease agents — Mycobacterium tuberculosis (tuberculosis), Mycobacterium leprae (leprosy) and Treponema pallidum pallidum (syphilis). Genomic data from these pathogens have extended earlier work by paleopathologists. There have been efforts to sequence the genomes of additional ancient pathogens, with the potential to broaden our understanding of the infectious disease burden common to past populations from the Bronze Age to the early 20th century. In this review we describe the state-of-the-art of this rapidly developing field, highlight the contributions of ancient pathogen genomics to multidisciplinary endeavors and describe some of the limitations in resolving questions about the emergence and long-term evolution of pathogens.
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Affiliation(s)
- Sebastián Duchêne
- Department of Microbiology and Immunology, Peter Doherty Institute for Infection and Immunity, University of Melbourne, Melbourne, VIC 3000, Australia.
| | - Simon Y W Ho
- School of Life and Environmental Sciences, University of Sydney, Sydney, NSW 2006, Australia
| | | | - Edward C Holmes
- Marie Bashir Institute for Infectious Diseases and Biosecurity, School of Life and Environmental Sciences and School of Medical Sciences, University of Sydney, Sydney, NSW 2006, Australia.
| | - Hendrik Poinar
- McMaster Ancient DNA Centre, Departments of Anthropology and Biochemistry, McMaster University, 1280 Main St. W., Hamilton, ON L8S 4L9, Canada; Michael G. DeGroote Institute for Infectious Disease Research, McMaster University, 1280 Main St. W., Hamilton, ON L8S 4L8, Canada; Humans and the Microbiome Program, Canadian Institute for Advanced Research, Toronto, Canada.
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21
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Tahoun M, Gee CT, McCoy VE, Sander PM, Müller CE. Chemistry of porphyrins in fossil plants and animals. RSC Adv 2021; 11:7552-7563. [PMID: 35423242 PMCID: PMC8695116 DOI: 10.1039/d0ra10688g] [Citation(s) in RCA: 19] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/20/2020] [Accepted: 02/08/2021] [Indexed: 11/30/2022] Open
Abstract
Porphyrins are macrocyclic tetrapyrrole derivatives that are widely distributed in nature. They are often complexed with a metal ion located in the center of the ring system and may be modified by various substituents including additional rings, or by ring opening, which leads to a plethora of different functions. Due to their extended conjugated aromatic ring system, porphyrins absorb light in the visible range and therefore show characteristic colors. Well-known natural porphyrins include the red-colored heme present in hemoglobin, which is responsible for blood oxygen transport, and the chlorophylls in some bacteria and in plants which are utilized for photosynthesis. Porphyrins are mostly lipophilic pigments that display relatively high chemical stability. Therefore, they can even survive hundreds of millions of years. The present review article provides an overview of natural porphyrins, their chemical structures, and properties. A special focus is put on porphyrins discovered in the fossil record. Examples will be highlighted, and information on their chemical analysis will be provided. We anticipate that the development of novel analytical methods with increased sensitivity will prompt new discoveries of porphyrins in fossils.
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Affiliation(s)
- Mariam Tahoun
- Pharmaceutical Institute, Pharmaceutical & Medicinal Chemistry, University of Bonn An der Immenburg 4 53121 Bonn Germany
| | - Carole T Gee
- Institute of Geosciences, Division of Paleontology, University of Bonn Nussallee 8 53115 Bonn Germany
- Huntington Botanical Gardens 1151 Oxford Road San Marino California 91108 USA
| | - Victoria E McCoy
- Department of Geosciences, University of Wisconsin-Milwaukee 3209 N Maryland Ave Milwaukee WI 53211 USA
| | - P Martin Sander
- Institute of Geosciences, Division of Paleontology, University of Bonn Nussallee 8 53115 Bonn Germany
| | - Christa E Müller
- Pharmaceutical Institute, Pharmaceutical & Medicinal Chemistry, University of Bonn An der Immenburg 4 53121 Bonn Germany
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22
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Armbrecht L, Hallegraeff G, Bolch CJS, Woodward C, Cooper A. Hybridisation capture allows DNA damage analysis of ancient marine eukaryotes. Sci Rep 2021; 11:3220. [PMID: 33547359 PMCID: PMC7864908 DOI: 10.1038/s41598-021-82578-6] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/22/2020] [Accepted: 01/20/2021] [Indexed: 11/09/2022] Open
Abstract
Marine sedimentary ancient DNA (sedaDNA) is increasingly used to study past ocean ecosystems, however, studies have been severely limited by the very low amounts of DNA preserved in the subseafloor, and the lack of bioinformatic tools to authenticate sedaDNA in metagenomic data. We applied a hybridisation capture 'baits' technique to target marine eukaryote sedaDNA (specifically, phyto- and zooplankton, 'Planktonbaits1'; and harmful algal bloom taxa, 'HABbaits1'), which resulted in up to 4- and 9-fold increases, respectively, in the relative abundance of eukaryotes compared to shotgun sequencing. We further used the bioinformatic tool 'HOPS' to authenticate the sedaDNA component, establishing a new proxy to assess sedaDNA authenticity, "% eukaryote sedaDNA damage", that is positively correlated with subseafloor depth. We used this proxy to report the first-ever DNA damage profiles from a marine phytoplankton species, the ubiquitous coccolithophore Emiliania huxleyi. Our approach opens new avenues for the detailed investigation of long-term change and evolution of marine eukaryotes over geological timescales.
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Affiliation(s)
- L Armbrecht
- Australian Centre for Ancient DNA, School of Biological Sciences, Faculty of Sciences, The University of Adelaide, Adelaide, SA, Australia.
| | - G Hallegraeff
- Institute for Marine and Antarctic Studies, University of Tasmania, Hobart, TAS, Australia
| | - C J S Bolch
- Institute for Marine and Antarctic Studies, University of Tasmania, Launceston, TAS, Australia
| | - C Woodward
- Australian Nuclear Science and Technology Organisation, Lucas Heights, NSW, Australia
| | - A Cooper
- South Australian Museum, Adelaide, SA, Australia
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23
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Suryanarayan A, Cubas M, Craig OE, Heron CP, Shinde VS, Singh RN, O'Connell TC, Petrie CA. Lipid residues in pottery from the Indus Civilisation in northwest India. JOURNAL OF ARCHAEOLOGICAL SCIENCE 2021; 125:105291. [PMID: 33519031 PMCID: PMC7829615 DOI: 10.1016/j.jas.2020.105291] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/04/2023]
Abstract
This paper presents novel insights into the archaeology of food in ancient South Asia by using lipid residue analysis to investigate what kinds of foodstuffs were used in ceramic vessels by populations of the Indus Civilisation in northwest India. It examines how vessels were used in urban and rural Indus settlements during the Mature Harappan period (c.2600/2500-1900 BC), the relationship between vessels and the products within them, and identifies whether changes in vessel use occurred from the Mature Harappan to Late Harappan periods, particularly during climatic instability after 4.2 ka BP (c.2100 BC). Despite low lipid concentrations, which highlight challenges with conducting residue analysis in arid, seasonally-wet and alkaline environments, 71% of the vessels yielded appreciable quantities of lipid. Lipid profiles revealed the use of animal fats in vessels, and contradictory to faunal evidence, a dominance of non-ruminant fats, with limited evidence of dairy processing. The absence of local modern reference fats makes this dataset challenging to interpret, and it is possible that plant products or mixtures of plant and animal products have led to ambiguous fatty acid-specific isotopic values. At the same time, it appears that urban and rural populations processed similar types of products in vessels, with limited evidence for change in vessel use from the urban to the post-urban period. This study is a systematic investigation into pot lipid residues from multiple sites, demonstrating the potential of the method for examining ancient Indus foodways and the need for the development of further research in ancient organic residues in South Asia.
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Affiliation(s)
- Akshyeta Suryanarayan
- Department of Archaeology, University of Cambridge, Downing Street, Cambridge, CB2 3DZ, UK
- CEPAM (Cultures et Environnements, Préhistoire, Antiquité,Moyen Âge), UMR7264-CNRS, Université Nice Côte d'Azur, Nice, 06300, France
- Corresponding author. CEPAM (Cultures et Environnements, Préhistoire, Antiquité,Moyen Âge), UMR7264-CNRS Université Nice Côte d'Azur, 06300 Nice, France
| | - Miriam Cubas
- Department of History, University of Oviedo, C/Amparo Pedregal s/n, E-33011, Oviedo, Asturias, Spain
- BioArch, University of York, Wentworth Way, York, YO10 5DD, UK
| | - Oliver E. Craig
- BioArch, University of York, Wentworth Way, York, YO10 5DD, UK
| | - Carl P. Heron
- Scientific Research, British Museum, Great Russell Street, London, WC1B 3DG, UK
| | | | - Ravindra N. Singh
- Department of Ancient Indian History, Culture and Archaeology, Banaras Hindu University, Varanasi, 221005, India
| | - Tamsin C. O'Connell
- Department of Archaeology, University of Cambridge, Downing Street, Cambridge, CB2 3DZ, UK
| | - Cameron A. Petrie
- Department of Archaeology, University of Cambridge, Downing Street, Cambridge, CB2 3DZ, UK
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24
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Thermal degradation and lifetime of β-chitin from Dosidicus gigas squid pen: Effect of impact at 9.7 GPa and a comparative study with α-chitin. Carbohydr Polym 2021; 251:116987. [PMID: 33142559 DOI: 10.1016/j.carbpol.2020.116987] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/18/2020] [Revised: 08/17/2020] [Accepted: 08/22/2020] [Indexed: 11/21/2022]
Abstract
The kinetics of thermal degradation of β-chitin extracted from Dosidicus gigas squid pen, was studied at normal conditions as well as after being subjected to the action of high-pressure impact of 9.7 GPa. The integral iso-conversional procedure of Kissinger-Akahira-Sunose (KAS) recommended by the ICTAC kinetics committee was applied to the non-isothermal data obtained from thermogravimetry (TGA). Lifetimes were predicted without assumption of any reaction model. Heating rates of β = 10, 15, 20 and 25 °C/min under nitrogen atmosphere were used from room temperature to 1300 °C. A comparative study with α-chitin was performed. All the samples were structurally and chemically characterized by several techniques. The extracted β-chitin was found to be in the monohydrate form; while with the action of high-pressure impact, it was transformed into β-chitin dehydrate showing slightly higher stability. Reliable prediction for lifetimes considering working temperatures over 425 K was found for α and β-chitin.
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25
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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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26
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The effect of cultivar and harvest season on the n-alkane and the n-alkene composition of virgin olive oil. Eur Food Res Technol 2020. [DOI: 10.1007/s00217-020-03604-x] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/23/2022]
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27
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Shillito LM, Whelton HL, Blong JC, Jenkins DL, Connolly TJ, Bull ID. Pre-Clovis occupation of the Americas identified by human fecal biomarkers in coprolites from Paisley Caves, Oregon. SCIENCE ADVANCES 2020; 6:eaba6404. [PMID: 32743069 PMCID: PMC7363456 DOI: 10.1126/sciadv.aba6404] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 12/19/2019] [Accepted: 05/28/2020] [Indexed: 06/11/2023]
Abstract
When and how people first settled in the Americas is an ongoing area of research and debate. The earliest sites typically only contain lithic artifacts that cannot be directly dated. The lack of human skeletal remains in these early contexts means that alternative sources of evidence are needed. Coprolites, and the DNA contained within them, are one such source, but unresolved issues concerning ancient DNA taphonomy and potential for contamination make this approach problematic. Here, we use fecal lipid biomarkers to demonstrate unequivocally that three coprolites dated to pre-Clovis are human, raise questions over the reliance on DNA methods, and present a new radiocarbon date on basketry further supporting pre-Clovis human occupation.
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Affiliation(s)
- Lisa-Marie Shillito
- School of History, Classics and Archaeology, Armstrong Building, Newcastle University, Newcastle upon Tyne NE1 7RU, UK
| | - Helen L. Whelton
- Organic Geochemistry Unit, School of Chemistry, University of Bristol, Cantock’s Close, Bristol BS8 1TS, UK
| | - John C. Blong
- School of History, Classics and Archaeology, Armstrong Building, Newcastle University, Newcastle upon Tyne NE1 7RU, UK
| | - Dennis L. Jenkins
- Museum of Natural and Cultural History, University of Oregon, Eugene, OR 97403, USA
| | - Thomas J. Connolly
- Museum of Natural and Cultural History, University of Oregon, Eugene, OR 97403, USA
| | - Ian D. Bull
- Organic Geochemistry Unit, School of Chemistry, University of Bristol, Cantock’s Close, Bristol BS8 1TS, UK
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n-Alkane Distribution—A Paleovegetation Change Indicator during the Period from Late Glacial to Late Holocene on Russian Plain (Bryansk Region). GEOSCIENCES 2020. [DOI: 10.3390/geosciences10030086] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
Abstract
Loess-paleosol series are well preserved in the south part of the Russian Plain. However, these sequences have a low number of studies on their organic matter, such as researches of isotope composition, n-alkane and other biomarkers. Thus, the purpose of the study was to reconstruct vegetation conditions from the Late Glacial to Late Holocene. We used the leaf wax-derived n-alkanes to detect vegetation evolution of the Bryansk Region. The stable carbon isotope composition of organic matter and pedogenic carbonates was carried out for the same aim. Three paleosols (of Lasko, Bølling-Allerød warmings and Holocene second humus horizons) and modern soils of different relief positions were investigated. n-Alkane distribution, as well as isotope composition indicates changes from grassy to woody vegetation during this period. The use of biomarkers such as n-alkanes helps to more clearly interpret isotopic data.
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Parry L, Caron JB. Canadia spinosa and the early evolution of the annelid nervous system. SCIENCE ADVANCES 2019; 5:eaax5858. [PMID: 31535028 PMCID: PMC6739095 DOI: 10.1126/sciadv.aax5858] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/05/2019] [Accepted: 08/09/2019] [Indexed: 05/19/2023]
Abstract
Annelid worms are a disparate, primitively segmented clade of bilaterians that first appear during the early Cambrian Period. Reconstructing their early evolution is complicated by the extreme morphological diversity in early diverging lineages, rapid diversification, and sparse fossil record. Canadia spinosa, a Burgess Shale fossil polychaete, is redescribed as having palps with feeding grooves, a dorsal median antenna and biramous parapodia associated with the head and flanking a ventral mouth. Carbonaceously preserved features are identified as a terminal brain, circumoral connectives, a midventral ganglionated nerve cord and prominent parapodial nerves. Phylogenetic analysis recovers neuroanatomically simple extant taxa as the sister group of other annelids, but the phylogenetic position of Canadia suggests that the annelid ancestor was reasonably complex neuroanatomically and that reduction of the nervous system occurred several times independently in the subsequent 500 million years of annelid evolution.
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Affiliation(s)
- Luke Parry
- Department of Natural History, Palaeobiology, Royal Ontario Museum, 100 Queen’s Park, Toronto, Ontario M5S 2C6, Canada
- Department of Geology and Geophysics, Yale University, New Haven, CT 06511, USA
- Corresponding author.
| | - Jean-Bernard Caron
- Department of Geology and Geophysics, Yale University, New Haven, CT 06511, USA
- Department of Ecology and Evolutionary Biology, University of Toronto, 25 Willcocks Street, Toronto, Ontario M5S 3B2, Canada
- Department of Earth Sciences, University of Toronto, Toronto, Ontario M5S 3B1, Canada
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30
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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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31
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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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32
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Latham KE, Miller JJ. DNA recovery and analysis from skeletal material in modern forensic contexts. Forensic Sci Res 2018; 4:51-59. [PMID: 30915417 PMCID: PMC6427720 DOI: 10.1080/20961790.2018.1515594] [Citation(s) in RCA: 55] [Impact Index Per Article: 9.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/30/2018] [Revised: 08/21/2018] [Accepted: 08/21/2018] [Indexed: 11/03/2022] Open
Abstract
The generation of a DNA profile from skeletal remains is an important part of the identification process in both mass disaster and unidentified person cases. Since bones and teeth are often the only biological materials remaining after exposure to environmental conditions, intense heat, certain traumatic events and in cases where a significant amount of time has passed since the death of the individual, the ability to purify large quantities of informative DNA from these hard tissues would be beneficial. Since sampling the hard tissues for genetic analysis is a destructive process, it is important to understand those environmental and intrinsic factors that contribute to DNA preservation. This will serve as a brief introduction to these topics, since skeletal sampling strategies and molecular taphonomy have been discussed in depth elsewhere. Additionally advances in skeletal DNA extraction and analysis will be discussed. Currently there is great variation in the DNA isolation methods used by laboratories to purify DNA from the hard tissues; however, a standardized set of short tandem repeat (STR) loci is analyzed by many US laboratories to allow for comparisons across samples and jurisdictions. Recent advances have allowed for the generation of DNA profiles from smaller quantities of template DNA and have expanded the number of loci analyzed for greater discriminatory power and predictions regarding the geographic ancestry and phenotype of the individual. Finally, utilizing databases and expanding the number of comparison samples will be discussed in light of their role in the identification process.
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Affiliation(s)
- Krista E. Latham
- Biology Department, Human Identification Center, University of Indianapolis, Indianapolis, IN, USA
| | - Jessica J. Miller
- Biology Department, Human Identification Center, University of Indianapolis, Indianapolis, IN, USA
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33
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Igisu M, Yokoyama T, Ueno Y, Nakashima S, Shimojima M, Ohta H, Maruyama S. Changes of aliphatic C-H bonds in cyanobacteria during experimental thermal maturation in the presence or absence of silica as evaluated by FTIR microspectroscopy. GEOBIOLOGY 2018; 16:412-428. [PMID: 29869829 DOI: 10.1111/gbi.12294] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/03/2017] [Accepted: 03/16/2018] [Indexed: 06/08/2023]
Abstract
Aliphatic C-H bonds are one of the major organic signatures detected in Proterozoic organic microfossils, and their origin is a topic of interest. To investigate the influence of the presence of silica on the thermal alteration of aliphatic C-H bonds in prokaryotic cells during diagenesis, cyanobacteria Synechocystis sp. PCC6803 were heated at temperatures of 250-450°C. Changes in the infrared (IR) signals were monitored by micro-Fourier transform infrared (FTIR) spectroscopy. Micro-FTIR shows that absorbances at 2,925 cm-1 band (aliphatic CH2 ) and 2,960 cm-1 band (aliphatic CH3 ) decrease during heating, indicating loss of the C-H bonds, which was delayed by the presence of silica. A theoretical approach using solid-state kinetics indicates that the most probable process for the aliphatic C-H decrease is three-dimensional diffusion of alteration products under both non-embedded and silica-embedded conditions. The extrapolation of the experimental results obtained at 250-450°C to lower temperatures implies that the rate constant for CH3 (kCH3 ) is similar to or lower than that for CH2 (kCH2 ; i.e., CH3 decreases at a similar rate or more slowly than CH2 ). The peak height ratio of 2,960 cm-1 band (CH3 )/2,925 cm-1 band (CH2 ; R3/2 values) either increased or remained constant during the heating. These results reveal that the presence of silica does affect the decreasing rate of the aliphatic C-H bonds in cyanobacteria during thermal maturation, but that it does not significantly decrease the R3/2 values. Meanwhile, studies of microfossils suggest that the R3/2 values of Proterozoic prokaryotic fossils from the Bitter Springs Group and Gunflint Formation have decreased during fossilization, which is inconsistent with the prediction from our experimental results that R3/2 values did not decrease after silicification. Some process other than thermal degradation, possibly preservation of specific classes of biomolecules with low R3/2 values, might have occurred during fossilization.
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Affiliation(s)
- Motoko Igisu
- School of Life Science and Technology, Tokyo Institute of Technology, Kanagawa, Japan
| | - Tadashi Yokoyama
- Graduate School of Integrated Arts and Sciences, Hiroshima University, Hiroshima, Japan
| | - Yuichiro Ueno
- Department of Subsurface Geobiology Analysis and Research, Japan Agency for Marine-Earth Science and Technology (JAMSTEC), Kanagawa, Japan
- Department of Earth and Planetary Sciences, Tokyo Institute of Technology, Tokyo, Japan
- Earth-Life Science Institute, Tokyo Institute of Technology, Tokyo, Japan
| | - Satoru Nakashima
- Department of Earth and Space Science, Osaka University, Osaka, Japan
| | - Mie Shimojima
- School of Life Science and Technology, Tokyo Institute of Technology, Kanagawa, Japan
| | - Hiroyuki Ohta
- Earth-Life Science Institute, Tokyo Institute of Technology, Tokyo, Japan
- School of Life Science and Technology, Tokyo Institute of Technology, Kanagawa, Japan
| | - Shigenori Maruyama
- Earth-Life Science Institute, Tokyo Institute of Technology, Tokyo, Japan
- Novosibirsk State University, Novosibirsk, Russia
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34
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Parry LA, Smithwick F, Nordén KK, Saitta ET, Lozano-Fernandez J, Tanner AR, Caron JB, Edgecombe GD, Briggs DEG, Vinther J. Soft-Bodied Fossils Are Not Simply Rotten Carcasses - Toward a Holistic Understanding of Exceptional Fossil Preservation. Bioessays 2017; 40. [DOI: 10.1002/bies.201700167] [Citation(s) in RCA: 56] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/12/2017] [Revised: 10/21/2017] [Indexed: 12/31/2022]
Affiliation(s)
- Luke A. Parry
- School of Earth Sciences, University of Bristol, Wills Memorial Building; Queen's Road Bristol BS8 1RJ UK
- Royal Ontario Museum; 100 Queen's Park Toronto ON M5S 2C6 Canada
- Department of Earth Sciences, The Natural History Museum; Cromwell Road London SW7 5BD UK
| | - Fiann Smithwick
- Royal Ontario Museum; 100 Queen's Park Toronto ON M5S 2C6 Canada
| | - Klara K. Nordén
- Royal Ontario Museum; 100 Queen's Park Toronto ON M5S 2C6 Canada
| | - Evan T. Saitta
- Royal Ontario Museum; 100 Queen's Park Toronto ON M5S 2C6 Canada
| | - Jesus Lozano-Fernandez
- School of Biological Sciences, University of Bristol; Life Sciences Building, 24 Tyndall Avenue Bristol BS8 1TQ UK
| | - Alastair R. Tanner
- School of Biological Sciences, University of Bristol; Life Sciences Building, 24 Tyndall Avenue Bristol BS8 1TQ UK
| | - Jean-Bernard Caron
- School of Earth Sciences, University of Bristol, Wills Memorial Building; Queen's Road Bristol BS8 1RJ UK
| | - Gregory D. Edgecombe
- Department of Earth Sciences, The Natural History Museum; Cromwell Road London SW7 5BD UK
| | - Derek E. G. Briggs
- Department of Geology and Geophysics, Yale University; 210 Whitney Avenue New Haven CT 06511 USA
- Yale Peabody Museum of Natural History; 170 Whitney Avenue New Haven CT 06520 USA
- Departments of Ecology and Evolutionary Biology and Earth Sciences, University of Toronto; Toronto ON M5S 3B2 Canada
| | - Jakob Vinther
- School of Earth Sciences, University of Bristol, Wills Memorial Building; Queen's Road Bristol BS8 1RJ UK
- Royal Ontario Museum; 100 Queen's Park Toronto ON M5S 2C6 Canada
- School of Biological Sciences, University of Bristol; Life Sciences Building, 24 Tyndall Avenue Bristol BS8 1TQ UK
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35
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Pérez-Martínez C, Pérez-Cárceles MD, Legaz I, Prieto-Bonete G, Luna A. Quantification of nitrogenous bases, DNA and Collagen type I for the estimation of the postmortem interval in bone remains. Forensic Sci Int 2017; 281:106-112. [PMID: 29125988 DOI: 10.1016/j.forsciint.2017.10.039] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/03/2017] [Revised: 10/02/2017] [Accepted: 10/29/2017] [Indexed: 11/28/2022]
Abstract
Estimating the postmortem interval (PMI) is an important goal in forensic medicine and continues to be one of the most difficult tasks of the forensic investigator. Few accurate methods exist to determine the time since death of skeletonized human remains due to the great number of intrinsic and external factors that may alter the normal course of postmortem change. The purpose of this research was to assess the usefulness of various biochemical parameters, such as nitrogenous bases (adenine, guanine, purines, cytosine, thymine, pyrimidines, hypoxanthine and xanthine), DNA and Collagen Type I peptides to estimate PMI. These parameters were analysed in cortical bone for the establishment of data in a total of 80 long bones of 80 corpses (50 males, 30 females) with a mean age of 68.31 years (S.D.=18.021, range=20-97). The bones were removed from the cement niches of a cemetery in Murcia (south-eastern Spain), where they had lain for between 5 and 47 years (mean time 23.83 years, S.D.=10.85). Our results show a significant decrease in adenine (p=0.0004), guanine (p=0.0001), purines (p=0.0001), cytosine (p=0.0001), thymine (p=0.0226), pyrimidines (p=0.0002) and the number of peptides of Collagen type I (p=0.0053) in those with a PMI≥20 years. In a curvilinear regression analysis the results show that 30.6% of the variable PMI could be explained by guanine concentration, in bones with a PMI<20 years, while in cases of a PMI≥20 years, the variable that best explained membership of this group was adenine (38.0%). In the discriminant analysis applied to the all the variables as a function of PMI when two groups were established, 86.7% of the cases were correctly classified. These results show that the quantification of Collagen type I proteins and nitrogenous bases could be used as a complementary tool, together with other analyses, in the estimation of PMI.
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Affiliation(s)
| | | | - Isabel Legaz
- Department of Legal and Forensic Medicine, University of Murcia, Spain
| | | | - Aurelio Luna
- Department of Legal and Forensic Medicine, University of Murcia, Spain
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36
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Alleon J, Bernard S, Le Guillou C, Daval D, Skouri-Panet F, Kuga M, Robert F. Organic molecular heterogeneities can withstand diagenesis. Sci Rep 2017; 7:1508. [PMID: 28473702 PMCID: PMC5431453 DOI: 10.1038/s41598-017-01612-8] [Citation(s) in RCA: 42] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/08/2017] [Accepted: 03/30/2017] [Indexed: 11/09/2022] Open
Abstract
Reconstructing the original biogeochemistry of organic fossils requires quantifying the extent of the chemical transformations that they underwent during burial-induced maturation processes. Here, we performed laboratory experiments on chemically different organic materials in order to simulate the thermal maturation processes that occur during diagenesis. Starting organic materials were microorganisms and organic aerosols. Scanning transmission X-ray microscopy (STXM) was used to collect X-ray absorption near edge spectroscopy (XANES) data of the organic residues. Results indicate that even after having been submitted to 250 °C and 250 bars for 100 days, the molecular signatures of microorganisms and aerosols remain different in terms of nitrogen-to-carbon atomic ratio and carbon and nitrogen speciation. These observations suggest that burial-induced thermal degradation processes may not completely obliterate the chemical and molecular signatures of organic molecules. In other words, the present study suggests that organic molecular heterogeneities can withstand diagenesis and be recognized in the fossil record.
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Affiliation(s)
- Julien Alleon
- Institut de Minéralogie, de Physique des Matériaux et de Cosmochimie (IMPMC), Sorbonne Universités - CNRS UMR 7590, Muséum National d'Histoire Naturelle, UPMC Univ. Paris 06, IRD UMR 206, 61 rue Buffon, 75005, Paris, France.,Department of Earth Atmospheric and Planetary Sciences, Massachusetts Institute of Technology, Cambridge, MA, 02139, USA
| | - Sylvain Bernard
- Institut de Minéralogie, de Physique des Matériaux et de Cosmochimie (IMPMC), Sorbonne Universités - CNRS UMR 7590, Muséum National d'Histoire Naturelle, UPMC Univ. Paris 06, IRD UMR 206, 61 rue Buffon, 75005, Paris, France.
| | | | - Damien Daval
- Laboratoire d'Hydrologie et de Géochimie de Strasbourg, Université de Strasbourg/EOST - CNRS UMR 7517, 1 Rue Blessig, 67084, Strasbourg, France
| | - Feriel Skouri-Panet
- Institut de Minéralogie, de Physique des Matériaux et de Cosmochimie (IMPMC), Sorbonne Universités - CNRS UMR 7590, Muséum National d'Histoire Naturelle, UPMC Univ. Paris 06, IRD UMR 206, 61 rue Buffon, 75005, Paris, France
| | - Maïa Kuga
- Department of Earth Sciences, ETH Zürich, 8092, Zürich, Switzerland
| | - François Robert
- Institut de Minéralogie, de Physique des Matériaux et de Cosmochimie (IMPMC), Sorbonne Universités - CNRS UMR 7590, Muséum National d'Histoire Naturelle, UPMC Univ. Paris 06, IRD UMR 206, 61 rue Buffon, 75005, Paris, France
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37
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Halter MC, Zahn JA. Degradation and half-life of DNA present in biomass from a genetically-modified organism during land application. ACTA ACUST UNITED AC 2017; 44:213-220. [DOI: 10.1007/s10295-016-1876-x] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/11/2016] [Accepted: 11/17/2016] [Indexed: 11/29/2022]
Abstract
Abstract
White biotechnology has made a positive impact on the chemical industry by providing safer, more efficient chemical manufacturing processes that have reduced the use of toxic chemicals, harsh reaction conditions, and expensive metal catalysts, which has improved alignment with the principles of Green Chemistry. The genetically-modified (GM) biocatalysts that are utilized in these processes are typically separated from high-value products and then recycled, or eliminated. Elimination routes include disposal in sanitary landfills, incineration, use as a fuel, animal feed, or reuse as an agricultural soil amendment or other value-added products. Elimination routes that have the potential to impact the food chain or environment have been more heavily scrutinized for the fate and persistence of biological products. In this study, we developed and optimized a method for monitoring the degradation of strain-specific DNA markers from a genetically-modified organism (GMO) used for the commercial production of 1,3-propanediol. Laboratory and field tests showed that a marker for heterologous DNA in the GM organism was no longer detectable by end-point polymerase chain reaction (PCR) after 14 days. The half-life of heterologous DNA was increased by 17% (from 42.4 to 49.7 h) after sterilization of the soil from a field plot, which indicated that abiotic factors were important in degradation of DNA under field conditions. There was no evidence for horizontal transfer of DNA target sequences from the GMO to viable organisms present in the soil.
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Affiliation(s)
- Mathew C Halter
- DuPont Tate and Lyle Bio Products 198 Blair Bend Drive 37774 Loudon TN USA
| | - James A Zahn
- DuPont Tate and Lyle Bio Products 198 Blair Bend Drive 37774 Loudon TN USA
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38
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Moyer AE, Zheng W, Schweitzer MH. Keratin Durability Has Implications for the Fossil Record: Results from a 10 Year Feather Degradation Experiment. PLoS One 2016; 11:e0157699. [PMID: 27384819 PMCID: PMC4934732 DOI: 10.1371/journal.pone.0157699] [Citation(s) in RCA: 27] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/18/2015] [Accepted: 05/03/2016] [Indexed: 11/19/2022] Open
Abstract
Keratinous ‘soft tissue’ structures (i.e. epidermally derived and originally non-biomineralized), include feathers, skin, claws, beaks, and hair. Despite their relatively common occurrence in the fossil record (second only to bone and teeth), few studies have addressed natural degradation processes that must occur in all organic material, including those keratinous structures that are incorporated into the rock record as fossils. Because feathers have high preservation potential and strong phylogenetic signal, in the current study we examine feathers subjected to different burial environments for a duration of ~10 years, using transmission electron microscopy (TEM) and in situ immunofluorescence (IF). We use morphology and persistence of specific immunoreactivity as indicators of preservation at the molecular and microstructural levels. We show that feather keratin is durable, demonstrates structural and microstructural integrity, and retains epitopes suitable for specific antibody recognition in even the harshest conditions. These data support the hypothesis that keratin antibody reactivity can be used to identify the nature and composition of epidermal structures in the rock record, and to address evolutionary questions by distinguishing between alpha- (widely distributed) and beta- (limited to sauropsids) keratin.
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Affiliation(s)
- Alison E. Moyer
- Department of Biological Science, North Carolina State University, Raleigh NC 27695, United States of America
- * E-mail:
| | - Wenxia Zheng
- Department of Biological Science, North Carolina State University, Raleigh NC 27695, United States of America
| | - Mary H. Schweitzer
- Department of Biological Science, North Carolina State University, Raleigh NC 27695, United States of America
- North Carolina Museum of Natural Sciences, Raleigh NC 27601, United States of America
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39
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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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40
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Papakosta V, Smittenberg RH, Gibbs K, Jordan P, Isaksson S. Extraction and derivatization of absorbed lipid residues from very small and very old samples of ceramic potsherds for molecular analysis by gas chromatography–mass spectrometry (GC–MS) and single compound stable carbon isotope analysis by gas chromatography–combustion–isotope ratio mass spectrometry (GC–C–IRMS). Microchem J 2015. [DOI: 10.1016/j.microc.2015.06.013] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/23/2022]
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41
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Sistiaga A, Wrangham R, Rothman JM, Summons RE. New Insights into the Evolution of the Human Diet from Faecal Biomarker Analysis in Wild Chimpanzee and Gorilla Faeces. PLoS One 2015; 10:e0128931. [PMID: 26061730 PMCID: PMC4465628 DOI: 10.1371/journal.pone.0128931] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/20/2015] [Accepted: 05/01/2015] [Indexed: 01/19/2023] Open
Abstract
Our understanding of early human diets is based on reconstructed biomechanics of hominin jaws, bone and teeth isotopic data, tooth wear patterns, lithic, taphonomic and zooarchaeological data, which do not provide information about the relative amounts of different types of foods that contributed most to early human diets. Faecal biomarkers are proving to be a valuable tool in identifying relative proportions of plant and animal tissues in Palaeolithic diets. A limiting factor in the application of the faecal biomarker approach is the striking absence of data related to the occurrence of faecal biomarkers in non-human primate faeces. In this study we explored the nature and proportions of sterols and stanols excreted by our closest living relatives. This investigation reports the first faecal biomarker data for wild chimpanzee (Pan troglodytes) and mountain gorilla (Gorilla beringei). Our results suggest that the chemometric analysis of faecal biomarkers is a useful tool for distinguishing between NHP and human faecal matter, and hence, it could provide information for palaeodietary research and early human diets.
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Affiliation(s)
- Ainara Sistiaga
- Massachusetts Institute of Technology, Cambridge, United States of America
- Universidad de La Laguna, La Laguna, Spain
| | | | | | - Roger E. Summons
- Massachusetts Institute of Technology, Cambridge, United States of America
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Rajčević N, Janaćković P, Dodoš T, Tešević V, Bojović S, Marin PD. Leaf n-alkanes as characters differentiating coastal and continental Juniperus deltoides populations from the Balkan Peninsula. Chem Biodivers 2014; 11:1042-52. [PMID: 25044590 DOI: 10.1002/cbdv.201300363] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/22/2013] [Indexed: 11/09/2022]
Abstract
The composition of the cuticular n-alkanes isolated from the leaves of nine populations of Juniperus deltoides R.P.Adams from continental and coastal areas of the Balkan Peninsula was characterized by GC-FID and GC/MS analyses. In the leaf waxes, 14 n-alkane homologues with chain-lengths ranging from C22 to C35 were identified. n-Tritriacontane (C33 ) was dominant in the waxes of all populations, but variations between the populations in the contents of all n-alkanes were observed. Several statistical methods (ANOVA, principal component, discriminant, and cluster analyses) were used to investigate the diversity and variability of the cuticular-leaf-n-alkane patterns of the nine J. deltoides populations. This is the first report on the n-alkane composition for this species. The multivariate statistical analyses evidenced a high correlation of the leaf-n-alkane pattern with the geographical distribution of the investigated samples, differentiating the coastal from the continental populations of this taxon.
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Affiliation(s)
- Nemanja Rajčević
- University of Belgrade, Faculty of Biology, Institute of Botany and Botanical Garden 'Jevremovac', Studentski trg 16, 11000 Belgrade, Serbia.
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43
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Briggs DEG, Summons RE. Ancient biomolecules: Their origins, fossilization, and role in revealing the history of life. Bioessays 2014; 36:482-90. [DOI: 10.1002/bies.201400010] [Citation(s) in RCA: 123] [Impact Index Per Article: 12.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
Affiliation(s)
- Derek E. G. Briggs
- Department of Geology and Geophysics; Yale University; New Haven CT USA
- Yale Peabody Museum of Natural History; New Haven CT USA
| | - Roger E. Summons
- Department of Earth, Atmospheric and Planetary Sciences; Massachusetts Institute of Technology; Cambridge MA USA
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44
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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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45
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Baldwin DS, Colloff MJ, Rees GN, Chariton AA, Watson GO, Court LN, Hartley DM, Morgan MJ, King AJ, Wilson JS, Hodda M, Hardy CM. Impacts of inundation and drought on eukaryote biodiversity in semi-arid floodplain soils. Mol Ecol 2013; 22:1746-58. [PMID: 23379967 DOI: 10.1111/mec.12190] [Citation(s) in RCA: 49] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/21/2012] [Revised: 11/18/2012] [Accepted: 11/21/2012] [Indexed: 01/15/2023]
Abstract
Floodplain ecosystems are characterized by alternating wet and dry phases and periodic inundation defines their ecological character. Climate change, river regulation and the construction of levees have substantially altered natural flooding and drying regimes worldwide with uncertain effects on key biotic groups. In southern Australia, we hypothesized that soil eukaryotic communities in climate change affected areas of a semi-arid floodplain would transition towards comprising mainly dry-soil specialist species with increasing drought severity. Here, we used 18S rRNA amplicon pyrosequencing to measure the eukaryote community composition in soils that had been depleted of water to varying degrees to confirm that reproducible transitional changes occur in eukaryotic biodiversity on this floodplain. Interflood community structures (3 years post-flood) were dominated by persistent rather than either aquatic or dry-specialist organisms. Only 2% of taxa were unique to dry locations by 8 years post-flood, and 10% were restricted to wet locations (inundated a year to 2 weeks post-flood). Almost half (48%) of the total soil biota were detected in both these environments. The discovery of a large suite of organisms able to survive nearly a decade of drought, and up to a year submerged supports the concept of inherent resilience of Australian semi-arid floodplain soil communities under increasing pressure from climatic induced changes in water availability.
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Affiliation(s)
- Darren S Baldwin
- CSIRO Land and Water and the Murray-Darling Freshwater Research Centre, PO Box 991, Wodonga, Vic., 3689, Australia
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46
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Allentoft ME, Collins M, Harker D, Haile J, Oskam CL, Hale ML, Campos PF, Samaniego JA, Gilbert MTP, Willerslev E, Zhang G, Scofield RP, Holdaway RN, Bunce M. The half-life of DNA in bone: measuring decay kinetics in 158 dated fossils. Proc Biol Sci 2012; 279:4724-33. [PMID: 23055061 PMCID: PMC3497090 DOI: 10.1098/rspb.2012.1745] [Citation(s) in RCA: 269] [Impact Index Per Article: 22.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/26/2012] [Accepted: 09/14/2012] [Indexed: 12/26/2022] Open
Abstract
Claims of extreme survival of DNA have emphasized the need for reliable models of DNA degradation through time. By analysing mitochondrial DNA (mtDNA) from 158 radiocarbon-dated bones of the extinct New Zealand moa, we confirm empirically a long-hypothesized exponential decay relationship. The average DNA half-life within this geographically constrained fossil assemblage was estimated to be 521 years for a 242 bp mtDNA sequence, corresponding to a per nucleotide fragmentation rate (k) of 5.50 × 10(-6) per year. With an effective burial temperature of 13.1°C, the rate is almost 400 times slower than predicted from published kinetic data of in vitro DNA depurination at pH 5. Although best described by an exponential model (R(2) = 0.39), considerable sample-to-sample variance in DNA preservation could not be accounted for by geologic age. This variation likely derives from differences in taphonomy and bone diagenesis, which have confounded previous, less spatially constrained attempts to study DNA decay kinetics. Lastly, by calculating DNA fragmentation rates on Illumina HiSeq data, we show that nuclear DNA has degraded at least twice as fast as mtDNA. These results provide a baseline for predicting long-term DNA survival in bone.
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Affiliation(s)
- Morten E. Allentoft
- Ancient DNA Laboratory, School of Biological Sciences and Biotechnology, Murdoch University, 90 South Street, Perth, Western Australia 6150, Australia
- School of Biological Sciences, University of Canterbury, Private Bag 4800, Christchurch, New Zealand
- Centre for GeoGenetics, Natural History Museum of Denmark, University of Copenhagen, Øster Voldgade 5-7, 1350 Copenhagen K, Denmark
| | - Matthew Collins
- Department of Archaeology, University of York, PO Box 373, York, UK
| | - David Harker
- Department of Archaeology, University of York, PO Box 373, York, UK
| | - James Haile
- Ancient DNA Laboratory, School of Biological Sciences and Biotechnology, Murdoch University, 90 South Street, Perth, Western Australia 6150, Australia
| | - Charlotte L. Oskam
- Ancient DNA Laboratory, School of Biological Sciences and Biotechnology, Murdoch University, 90 South Street, Perth, Western Australia 6150, Australia
| | - Marie L. Hale
- School of Biological Sciences, University of Canterbury, Private Bag 4800, Christchurch, New Zealand
| | - Paula F. Campos
- Centre for GeoGenetics, Natural History Museum of Denmark, University of Copenhagen, Øster Voldgade 5-7, 1350 Copenhagen K, Denmark
- Museu da Ciência, University of Coimbra, Laboratorio Chimico, Largo Marquês de Pombal, 3000-272 Coimbra, Portugal
| | - Jose A. Samaniego
- Centre for GeoGenetics, Natural History Museum of Denmark, University of Copenhagen, Øster Voldgade 5-7, 1350 Copenhagen K, Denmark
| | - M. Thomas P. Gilbert
- Ancient DNA Laboratory, School of Biological Sciences and Biotechnology, Murdoch University, 90 South Street, Perth, Western Australia 6150, Australia
- Centre for GeoGenetics, Natural History Museum of Denmark, University of Copenhagen, Øster Voldgade 5-7, 1350 Copenhagen K, Denmark
| | - Eske Willerslev
- Centre for GeoGenetics, Natural History Museum of Denmark, University of Copenhagen, Øster Voldgade 5-7, 1350 Copenhagen K, Denmark
| | - Guojie Zhang
- Beijing Genomics Institute-Shenzhen, Shenzhen 518083, People's Republic of China
| | - R. Paul Scofield
- Canterbury Museum, Rolleston Avenue, Christchurch 8050, New Zealand
| | - Richard N. Holdaway
- School of Biological Sciences, University of Canterbury, Private Bag 4800, Christchurch, New Zealand
- Palaecol Research Ltd, 167 Springs Road, Hornby, Christchurch 8042, New Zealand
| | - Michael Bunce
- Ancient DNA Laboratory, School of Biological Sciences and Biotechnology, Murdoch University, 90 South Street, Perth, Western Australia 6150, Australia
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Abstract
The preservation of microstructures consistent with soft tissues, cells, and other biological components in demineralized fragments of dinosaur bone tens of millions of years old was unexpected, and counter to current hypotheses of tissue, cellular, and molecular degradation. Although the morphological similarity of these tissues to extant counterparts was unmistakable, after at least 80 million years exposed to geochemical influences, morphological similarity is insufficient to support an endogenous source. To test this hypothesis, and to characterize these materials at a molecular level, we applied multiple independent chemical, molecular, and microscopic analyses to identify the presence of original components produced by the extinct organisms. Microscopic techniques included field emission scanning electron microscopy, analytical transmission electron microscopy, transmitted light microscopy (LM), and fluorescence microscopy (FM). The chemical and molecular techniques include enzyme-linked immunosorbant assay, sodium dodecyl sulfate polyacrylamide gel electrophoresis, western blot (immunoblot), and attenuated total reflectance infrared spectroscopy. In situ analyses performed directly on tissues included immunohistochemistry and time-of-flight secondary ion mass spectrometry. The details of sample preparation and methodology are described in detail herein.
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Affiliation(s)
- Wenxia Zheng
- Department of Marine, Earth and Atmospheric Sciences, North Carolina State University, Raleigh, NC, USA.
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Weaver PG, Doguzhaeva LA, Lawver DR, Tacker RC, Ciampaglio CN, Crate JM, Zheng W. Characterization of organics consistent with β-chitin preserved in the Late Eocene cuttlefish Mississaepia mississippiensis. PLoS One 2011; 6:e28195. [PMID: 22132239 PMCID: PMC3223232 DOI: 10.1371/journal.pone.0028195] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/09/2011] [Accepted: 11/02/2011] [Indexed: 12/30/2022] Open
Abstract
BACKGROUND Preservation of original organic components in fossils across geological time is controversial, but the potential such molecules have for elucidating evolutionary processes and phylogenetic relationships is invaluable. Chitin is one such molecule. Ancient chitin has been recovered from both terrestrial and marine arthropods, but prior to this study had not been recovered from fossil marine mollusks. METHODOLOGY/PRINCIPAL FINDINGS Organics consistent with β-chitin are recovered in cuttlebones of Mississaepia mississippiensis from the Late Eocene (34.36 million years ago) marine clays of Hinds County, Mississippi, USA. These organics were determined and characterized through comparisons with extant taxa using Scanning Electron Microscopy/Energy Dispersive Spectrometry (SEM/EDS), Field Emission Scanning Electron Microscopy (Hyperprobe), Fourier Transmission Infrared Spectroscopy (FTIR) and Immunohistochemistry (IHC). CONCLUSIONS/SIGNIFICANCE Our study presents the first evidence for organics consistent with chitin from an ancient marine mollusk and discusses how these organics have been degraded over time. As mechanisms for their preservation, we propose that the inorganic/organic lamination of the cuttlebone, combined with a suboxic depositional environment with available free Fe(2+) ions, inhibited microbial or enzymatic degradation.
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Affiliation(s)
- Patricia G Weaver
- Research and Collections, North Carolina Museum of Natural Sciences, Raleigh, North Carolina, United States of America.
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Molak M, Ho SYW. Evaluating the impact of post-mortem damage in ancient DNA: a theoretical approach. J Mol Evol 2011; 73:244-55. [PMID: 22101653 DOI: 10.1007/s00239-011-9474-z] [Citation(s) in RCA: 22] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/04/2011] [Accepted: 11/07/2011] [Indexed: 01/08/2023]
Abstract
The growth of ancient DNA research has offered exceptional opportunities and raised great expectations, but has also presented some considerable challenges. One of the ongoing issues is the impact of post-mortem damage in DNA molecules. Nucleotide alterations and DNA strand breakages lead to a significant decrease in the quantity of DNA molecules of useful length in a sample and to errors in the final DNA sequences obtained. We present a model of age-dependent DNA damage and quantify the influence of that damage on subsequent steps in the sequencing process, including the polymerase chain reaction and cloning. Calculations using our model show that deposition conditions, rather than the age of a sample, have the greatest influence on the level of DNA damage. In turn, this affects the probability of interpreting an erroneous (possessing damage-derived mutations) sequence as being authentic. We also evaluated the effect of post-mortem damage on real data sets using a Bayesian phylogenetic approach. According to our study, damage-derived sequence alterations appear to have little impact on the final DNA sequences. This indicates the effectiveness of current methods for sequence authentication and validation.
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Affiliation(s)
- Martyna Molak
- School of Biological Sciences, University of Sydney, Sydney, NSW 2006, Australia.
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50
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Regert M. Analytical strategies for discriminating archeological fatty substances from animal origin. MASS SPECTROMETRY REVIEWS 2011; 30:177-220. [PMID: 21337597 DOI: 10.1002/mas.20271] [Citation(s) in RCA: 39] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/17/2008] [Revised: 07/21/2009] [Accepted: 07/21/2009] [Indexed: 05/21/2023]
Abstract
Mass spectrometry (MS) is an essential tool in the field of biomolecular archeology to characterize amorphous organic residues preserved in ancient ceramic vessels. Animal fats of various nature and origin, namely subcutaneous fats of cattle, sheep, goats, pigs, horses, and also of dairy products, are those most commonly identified in organic residues in archeological pottery. Fats and oils of marine origin have also been revealed. Since the first applications of MS coupled with gas chromatography (GC) in archeology at the end of 1980s, several developments have occurred, including isotopic determinations by GC coupled to isotope ratio MS and identification of triacylglycerols (TAGs) structure by soft ionization techniques (ESI and APCI). The combination of these methods provides invaluable insights into the strategies of exploitation of animal products in prehistory. In this review, I focus on the analytical strategies based upon MS that allow elucidation of the structure of biomolecular constituents and determination of their isotopic values to identify the nature of animal fat components preserved in highly complex and degraded archeological matrices.
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Affiliation(s)
- M Regert
- Centre d'Etudes Préhistoire, Antiquité, Moyen Âge, UMR 6130, Université Nice Sophia Antipolis, CNRS, Bât. 1; 250, rue Albert Einstein, F-06560 Valbonne, France.
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