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Duan Y, Zhang M, Min C, Lin Y, Li L. Proteomic Analysis of Collagen: a Mass Spectrometry Approach to Material Identification of Shadow Puppet Cultural Relics. Appl Biochem Biotechnol 2024:10.1007/s12010-023-04822-1. [PMID: 38165589 DOI: 10.1007/s12010-023-04822-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 12/19/2023] [Indexed: 01/04/2024]
Abstract
Shadow puppets are a popular art form in various regions, including China, Indonesia, and Turkey, and are rich in cultural significance. However, there is a considerable lack of research on the materials, diseases and conservation techniques related to shadow puppet relics. Material identification is the basis for understanding the production process of ancient shadow puppet relics and evaluating their deterioration degree. The microscopic morphology and infrared spectroscopy results in our experiments showed that the traditional methods of ancient skin identification were not effective in the shadow puppet samples. In order to achieve accurate identification, we used biological mass-spectrometry in proteomics to examine two puppet relics and commercially available modern shadow puppets. The results showed that the above samples could be detected by mass spectrometry with abundant peptides, including peptides specific for bovine skin. These peptides cannot be found in other commonly used materials for making shadow puppets, including the skins of pig, sheep, deer and horse. It is worth mentioning that we have found the peptides specific to yellow cowhide in two ancient shadow puppet relics samples. Therefore, the proteomic evidence shows that the raw materials of the two shadow puppet relics samples are yellow cowhide. Four modern samples also confirmed the reliability of material identification using proteomics. The proteomic evidence shows that the biological mass spectrometry will contribute to the scientific research of shadow puppet relics and other skin and leather cultural relics.
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Affiliation(s)
- Yangbo Duan
- School of Archaeology and Museology, Sichuan University, Chengdu, 610065, Sichuan, China
| | - Muzi Zhang
- Joint International Research Laboratory of Environmental and Social Archaeology, Institute of Cultural Heritage, Shandong University, Qingdao, 266237, Shandong, China
| | - Chen Min
- Chengdu Museum (National Shadow Puppetry Museum in Chengdu), Chengdu, 610015, Sichuan, China
| | - Yalun Lin
- Chengdu Museum (National Shadow Puppetry Museum in Chengdu), Chengdu, 610015, Sichuan, China
| | - Li Li
- Joint International Research Laboratory of Environmental and Social Archaeology, Institute of Cultural Heritage, Shandong University, Qingdao, 266237, Shandong, China.
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2
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SPIN enables high throughput species identification of archaeological bone by proteomics. Nat Commun 2022; 13:2458. [PMID: 35513387 PMCID: PMC9072323 DOI: 10.1038/s41467-022-30097-x] [Citation(s) in RCA: 15] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/23/2021] [Accepted: 04/18/2022] [Indexed: 12/29/2022] Open
Abstract
Species determination based on genetic evidence is an indispensable tool in archaeology, forensics, ecology, and food authentication. Most available analytical approaches involve compromises with regard to the number of detectable species, high cost due to low throughput, or a labor-intensive manual process. Here, we introduce "Species by Proteome INvestigation" (SPIN), a shotgun proteomics workflow for analyzing archaeological bone capable of querying over 150 mammalian species by liquid chromatography-tandem mass spectrometry (LC-MS/MS). Rapid peptide chromatography and data-independent acquisition (DIA) with throughput of 200 samples per day reduce expensive MS time, whereas streamlined sample preparation and automated data interpretation save labor costs. We confirm the successful classification of known reference bones, including domestic species and great apes, beyond the taxonomic resolution of the conventional peptide mass fingerprinting (PMF)-based Zooarchaeology by Mass Spectrometry (ZooMS) method. In a blinded study of degraded Iron-Age material from Scandinavia, SPIN produces reproducible results between replicates, which are consistent with morphological analysis. Finally, we demonstrate the high throughput capabilities of the method in a high-degradation context by analyzing more than two hundred Middle and Upper Palaeolithic bones from Southern European sites with late Neanderthal occupation. While this initial study is focused on modern and archaeological mammalian bone, SPIN will be open and expandable to other biological tissues and taxa.
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Abstract
Archaeological and paleontological records offer tremendous yet often untapped potential for examining long-term biodiversity trends and the impact of climate change and human activity on ecosystems. Yet, zooarchaeological and fossil remains suffer various limitations, including that they are often highly fragmented and morphologically unidentifiable, preventing them from being optimally leveraged for addressing fundamental research questions in archaeology, paleontology, and conservation paleobiology. Here, we explore the potential of palaeoproteomics—the study of ancient proteins—to serve as a critical tool for creating richer, more informative datasets about biodiversity change that can be leveraged to generate more realistic, constructive, and effective conservation and restoration strategies into the future.
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Chen B, Wang Z, Wang J, Zheng H, Zhou J, Chen X, Wang B, Zhou Y, Peng Z. Ultrasensitive dual enhanced electrochemical immunosensor to detect ancient wool relics. ANALYTICAL METHODS : ADVANCING METHODS AND APPLICATIONS 2022; 14:394-400. [PMID: 34981794 DOI: 10.1039/d1ay01514a] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/14/2023]
Abstract
The identification of ancient wool is of great significance in archaeology; however, conventional methods are unwieldy or even ineffective when testing contaminated or severely degraded ancient samples. Therefore, it is highly desirable to develop an ultrasensitive detection method for ancient wool. In this study, an ultrasensitive electrochemical immunosensor is proposed and developed to detect ancient wool, where graphene oxide (GO), aldehyde-functionalized ionic liquid (AFIL) composites and gold nanoparticles (AuNPs) are synthesized as efficient signal amplifiers. With their large surface area and excellent electron transfer efficiency, the combination of GO-AFIL and AuNPs endows the immunosensor with excellent electrochemical properties. The fabricated immunosensor measures over a wide linear range of 0.01-100 ng mL-1 with a low detection limit of 0.9 ± 0.2 pg mL-1. Moreover, the immunosensor demonstrates excellent performance for detecting ancient wool. The identification of wool fabrics unearthed from Xinjiang, Tibet and Kazakhstan supports the historicity of prosperous sheepherding and wool trade in Central Asia during the Bronze Age.
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Affiliation(s)
- Boyi Chen
- School of Materials Science & Engineering, Zhejiang Sci-Tech University, Hangzhou 310018, China.
| | - Zhongyuan Wang
- School of Materials Science & Engineering, Zhejiang Sci-Tech University, Hangzhou 310018, China.
| | - Junsen Wang
- School of Materials Science & Engineering, Zhejiang Sci-Tech University, Hangzhou 310018, China.
| | - Hailing Zheng
- Key Scientific Research Base of Textile Conservation, State Administration for Cultural Heritage, China National Silk Museum, Hangzhou 310002, China.
| | - Junyi Zhou
- School of Materials Science & Engineering, Zhejiang Sci-Tech University, Hangzhou 310018, China.
| | - Xushi Chen
- School of Materials Science & Engineering, Zhejiang Sci-Tech University, Hangzhou 310018, China.
| | - Bing Wang
- School of Materials Science & Engineering, Zhejiang Sci-Tech University, Hangzhou 310018, China.
| | - Yang Zhou
- Key Scientific Research Base of Textile Conservation, State Administration for Cultural Heritage, China National Silk Museum, Hangzhou 310002, China.
| | - Zhiqin Peng
- School of Materials Science & Engineering, Zhejiang Sci-Tech University, Hangzhou 310018, China.
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Goecker ZC, Legg KM, Salemi MR, Herren AW, Phinney BS, McKiernan HE, Parker GJ. Alternative LC-MS/MS Platforms and Data Acquisition Strategies for Proteomic Genotyping of Human Hair Shafts. J Proteome Res 2021; 20:4655-4666. [PMID: 34491751 DOI: 10.1021/acs.jproteome.1c00209] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Protein is a major component of all biological evidence. Proteomic genotyping is the use of genetically variant peptides (GVPs) that contain single-amino-acid polymorphisms to infer the genotype of matching nonsynonymous single-nucleotide polymorphisms for the individual from whom the protein sample originated. This can be used to statistically associate an individual to evidence found at a crime scene. The utility of the inferred genotype increases as the detection of GVPs increases, which is the direct result of technology transfer to mass spectrometry platforms typically available. Digests of single (2 cm) human hair shafts from three European and two African subjects were analyzed using data-dependent acquisition on a Q-Exactive Plus Hybrid Quadrupole-Orbitrap system, data-independent acquisition and a variant of parallel reaction monitoring (PRM) on an Orbitrap Fusion Lumos Tribrid system, and multiple reaction monitoring (MRM) on an Agilent 6495 triple quadrupole system. In our hands, average GVP detection from a selected panel of 24 GVPs increased from 6.5 ± 1.1 and 3.1 ± 0.8 using data-dependent and -independent acquisition to 9.5 ± 0.7 and 11.7 ± 1.7 using PRM and MRM (p < 0.05), respectively. PRM resulted in a 1.3-fold increase in detection sensitivity, and MRM resulted in a 1.6-fold increase in detection sensitivity. This increase in biomarker detection has a functional impact on the statistical association of a protein sample and an individual. Increased biomarker sensitivity, using Markov Chain Monte Carlo modeling, produced a median-estimated random match probability of over 1 in 10 trillion from a single hair using targeted proteomics. For PRM and MRM, detected GVPs were validated by the inclusion of stable isotope-labeled peptides in each sample, which served also as a detection trigger. This research accomplishes two aims: the demonstration of utility for alternative analytical platforms in proteomic genotyping and the establishment of validation methods for the evaluation of inferred genotypes.
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Affiliation(s)
- Zachary C Goecker
- Department of Environmental Toxicology, University of California, Davis, California 95616, United States
| | - Kevin M Legg
- The Center for Forensic Science Research and Education, Willow Grove, Pennsylvania 19090, United States
| | - Michelle R Salemi
- Proteomics Core Facility, University of California, Davis, California 95616, United States
| | - Anthony W Herren
- Proteomics Core Facility, University of California, Davis, California 95616, United States
| | - Brett S Phinney
- Proteomics Core Facility, University of California, Davis, California 95616, United States
| | - Heather E McKiernan
- The Center for Forensic Science Research and Education, Willow Grove, Pennsylvania 19090, United States
| | - Glendon J Parker
- Department of Environmental Toxicology, University of California, Davis, California 95616, United States
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Forensic proteomics. Forensic Sci Int Genet 2021; 54:102529. [PMID: 34139528 DOI: 10.1016/j.fsigen.2021.102529] [Citation(s) in RCA: 19] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/24/2020] [Revised: 05/06/2021] [Accepted: 05/07/2021] [Indexed: 12/19/2022]
Abstract
Protein is a major component of all biological evidence, often the matrix that embeds other biomolecules such as polynucleotides, lipids, carbohydrates, and small molecules. The proteins in a sample reflect the transcriptional and translational program of the originating cell types. Because of this, proteins can be used to identify body fluids and tissues, as well as convey genetic information in the form of single amino acid polymorphisms, the result of non-synonymous SNPs. This review explores the application and potential of forensic proteomics. The historical role that protein analysis played in the development of forensic science is examined. This review details how innovations in proteomic mass spectrometry have addressed many of the historical limitations of forensic protein science, and how the application of forensic proteomics differs from proteomics in the life sciences. Two more developed applications of forensic proteomics are examined in detail: body fluid and tissue identification, and proteomic genotyping. The review then highlights developing areas of proteomics that have the potential to impact forensic science in the near future: fingermark analysis, species identification, peptide toxicology, proteomic sex estimation, and estimation of post-mortem intervals. Finally, the review highlights some of the newer innovations in proteomics that may drive further development of the field. In addition to potential impact, this review also attempts to evaluate the stage of each application in the development, validation and implementation process. This review is targeted at investigators who are interested in learning about proteomics in a forensic context and expanding the amount of information they can extract from biological evidence.
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Nodari R, Drancourt M, Barbieri R. Paleomicrobiology of the human digestive tract: A review. Microb Pathog 2021; 157:104972. [PMID: 34029658 DOI: 10.1016/j.micpath.2021.104972] [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: 12/08/2020] [Revised: 04/23/2021] [Accepted: 05/14/2021] [Indexed: 10/21/2022]
Abstract
The microbiota is a hot topic of research in medical microbiology, boosted by culturomics and metagenomics, with unanticipated knowledge outputs in physiology and pathology. Knowledge of the microbiota in ancient populations may therefore be of prime interest in understanding factors shaping the coevolution of the microbiota and populations. Studies on ancient human microbiomes can help us understand how the community of microorganisms presents in the oral cavity and the gut was shaped during the evolution of our species and what environmental, social or cultural changes may have changed it. This review cumulates and summarizes the discoveries in the field of the ancient human microbiota, focusing on the remains used as samples and techniques used to handle and analyze them.
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Affiliation(s)
- Riccardo Nodari
- Department of Biosciences and Pediatric Clinical Research Center "Romeo and Enrica Invernizzi", University of Milan, Milan, 20133, Italy
| | - Michel Drancourt
- Aix-Marseille Univ., IRD, MEPHI, IHU Méditerranée Infection, Marseille, France
| | - Rémi Barbieri
- Aix-Marseille Univ., IRD, MEPHI, IHU Méditerranée Infection, Marseille, France; UMR 7268, Anthropologie Bioculturelle, Droit, Ethique et Santé, Aix Marseille Univ., 11 CNRS, EFS, ADES, Marseille, France.
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Tanasi D, Cucina A, Cunsolo V, Saletti R, Di Francesco A, Greco E, Foti S. Paleoproteomic profiling of organic residues on prehistoric pottery from Malta. Amino Acids 2021; 53:295-312. [PMID: 33582869 PMCID: PMC7910365 DOI: 10.1007/s00726-021-02946-4] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/26/2020] [Accepted: 01/22/2021] [Indexed: 11/02/2022]
Abstract
Mass spectrometry-based approaches have been successfully applied for identifying ancient proteins in bones and other tissues. On the contrary, there are relatively few examples of the successful recovery and identification of archeological protein residues from ceramic artifacts; this is because ceramics contain much lower levels of proteins which are extensively degraded by diagenetic effects. In this paper, we report the results of the characterization of proteins extracted from pottery of the Maltese site of Baħrija, the guide-site for the Baħrija period (half of 9th-second half of eighth century BCE), recently identified as the final part of the Borġ in-Nadur culture. Proteomic data here reported confirm that one of the major issue of these kind of studies is represented by contamination of animal and human agents that may complicate endogenous protein identification and authentication. The samples tested included a small group of ceramic forms, namely three tableware and six coarse ware thought to have been used in food preparation and/or storage. In this context, the limited availability of paleobotanical and archeozoological analyses may be compensated by the outcomes of the first proteomics profiling which, even if obtained on a limited selection of vessels, revealed the centrality of wheat in the diet of the ancient community of Baħrija. The data have been deposited to the ProteomeXchange with identifier < PXD022848 > .
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Affiliation(s)
- Davide Tanasi
- Department of History, University of South Florida, SOC107 4202 E. Fowler Ave, Tampa, FL, 33620, USA
| | - Annamaria Cucina
- Laboratory of Organic Mass Spectrometry, Department of Chemical Sciences, University of Catania, Viale A. Doria 6, 95125, Catania, Italy
| | - Vincenzo Cunsolo
- Laboratory of Organic Mass Spectrometry, Department of Chemical Sciences, University of Catania, Viale A. Doria 6, 95125, Catania, Italy.
| | - Rosaria Saletti
- Laboratory of Organic Mass Spectrometry, Department of Chemical Sciences, University of Catania, Viale A. Doria 6, 95125, Catania, Italy
| | - Antonella Di Francesco
- Laboratory of Organic Mass Spectrometry, Department of Chemical Sciences, University of Catania, Viale A. Doria 6, 95125, Catania, Italy
| | - Enrico Greco
- Aix-Marseille Université, Institut de Chimie Radicalaire, Service 512, Avenue Escadrille Normandie Niemen, 13013, Marseille, France
| | - Salvatore Foti
- Laboratory of Organic Mass Spectrometry, Department of Chemical Sciences, University of Catania, Viale A. Doria 6, 95125, Catania, Italy
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Froment C, Zanolli C, Hourset M, Mouton-Barbosa E, Moreira A, Burlet-Schiltz O, Mollereau C. Protein sequence comparison of human and non-human primate tooth proteomes. J Proteomics 2020; 231:104045. [PMID: 33189847 DOI: 10.1016/j.jprot.2020.104045] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/18/2020] [Revised: 11/02/2020] [Accepted: 11/05/2020] [Indexed: 10/23/2022]
Abstract
In the context of human evolution, the study of proteins may overcome the limitation of the high degradation of ancient DNA over time to provide biomolecular information useful for the phylogenetic reconstruction of hominid taxa. In this study, we used a shotgun proteomics approach to compare the tooth proteomes of extant human and non-human primates (gorilla, chimpanzee, orangutan and baboon) in order to search for a panel of peptides able to discriminate between taxa and further help reconstructing the evolutionary relationships of fossil primates. Among the 25 proteins shared by the five genera datasets, we found a combination of peptides with sequence variations allowing to differentiate the hominid taxa in the proteins AHSG, AMBN, APOA1, BGN, C9, COL11A2, COL22A1, COL3A1, DSPP, F2, LUM, OMD, PCOLCE and SERPINA1. The phylogenetic tree confirms the placement of the samples in the appropriate genus branches. Altogether, the results provide experimental evidence that a shotgun proteomics approach on dental tissue has the potential to detect taxonomic variation, which is promising for future investigations of uncharacterized and/or fossil hominid/hominin specimens. SIGNIFICANCE: A shotgun proteomics approach on human and non-human primate teeth allowed to identify peptides with taxonomic interest, highlighting the potential for future studies on hominid fossils.
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Affiliation(s)
- Carine Froment
- Institut de Pharmacologie et Biologie Structurale (IPBS), Université de Toulouse, CNRS, UPS, Toulouse, France
| | - Clément Zanolli
- Laboratoire PACEA, UMR 5199 CNRS, Université de Bordeaux, Pessac, France
| | - Mathilde Hourset
- Laboratoire d'Anthropobiologie Moléculaire et Imagerie de Synthèse (AMIS), UMR 5288 CNRS, Université de Toulouse, UPS, Toulouse, France; Faculté de chirurgie dentaire de Toulouse, Université de Toulouse, UPS, Toulouse, France
| | - Emmanuelle Mouton-Barbosa
- Institut de Pharmacologie et Biologie Structurale (IPBS), Université de Toulouse, CNRS, UPS, Toulouse, France
| | - Andreia Moreira
- Laboratoire d'Anthropobiologie Moléculaire et Imagerie de Synthèse (AMIS), UMR 5288 CNRS, Université de Toulouse, UPS, Toulouse, France
| | - Odile Burlet-Schiltz
- Institut de Pharmacologie et Biologie Structurale (IPBS), Université de Toulouse, CNRS, UPS, Toulouse, France.
| | - Catherine Mollereau
- Laboratoire d'Anthropobiologie Moléculaire et Imagerie de Synthèse (AMIS), UMR 5288 CNRS, Université de Toulouse, UPS, Toulouse, France.
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Azémard C, Dufour E, Zazzo A, Wheeler JC, Goepfert N, Marie A, Zirah S. Untangling the fibre ball: Proteomic characterization of South American camelid hair fibres by untargeted multivariate analysis and molecular networking. J Proteomics 2020; 231:104040. [PMID: 33152504 DOI: 10.1016/j.jprot.2020.104040] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/25/2020] [Revised: 08/27/2020] [Accepted: 10/29/2020] [Indexed: 12/24/2022]
Abstract
The proteomic analysis of hairs, yarns or textiles has emerged as a powerful method to determine species of origin, mainly used in archaeozoological research and fraud control. Differentiation between the South American camelid (SAC) species (the wild guanaco and vicuña and their respective domesticates the llama and alpaca) is particularly challenging due to poor database information and significant hybridization between species. In this study, we analysed 41 modern and 4 archaeological samples from the four SACs species. Despite strong similarities with Old World Camelidae, we identified 7 peptides specific to SACs assigned to keratin K86 and the keratin-associated proteins KAP13-1 and KAP11-1. Untargeted multivariate analysis of the LC-MS data permitted to distinguish SAC species and propose discriminant features. MS/MS-based molecular networking combined with database-assisted de novo sequencing permitted to identify 5 new taxonomic peptides assigned to K33a, K81 and/or K83 keratins and KAP19-1. These peptides differentiate the two wild species, guanaco and vicuña. These results show the value of combining database search and untargeted metabolomic approaches for paleoproteomics, and reveal for the first time the potential of molecular networks to highlight deamidation related to diagenesis and cluster highly similar peptides related to interchain homologies or intra- or inter-specific polymorphism. SIGNIFICANCE: This study used an innovative approach combining multivariate analysis of LC-MS data together with molecular networking and database-assisted de novo sequencing to identify taxonomic peptides in palaeoproteomics. It constitutes the first attempt to differentiate between hair fibres from the four South American camelids (SACs) based on proteomic analysis of modern and archaeological samples. It provides different proteomic signatures for each of the four SAC species and proposes new SAC taxonomic peptides of interest in archaeozoology and fraud control. SACs have been extensively exploited since human colonization of South America but have not been studied to the extent of their economic, cultural and heritage importance. Applied to the analysis of ancient Andean textiles, our results should permit a better understanding of cultural and pastoral practices in South America. The wild SACs are endangered by poaching and black-market sale of their fibre. For the first time, our results provide discriminant features for the determination of species of origin of contraband fibre.
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Affiliation(s)
- Clara Azémard
- Unité Molécules de Communication et Adaptations des Microorganismes (MCAM), Muséum National d'Histoire Naturelle, CNRS, CP 54, 63 rue Buffon, 75005 Paris, France; Archéozoologie, Archéobotanique: Sociétés, Pratiques et Environnements (AASPE), Muséum National d'Histoire Naturelle, CNRS, CP 56, 55 rue Buffon, 75005 Paris, France
| | - Elise Dufour
- Archéozoologie, Archéobotanique: Sociétés, Pratiques et Environnements (AASPE), Muséum National d'Histoire Naturelle, CNRS, CP 56, 55 rue Buffon, 75005 Paris, France
| | - Antoine Zazzo
- Archéozoologie, Archéobotanique: Sociétés, Pratiques et Environnements (AASPE), Muséum National d'Histoire Naturelle, CNRS, CP 56, 55 rue Buffon, 75005 Paris, France
| | - Jane C Wheeler
- CONOPA - Instituto de Investigación y Desarrollo de Camélidos Sudamericanos, Av. Reusche M4, Pachacamac, Lima 19, Peru
| | - Nicolas Goepfert
- Archéologie des Amériques, UMR 8096, CNRS - Université Paris 1 Panthéon-Sorbonne, MSH Mondes, 21 allée de l'université, 92023 Nanterre, France
| | - Arul Marie
- Unité Molécules de Communication et Adaptations des Microorganismes (MCAM), Muséum National d'Histoire Naturelle, CNRS, CP 54, 63 rue Buffon, 75005 Paris, France
| | - Séverine Zirah
- Unité Molécules de Communication et Adaptations des Microorganismes (MCAM), Muséum National d'Histoire Naturelle, CNRS, CP 54, 63 rue Buffon, 75005 Paris, France.
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Petzold A, Lu CH, Groves M, Gobom J, Zetterberg H, Shaw G, O'Connor S. Protein aggregate formation permits millennium-old brain preservation. J R Soc Interface 2020; 17:20190775. [PMID: 31910770 DOI: 10.1098/rsif.2019.0775] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/09/2023] Open
Abstract
Human proteins have not been reported to survive in free nature, at ambient temperature, for long periods. Particularly, the human brain rapidly dissolves after death due to auto-proteolysis and putrefaction. The here presented discovery of 2600-year-old brain proteins from a radiocarbon dated human brain provides new evidence for extraordinary long-term stability of non-amyloid protein aggregates. Immunoelectron microscopy confirmed the preservation of neurocytoarchitecture in the ancient brain, which appeared shrunken and compact compared to a modern brain. Resolution of intermediate filaments (IFs) from protein aggregates took 2-12 months. Immunoassays on micro-dissected brain tissue homogenates revealed the preservation of the known protein topography for grey and white matter for type III (glial fibrillary acidic protein, GFAP) and IV (neurofilaments, Nfs) IFs. Mass spectrometry data could be matched to a number of peptide sequences, notably for GFAP and Nfs. Preserved immunogenicity of the prehistoric human brain proteins was demonstrated by antibody generation (GFAP, Nfs, myelin basic protein). Unlike brain proteins, DNA was of poor quality preventing reliable sequencing. These long-term data from a unique ancient human brain demonstrate that aggregate formation permits for the preservation of brain proteins for millennia.
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Affiliation(s)
- Axel Petzold
- Department of Neuroinflammation and National Hospital for Neurology and Neurosurgery, UCL Institute of Neurology, UCLH, Queen Square, London WC1N 3BG, UK.,Moorfields Eye Hospital, City Road, London EC1V 2PD, UK.,Department of Neurology, Neuroscience Campus Amsterdam, Amsterdam, The Netherlands.,Department of Ophthalmology, Neuroscience Campus Amsterdam, Amsterdam, The Netherlands
| | - Ching-Hua Lu
- Neurology, School of Medicine, China Medical University and Hospital, Taichung City, Taiwan.,Sobell Department of Motor Neuroscience and Movement Disorders, UCL Institute of Neurology, Queen Square, London WC1N 3BG, UK
| | - Mike Groves
- Division of Neuropathology, UCL Institute of Neurology, Queen Square, London WC1N 3BG, UK
| | - Johan Gobom
- Department of Psychiatry and Neurochemistry, Institute of Neuroscience and Physiology, The Sahlgrenska Academy at the University of Gothenburg and Clinical Neurochemistry Laboratory, Sahlgrenska University Hospital, Mölndal, Sweden
| | - Henrik Zetterberg
- Department of Psychiatry and Neurochemistry, Institute of Neuroscience and Physiology, The Sahlgrenska Academy at the University of Gothenburg and Clinical Neurochemistry Laboratory, Sahlgrenska University Hospital, Mölndal, Sweden.,UK Dementia Research Institute at UCL, London WC1E 6BT, UK.,Department of Neurodegenerative Disease, UCL Institute of Neurology, Queen Square, London WC1N 3BG, UK
| | - Gerry Shaw
- EnCor Biotechnology Inc., 4949 SW 41st Boulevard, Ste 40., Gainesville, FL 32608, USA
| | - Sonia O'Connor
- Archaeological and Forensic Sciences, University of Bradford, Richmond Road, Bradford, West Yorkshire BD7 1DP, UK
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13
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Froment C, Hourset M, Sáenz-Oyhéréguy N, Mouton-Barbosa E, Willmann C, Zanolli C, Esclassan R, Donat R, Thèves C, Burlet-Schiltz O, Mollereau C. Analysis of 5000 year-old human teeth using optimized large-scale and targeted proteomics approaches for detection of sex-specific peptides. J Proteomics 2019; 211:103548. [PMID: 31626997 DOI: 10.1016/j.jprot.2019.103548] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/24/2019] [Revised: 08/30/2019] [Accepted: 10/07/2019] [Indexed: 12/27/2022]
Abstract
The study demonstrates the high potential of MS-based proteomics coupled to an iterative database search strategy for the in-depth investigation of ancient proteomes. An efficient targeted PRM MS-based approach, although limited to the detection of a single pair of sex-specific amelogenin peptides, allowed confirming the sex of individuals in ancient dental remains, an essential information for paleoanthropologists facing the issue of sex determination and dimorphism.
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Affiliation(s)
- Carine Froment
- Institut de Pharmacologie et Biologie Structurale (IPBS), Université de Toulouse, CNRS, UPS, Toulouse, France
| | - Mathilde Hourset
- Laboratoire d'Anthropobiologie Moléculaire et Imagerie de Synthèse (AMIS), Université de Toulouse, CNRS, UPS, Toulouse, France; Faculté de chirurgie dentaire de Toulouse, Université de Toulouse, UPS, Toulouse, France
| | - Nancy Sáenz-Oyhéréguy
- Laboratoire d'Anthropobiologie Moléculaire et Imagerie de Synthèse (AMIS), Université de Toulouse, CNRS, UPS, Toulouse, France
| | - Emmanuelle Mouton-Barbosa
- Institut de Pharmacologie et Biologie Structurale (IPBS), Université de Toulouse, CNRS, UPS, Toulouse, France
| | - Claire Willmann
- Laboratoire d'Anthropobiologie Moléculaire et Imagerie de Synthèse (AMIS), Université de Toulouse, CNRS, UPS, Toulouse, France; Faculté de chirurgie dentaire de Toulouse, Université de Toulouse, UPS, Toulouse, France
| | - Clément Zanolli
- Laboratoire PACEA, UMR 5199 CNRS, Université de Bordeaux, Pessac, France
| | - Rémi Esclassan
- Laboratoire d'Anthropobiologie Moléculaire et Imagerie de Synthèse (AMIS), Université de Toulouse, CNRS, UPS, Toulouse, France; Faculté de chirurgie dentaire de Toulouse, Université de Toulouse, UPS, Toulouse, France
| | - Richard Donat
- Laboratoire d'Anthropobiologie Moléculaire et Imagerie de Synthèse (AMIS), Université de Toulouse, CNRS, UPS, Toulouse, France
| | - Catherine Thèves
- Laboratoire d'Anthropobiologie Moléculaire et Imagerie de Synthèse (AMIS), Université de Toulouse, CNRS, UPS, Toulouse, France
| | - Odile Burlet-Schiltz
- Institut de Pharmacologie et Biologie Structurale (IPBS), Université de Toulouse, CNRS, UPS, Toulouse, France.
| | - Catherine Mollereau
- Laboratoire d'Anthropobiologie Moléculaire et Imagerie de Synthèse (AMIS), Université de Toulouse, CNRS, UPS, Toulouse, France.
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14
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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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15
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Abstract
Ancient protein analysis is a rapidly developing field of research. Proteins ranging in age from the Quaternary to Jurassic are being used to answer questions about phylogeny, evolution, and extinction. However, these analyses are sometimes contentious, and focus primarily on large vertebrates in sedimentary fossilisation environments; there are few studies of protein preservation in fossils in amber. Here we show exceptionally slow racemisation rates during thermal degradation experiments of resin enclosed feathers, relative to previous thermal degradation experiments of ostrich eggshell, coral skeleton, and limpet shell. We also recover amino acids from two specimens of fossil feathers in amber. The amino acid compositions are broadly similar to those of degraded feathers, but concentrations are very low, suggesting that much of the original protein has been degraded and lost. High levels of racemisation in more apolar, slowly racemising amino acids suggest that some of the amino acids were ancient and therefore original. Our findings indicate that the unique fossilisation environment inside amber shows potential for the recovery of ancient amino acids and proteins.
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16
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Wasinger VC, Curnoe D, Bustamante S, Mendoza R, Shoocongdej R, Adler L, Baker A, Chintakanon K, Boel C, Tacon PS. Analysis of the Preserved Amino Acid Bias in Peptide Profiles of Iron Age Teeth from a Tropical Environment Enable Sexing of Individuals Using Amelogenin MRM. Proteomics 2019; 19:e1800341. [DOI: 10.1002/pmic.201800341] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/13/2018] [Revised: 01/18/2019] [Indexed: 01/22/2023]
Affiliation(s)
- Valerie C. Wasinger
- Bioanalytical Mass Spectrometry Facility Mark Wainwright Analytical Centre University of New South Wales Sydney NSW 2052 Australia
- Palaeontology, Geobiology and Earth Archives Research Centre University of New South Wales Sydney NSW 2052 Australia
| | - Darren Curnoe
- Palaeontology, Geobiology and Earth Archives Research Centre University of New South Wales Sydney NSW 2052 Australia
- ARC Centre of Excellence for Australian Biodiversity and Heritage University of New South Wales Sydney NSW 2052 Australia
| | - Sonia Bustamante
- Bioanalytical Mass Spectrometry Facility Mark Wainwright Analytical Centre University of New South Wales Sydney NSW 2052 Australia
| | - Raynold Mendoza
- Palaeontology, Geobiology and Earth Archives Research Centre University of New South Wales Sydney NSW 2052 Australia
- ARC Centre of Excellence for Australian Biodiversity and Heritage University of New South Wales Sydney NSW 2052 Australia
| | - Rasmi Shoocongdej
- Department of Archaeology Silpakorn University Bangkok 10200 Thailand
- Interaction between Prehistoric Population and Environments in Highland Pang Mapha Project Bangkok 10170 Thailand
| | - Lewis Adler
- Bioanalytical Mass Spectrometry Facility Mark Wainwright Analytical Centre University of New South Wales Sydney NSW 2052 Australia
| | - Andy Baker
- Palaeontology, Geobiology and Earth Archives Research Centre University of New South Wales Sydney NSW 2052 Australia
| | - Kanoknart Chintakanon
- Interaction between Prehistoric Population and Environments in Highland Pang Mapha Project Bangkok 10170 Thailand
- Advanced Dental Technology Center Thailand Science Park Amphoe Khlong Luang, Chang Wat Pathum Thani 12120 Thailand
| | - Ceridwen Boel
- Palaeontology, Geobiology and Earth Archives Research Centre University of New South Wales Sydney NSW 2052 Australia
- ARC Centre of Excellence for Australian Biodiversity and Heritage University of New South Wales Sydney NSW 2052 Australia
| | - Paul S.C. Tacon
- PERAHU Griffith Centre for Social and Cultural Research & School of Humanities Languages and Social Science Griffith University Gold Coast campus QLD 4222 Australia
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17
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Abstract
Ancient plant remains from archaeological sites, paleoenvironmental contexts, and herbaria provide excellent opportunities for interrogating plant genetics over Quaternary timescales using ancient DNA (aDNA)-based analyses. A variety of plant tissues, preserved primarily by desiccation and anaerobic waterlogging, have proven to be viable sources of aDNA. Plant tissues are anatomically and chemically diverse and therefore require optimized DNA extraction approaches. Here, we describe a plant DNA isolation protocol that performs well in most contexts. We include recommendations for optimization to retain the very short DNA fragments that are expected to be preserved in degraded tissues.
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Affiliation(s)
- Nathan Wales
- Department of Plant and Microbial Biology, University of California, Berkeley, CA, USA
- Laboratory of Molecular Anthropology and Image Synthesis, University Paul Sabatier, Toulouse, France
- Department of Archaeology, University of York, York, UK
| | - Logan Kistler
- Department of Anthropology, National Museum of Natural History, Smithsonian Institution, Washington, DC, USA.
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18
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Hendy J, Colonese AC, Franz I, Fernandes R, Fischer R, Orton D, Lucquin A, Spindler L, Anvari J, Stroud E, Biehl PF, Speller C, Boivin N, Mackie M, Jersie-Christensen RR, Olsen JV, Collins MJ, Craig OE, Rosenstock E. Ancient proteins from ceramic vessels at Çatalhöyük West reveal the hidden cuisine of early farmers. Nat Commun 2018; 9:4064. [PMID: 30283003 PMCID: PMC6170438 DOI: 10.1038/s41467-018-06335-6] [Citation(s) in RCA: 76] [Impact Index Per Article: 12.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/22/2018] [Accepted: 08/28/2018] [Indexed: 02/08/2023] Open
Abstract
The analysis of lipids (fats, oils and waxes) absorbed within archaeological pottery has revolutionized the study of past diets and culinary practices. However, this technique can lack taxonomic and tissue specificity and is often unable to disentangle signatures resulting from the mixing of different food products. Here, we extract ancient proteins from ceramic vessels from the West Mound of the key early farming site of Çatalhöyük in Anatolia, revealing that this community processed mixes of cereals, pulses, dairy and meat products, and that particular vessels may have been reserved for specialized foods (e.g., cow milk and milk whey). Moreover, we demonstrate that dietary proteins can persist on archaeological artefacts for at least 8000 years, and that this approach can reveal past culinary practices with more taxonomic and tissue-specific clarity than has been possible with previous biomolecular techniques.
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Affiliation(s)
- Jessica Hendy
- Department of Archaeology, Max Planck Institute for the Science of Human History, 07745, Jena, Germany. .,BioArCh, Department of Archaeology, University of York, York, YO10 5DD, UK.
| | - Andre C Colonese
- BioArCh, Department of Archaeology, University of York, York, YO10 5DD, UK
| | - Ingmar Franz
- Institute of Prehistoric and Protohistoric Archaeology, Christian-Albrechts-Universität zu Kiel, D-24098, Kiel, Germany
| | - Ricardo Fernandes
- Department of Archaeology, Max Planck Institute for the Science of Human History, 07745, Jena, Germany.,School of Archaeology, University of Oxford, Oxford, OX1 2PG, UK
| | - Roman Fischer
- Target Discovery Institute, University of Oxford, Oxford, OX3 7FZ, UK
| | - David Orton
- BioArCh, Department of Archaeology, University of York, York, YO10 5DD, UK
| | - Alexandre Lucquin
- BioArCh, Department of Archaeology, University of York, York, YO10 5DD, UK
| | - Luke Spindler
- BioArCh, Department of Archaeology, University of York, York, YO10 5DD, UK.,Oxford Radiocarbon Accelerator Unit, University of Oxford, 1 South Parks Road, Oxford, OX1 3TG, UK
| | - Jana Anvari
- Institute of Prehistoric Archaeology, Freie Universität Berlin, 14195, Berlin, Germany
| | - Elizabeth Stroud
- School of Archaeology, University of Oxford, Oxford, OX1 2PG, UK
| | - Peter F Biehl
- Department of Anthropology, University at Buffalo, Buffalo, NY, 14261-0026, USA
| | - Camilla Speller
- BioArCh, Department of Archaeology, University of York, York, YO10 5DD, UK.,Department of Anthropology, The University of British Columbia, Vancouver, BC, V6T 1Z1, Canada
| | - Nicole Boivin
- Department of Archaeology, Max Planck Institute for the Science of Human History, 07745, Jena, Germany
| | - Meaghan Mackie
- EvoGenomics, Natural History Museum of Denmark, University of Copenhagen, 2100, Copenhagen, Denmark.,Novo Nordisk Foundation Center for Protein Research, Faculty of Health and Medical Sciences, University of Copenhagen, 2200, Copenhagen, Denmark
| | - Rosa R Jersie-Christensen
- Novo Nordisk Foundation Center for Protein Research, Faculty of Health and Medical Sciences, University of Copenhagen, 2200, Copenhagen, Denmark
| | - Jesper V Olsen
- Novo Nordisk Foundation Center for Protein Research, Faculty of Health and Medical Sciences, University of Copenhagen, 2200, Copenhagen, Denmark
| | - Matthew J Collins
- BioArCh, Department of Archaeology, University of York, York, YO10 5DD, UK.,EvoGenomics, Natural History Museum of Denmark, University of Copenhagen, 2100, Copenhagen, Denmark
| | - Oliver E Craig
- BioArCh, Department of Archaeology, University of York, York, YO10 5DD, UK.
| | - Eva Rosenstock
- Institute of Prehistoric Archaeology, Freie Universität Berlin, 14195, Berlin, Germany.
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19
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Hendy J, Warinner C, Bouwman A, Collins MJ, Fiddyment S, Fischer R, Hagan R, Hofman CA, Holst M, Chaves E, Klaus L, Larson G, Mackie M, McGrath K, Mundorff AZ, Radini A, Rao H, Trachsel C, Velsko IM, Speller CF. Proteomic evidence of dietary sources in ancient dental calculus. Proc Biol Sci 2018; 285:20180977. [PMID: 30051838 PMCID: PMC6083251 DOI: 10.1098/rspb.2018.0977] [Citation(s) in RCA: 44] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/10/2018] [Accepted: 06/25/2018] [Indexed: 12/18/2022] Open
Abstract
Archaeological dental calculus has emerged as a rich source of ancient biomolecules, including proteins. Previous analyses of proteins extracted from ancient dental calculus revealed the presence of the dietary milk protein β-lactoglobulin, providing direct evidence of dairy consumption in the archaeological record. However, the potential for calculus to preserve other food-related proteins has not yet been systematically explored. Here we analyse shotgun metaproteomic data from 100 archaeological dental calculus samples ranging from the Iron Age to the post-medieval period (eighth century BC to nineteenth century AD) in England, as well as 14 dental calculus samples from contemporary dental patients and recently deceased individuals, to characterize the range and extent of dietary proteins preserved in dental calculus. In addition to milk proteins, we detect proteomic evidence of foodstuffs such as cereals and plant products, as well as the digestive enzyme salivary amylase. We discuss the importance of optimized protein extraction methods, data analysis approaches and authentication strategies in the identification of dietary proteins from archaeological dental calculus. This study demonstrates that proteomic approaches can robustly identify foodstuffs in the archaeological record that are typically under-represented due to their poor macroscopic preservation.
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Affiliation(s)
- Jessica Hendy
- Department of Archaeology, Max Planck Institute for the Science of Human History, Jena, Germany
- BioArCh, Department of Archaeology, University of York, York, UK
| | - Christina Warinner
- Department of Archaeogenetics, Max Planck Institute for the Science of Human History, Jena, Germany
- Laboratories of Molecular Anthropology and Microbiome Research, Department of Anthropology, University of Oklahoma, Norman, USA
- Institute for Evolutionary Medicine, ETH-Zürich, University of Zürich, Zürich, Switzerland
- Department of Periodontology, College of Dentistry, University of Oklahoma Health Sciences Center, Oklahoma, OK, USA
| | - Abigail Bouwman
- Institute for Evolutionary Medicine, ETH-Zürich, University of Zürich, Zürich, Switzerland
| | - Matthew J Collins
- BioArCh, Department of Archaeology, University of York, York, UK
- EvoGenomics, Natural History Museum of Denmark, University of Copenhagen, Copenhagen, Denmark
| | - Sarah Fiddyment
- BioArCh, Department of Archaeology, University of York, York, UK
| | - Roman Fischer
- Discovery Proteomics Facility, Target Discovery Institute, University of Oxford, Oxford, UK
| | - Richard Hagan
- Department of Archaeogenetics, Max Planck Institute for the Science of Human History, Jena, Germany
- Laboratories of Molecular Anthropology and Microbiome Research, Department of Anthropology, University of Oklahoma, Norman, USA
| | - Courtney A Hofman
- Laboratories of Molecular Anthropology and Microbiome Research, Department of Anthropology, University of Oklahoma, Norman, USA
| | - Malin Holst
- BioArCh, Department of Archaeology, University of York, York, UK
- York Osteoarchaeology Ltd, Bishop Wilton, York, UK
| | - Eros Chaves
- Department of Periodontology, College of Dentistry, University of Oklahoma Health Sciences Center, Oklahoma, OK, USA
- Pinellas Dental Specialties, Largo, FL 33776, USA
| | - Lauren Klaus
- Laboratories of Molecular Anthropology and Microbiome Research, Department of Anthropology, University of Oklahoma, Norman, USA
- Department of Periodontology, College of Dentistry, University of Oklahoma Health Sciences Center, Oklahoma, OK, USA
| | - Greger Larson
- The Palaeogenomics and Bio-Archaeology Research Network, Research Laboratory for Archaeology and the History of Art, University of Oxford, Oxford, UK
| | - Meaghan Mackie
- EvoGenomics, Natural History Museum of Denmark, University of Copenhagen, Copenhagen, Denmark
- Novo Nordisk Foundation Center for Protein Research, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark
| | - Krista McGrath
- BioArCh, Department of Archaeology, University of York, York, UK
| | - Amy Z Mundorff
- Department of Anthropology, College of Arts and Sciences, University of Tennessee, Knoxville, TN, USA
| | - Anita Radini
- BioArCh, Department of Archaeology, University of York, York, UK
| | - Huiyun Rao
- Key Laboratory of Vertebrate Evolution and Human Origins of Chinese Academy of Sciences, Institute of Vertebrate Paleontology and Paleoanthropology, Chinese Academy of Sciences, Beijing, People's Republic of China
| | - Christian Trachsel
- Functional Genomics Center, ETH-Zürich, University of Zürich, Zürich, Switzerland
| | - Irina M Velsko
- The Palaeogenomics and Bio-Archaeology Research Network, Research Laboratory for Archaeology and the History of Art, University of Oxford, Oxford, UK
| | - Camilla F Speller
- BioArCh, Department of Archaeology, University of York, York, UK
- Department of Anthropology, University of British Columbia, Vancouver, BC, Canada
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20
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Mason KE, Anex D, Grey T, Hart B, Parker G. Protein-based forensic identification using genetically variant peptides in human bone. Forensic Sci Int 2018; 288:89-96. [DOI: 10.1016/j.forsciint.2018.04.016] [Citation(s) in RCA: 39] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/24/2018] [Revised: 04/04/2018] [Accepted: 04/10/2018] [Indexed: 01/17/2023]
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21
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Mackie M, Rüther P, Samodova D, Di Gianvincenzo F, Granzotto C, Lyon D, Peggie DA, Howard H, Harrison L, Jensen LJ, Olsen JV, Cappellini E. Palaeoproteomic Profiling of Conservation Layers on a 14th Century Italian Wall Painting. Angew Chem Int Ed Engl 2018. [DOI: 10.1002/ange.201713020] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/07/2022]
Affiliation(s)
- Meaghan Mackie
- Natural History Museum of Denmark; University of Copenhagen; Øster Voldgade 5-7 1350 Copenhagen Denmark
- Proteomics Program, Novo Nordisk Foundation Center for Protein Research, Faculty of Health Science; University of Copenhagen; Blegdamsvej 3b 2200 Copenhagen Denmark
| | - Patrick Rüther
- Proteomics Program, Novo Nordisk Foundation Center for Protein Research, Faculty of Health Science; University of Copenhagen; Blegdamsvej 3b 2200 Copenhagen Denmark
| | - Diana Samodova
- Proteomics Program, Novo Nordisk Foundation Center for Protein Research, Faculty of Health Science; University of Copenhagen; Blegdamsvej 3b 2200 Copenhagen Denmark
| | - Fabiana Di Gianvincenzo
- Natural History Museum of Denmark; University of Copenhagen; Øster Voldgade 5-7 1350 Copenhagen Denmark
| | - Clara Granzotto
- Natural History Museum of Denmark; University of Copenhagen; Øster Voldgade 5-7 1350 Copenhagen Denmark
| | - David Lyon
- Disease Systems Biology Program, Novo Nordisk Foundation Center for Protein Research; Faculty of Health Science; University of Copenhagen; Blegdamsvej 3b 2200 Copenhagen Denmark
| | - David A. Peggie
- Scientific Department; National Gallery London; Trafalgar Square London WC2N 5DN UK
| | - Helen Howard
- Scientific Department; National Gallery London; Trafalgar Square London WC2N 5DN UK
| | - Lynne Harrison
- Conservation Department; National Gallery London; Trafalgar Square London WC2N 5DN UK
| | - Lars Juhl Jensen
- Disease Systems Biology Program, Novo Nordisk Foundation Center for Protein Research; Faculty of Health Science; University of Copenhagen; Blegdamsvej 3b 2200 Copenhagen Denmark
| | - Jesper V. Olsen
- Proteomics Program, Novo Nordisk Foundation Center for Protein Research, Faculty of Health Science; University of Copenhagen; Blegdamsvej 3b 2200 Copenhagen Denmark
| | - Enrico Cappellini
- Natural History Museum of Denmark; University of Copenhagen; Øster Voldgade 5-7 1350 Copenhagen Denmark
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22
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Mackie M, Rüther P, Samodova D, Di Gianvincenzo F, Granzotto C, Lyon D, Peggie DA, Howard H, Harrison L, Jensen LJ, Olsen JV, Cappellini E. Palaeoproteomic Profiling of Conservation Layers on a 14th Century Italian Wall Painting. Angew Chem Int Ed Engl 2018; 57:7369-7374. [PMID: 29603563 PMCID: PMC6032867 DOI: 10.1002/anie.201713020] [Citation(s) in RCA: 50] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/18/2017] [Revised: 03/08/2018] [Indexed: 01/24/2023]
Abstract
Ahead of display, a non-original layer was observed on the surface of a fragment of a wall painting by Ambrogio Lorenzetti (active 1319, died 1348/9). FTIR analysis suggested proteinaceous content. Mass spectrometry was used to better characterise this layer and revealed two protein components: sheep and cow glue and chicken and duck egg white. Analysis of post-translational modifications detected several photo-oxidation products, which suggest that the egg experienced prolonged exposure to UV light and was likely applied long before the glue layer. Additionally, glycation products detected may indicate naturally occurring glycoprotein degradation or reaction with a carbohydrate material such as starch, identified by ATR-FTIR in a cross-section of a sample taken from the painting. Palaeoproteomics is shown to provide detailed characterisation of organic layers associated with mural paintings and therefore aids reconstruction of the conservation history of these objects.
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Affiliation(s)
- Meaghan Mackie
- Natural History Museum of DenmarkUniversity of CopenhagenØster Voldgade 5–71350CopenhagenDenmark
- Proteomics Program, Novo Nordisk Foundation Center for Protein Research, Faculty of Health ScienceUniversity of CopenhagenBlegdamsvej 3b2200CopenhagenDenmark
| | - Patrick Rüther
- Proteomics Program, Novo Nordisk Foundation Center for Protein Research, Faculty of Health ScienceUniversity of CopenhagenBlegdamsvej 3b2200CopenhagenDenmark
| | - Diana Samodova
- Proteomics Program, Novo Nordisk Foundation Center for Protein Research, Faculty of Health ScienceUniversity of CopenhagenBlegdamsvej 3b2200CopenhagenDenmark
| | - Fabiana Di Gianvincenzo
- Natural History Museum of DenmarkUniversity of CopenhagenØster Voldgade 5–71350CopenhagenDenmark
| | - Clara Granzotto
- Natural History Museum of DenmarkUniversity of CopenhagenØster Voldgade 5–71350CopenhagenDenmark
| | - David Lyon
- Disease Systems Biology Program, Novo Nordisk Foundation Center for Protein ResearchFaculty of Health ScienceUniversity of CopenhagenBlegdamsvej 3b2200CopenhagenDenmark
| | - David A. Peggie
- Scientific DepartmentNational Gallery LondonTrafalgar SquareLondonWC2N 5DNUK
| | - Helen Howard
- Scientific DepartmentNational Gallery LondonTrafalgar SquareLondonWC2N 5DNUK
| | - Lynne Harrison
- Conservation DepartmentNational Gallery LondonTrafalgar SquareLondonWC2N 5DNUK
| | - Lars Juhl Jensen
- Disease Systems Biology Program, Novo Nordisk Foundation Center for Protein ResearchFaculty of Health ScienceUniversity of CopenhagenBlegdamsvej 3b2200CopenhagenDenmark
| | - Jesper V. Olsen
- Proteomics Program, Novo Nordisk Foundation Center for Protein Research, Faculty of Health ScienceUniversity of CopenhagenBlegdamsvej 3b2200CopenhagenDenmark
| | - Enrico Cappellini
- Natural History Museum of DenmarkUniversity of CopenhagenØster Voldgade 5–71350CopenhagenDenmark
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23
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Welker F. Elucidation of cross-species proteomic effects in human and hominin bone proteome identification through a bioinformatics experiment. BMC Evol Biol 2018; 18:23. [PMID: 29463217 PMCID: PMC5819086 DOI: 10.1186/s12862-018-1141-1] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/23/2017] [Accepted: 02/15/2018] [Indexed: 12/27/2022] Open
Abstract
BACKGROUND The study of ancient protein sequences is increasingly focused on the analysis of older samples, including those of ancient hominins. The analysis of such ancient proteomes thereby potentially suffers from "cross-species proteomic effects": the loss of peptide and protein identifications at increased evolutionary distances due to a larger number of protein sequence differences between the database sequence and the analyzed organism. Error-tolerant proteomic search algorithms should theoretically overcome this problem at both the peptide and protein level; however, this has not been demonstrated. If error-tolerant searches do not overcome the cross-species proteomic issue then there might be inherent biases in the identified proteomes. Here, a bioinformatics experiment is performed to test this using a set of modern human bone proteomes and three independent searches against sequence databases at increasing evolutionary distances: the human (0 Ma), chimpanzee (6-8 Ma) and orangutan (16-17 Ma) reference proteomes, respectively. RESULTS Incorrectly suggested amino acid substitutions are absent when employing adequate filtering criteria for mutable Peptide Spectrum Matches (PSMs), but roughly half of the mutable PSMs were not recovered. As a result, peptide and protein identification rates are higher in error-tolerant mode compared to non-error-tolerant searches but did not recover protein identifications completely. Data indicates that peptide length and the number of mutations between the target and database sequences are the main factors influencing mutable PSM identification. CONCLUSIONS The error-tolerant results suggest that the cross-species proteomics problem is not overcome at increasing evolutionary distances, even at the protein level. Peptide and protein loss has the potential to significantly impact divergence dating and proteome comparisons when using ancient samples as there is a bias towards the identification of conserved sequences and proteins. Effects are minimized between moderately divergent proteomes, as indicated by almost complete recovery of informative positions in the search against the chimpanzee proteome (≈90%, 6-8 Ma). This provides a bioinformatic background to future phylogenetic and proteomic analysis of ancient hominin proteomes, including the future description of novel hominin amino acid sequences, but also has negative implications for the study of fast-evolving proteins in hominins, non-hominin animals, and ancient bacterial proteins in evolutionary contexts.
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Affiliation(s)
- F Welker
- Department of Human Evolution, Max-Planck-Institute for Evolutionary Anthropology, Leipzig, Germany.
- Natural History Museum of Denmark, University of Copenhagen, Copenhagen, Denmark.
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24
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Cleland TP, Schroeter ER. A Comparison of Common Mass Spectrometry Approaches for Paleoproteomics. J Proteome Res 2018; 17:936-945. [PMID: 29384680 DOI: 10.1021/acs.jproteome.7b00703] [Citation(s) in RCA: 41] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
The last two decades have seen a broad diversity of methods used to identify and/or characterize proteins in the archeological and paleontological record. Of these, mass spectrometry has opened an unprecedented window into the proteomes of the past, providing protein sequence data from long extinct animals as well as historical and prehistorical artifacts. Thus, application of mass spectrometry to fossil remains has become an attractive source for ancient molecular sequences with which to conduct evolutionary studies, particularly in specimens older than the proposed limit of amplifiable DNA detection. However, "mass spectrometry" covers a range of mass-based proteomic approaches, each of which utilize different technology and physical principles to generate unique types of data, with their own strengths and challenges. Here, we discuss a variety of mass spectrometry techniques that have or may be used to detect and characterize archeological and paleontological proteins, with a particular focus on MALDI-MS, LC-MS/MS, TOF-SIMS, and MSi. The main differences in their functionality, the types of data they produce, and the potential effects of diagenesis on their results are considered.
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Affiliation(s)
- Timothy P Cleland
- Museum Conservation Institute, Smithsonian Institution , Suitland, Maryland 20746, United States
| | - Elena R Schroeter
- Department of Biological Sciences, North Carolina State University , Raleigh, North Carolina 27695, United States
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25
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Fox S, Strasdeit H. Inhabited or Uninhabited? Pitfalls in the Interpretation of Possible Chemical Signatures of Extraterrestrial Life. Front Microbiol 2017; 8:1622. [PMID: 28970819 PMCID: PMC5609592 DOI: 10.3389/fmicb.2017.01622] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/02/2017] [Accepted: 08/09/2017] [Indexed: 02/02/2023] Open
Abstract
The "Rare Earth" hypothesis-put forward by Ward and Brownlee in their 2000 book of the same title-states that prokaryote-type organisms may be common in the universe but animals and higher plants are exceedingly rare. If this idea is correct, the search for extraterrestrial life is essentially the search for microorganisms. Various indicators may be used to detect extant or extinct microbial life beyond Earth. Among them are chemical biosignatures, such as biomolecules and stable isotope ratios. The present minireview focuses on the major problems associated with the identification of chemical biosignatures. Two main types of misinterpretation are distinguished, namely false positive and false negative results. The former can be caused by terrestrial biogenic contaminants or by abiotic products. Terrestrial contamination is a common problem in space missions that search for biosignatures on other planets and moons. Abiotic organics can lead to false positive results if erroneously interpreted as biomolecules, but also to false negatives, for example when an abiotic source obscures a less productive biological one. In principle, all types of putative chemical biosignatures are prone to misinterpretation. Some, however, are more reliable ("stronger") than others. These include: (i) homochiral polymers of defined length and sequence, comparable to proteins and polynucleotides; (ii) enantiopure compounds; (iii) the existence of only a subset of molecules when abiotic syntheses would produce a continuous range of molecules; the proteinogenic amino acids constitute such a subset. These considerations are particularly important for life detection missions to solar system bodies such as Mars, Europa, and Enceladus.
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Affiliation(s)
- Stefan Fox
- Department of Bioinorganic Chemistry, Institute of Chemistry, University of HohenheimStuttgart, Germany
| | - Henry Strasdeit
- Department of Bioinorganic Chemistry, Institute of Chemistry, University of HohenheimStuttgart, Germany
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26
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Green EJ, Speller CF. Novel Substrates as Sources of Ancient DNA: Prospects and Hurdles. Genes (Basel) 2017; 8:E180. [PMID: 28703741 PMCID: PMC5541313 DOI: 10.3390/genes8070180] [Citation(s) in RCA: 30] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/30/2017] [Revised: 06/22/2017] [Accepted: 07/10/2017] [Indexed: 12/17/2022] Open
Abstract
Following the discovery in the late 1980s that hard tissues such as bones and teeth preserve genetic information, the field of ancient DNA analysis has typically concentrated upon these substrates. The onset of high-throughput sequencing, combined with optimized DNA recovery methods, has enabled the analysis of a myriad of ancient species and specimens worldwide, dating back to the Middle Pleistocene. Despite the growing sophistication of analytical techniques, the genetic analysis of substrates other than bone and dentine remain comparatively "novel". Here, we review analyses of other biological substrates which offer great potential for elucidating phylogenetic relationships, paleoenvironments, and microbial ecosystems including (1) archaeological artifacts and ecofacts; (2) calcified and/or mineralized biological deposits; and (3) biological and cultural archives. We conclude that there is a pressing need for more refined models of DNA preservation and bespoke tools for DNA extraction and analysis to authenticate and maximize the utility of the data obtained. With such tools in place the potential for neglected or underexploited substrates to provide a unique insight into phylogenetics, microbial evolution and evolutionary processes will be realized.
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Affiliation(s)
- Eleanor Joan Green
- BioArCh, Department of Archaeology, University of York, Wentworth Way, York YO10 5DD, UK.
| | - Camilla F Speller
- BioArCh, Department of Archaeology, University of York, Wentworth Way, York YO10 5DD, UK.
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27
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Zaucha J, Heddle JG. Resurrecting the Dead (Molecules). Comput Struct Biotechnol J 2017; 15:351-358. [PMID: 28652896 PMCID: PMC5472138 DOI: 10.1016/j.csbj.2017.05.002] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/15/2017] [Revised: 05/11/2017] [Accepted: 05/21/2017] [Indexed: 12/15/2022] Open
Abstract
Biological molecules, like organisms themselves, are subject to genetic drift and may even become "extinct". Molecules that are no longer extant in living systems are of high interest for several reasons including insight into how existing life forms evolved and the possibility that they may have new and useful properties no longer available in currently functioning molecules. Predicting the sequence/structure of such molecules and synthesizing them so that their properties can be tested is the basis of "molecular resurrection" and may lead not only to a deeper understanding of evolution, but also to the production of artificial proteins with novel properties and even to insight into how life itself began.
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Affiliation(s)
- Jan Zaucha
- Departament of Computer Science, University of Bristol, Life Sciences Building, 24 Tyndall Avenue, Bristol BS8 1TQ, United Kingdom
| | - Jonathan G. Heddle
- Bionanoscience and Biochemistry Laboratory, Jagiellonian University, Malopolska Centre of Biotechnology, Gronstajowa 7A, 30-387 Kraków, Poland
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28
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Jones J, Mirzaei M, Ravishankar P, Xavier D, Lim DS, Shin DH, Bianucci R, Haynes PA. Identification of proteins from 4200-year-old skin and muscle tissue biopsies from ancient Egyptian mummies of the first intermediate period shows evidence of acute inflammation and severe immune response. PHILOSOPHICAL TRANSACTIONS. SERIES A, MATHEMATICAL, PHYSICAL, AND ENGINEERING SCIENCES 2016; 374:rsta.2015.0373. [PMID: 27644972 PMCID: PMC5031639 DOI: 10.1098/rsta.2015.0373] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Accepted: 06/28/2016] [Indexed: 05/18/2023]
Abstract
We performed proteomics analysis on four skin and one muscle tissue samples taken from three ancient Egyptian mummies of the first intermediate period, approximately 4200 years old. The mummies were first dated by radiocarbon dating of the accompany-\break ing textiles, and morphologically examined by scanning electron microscopy of additional skin samples. Proteins were extracted, separated on SDS-PAGE (sodium dodecyl sulfate polyacrylamide gel electrophoresis) gels, and in-gel digested with trypsin. The resulting peptides were analysed using nanoflow high-performance liquid chromatography-mass spectrometry. We identified a total of 230 unique proteins from the five samples, which consisted of 132 unique protein identifications. We found a large number of collagens, which was confirmed by our microscopy data, and is in agreement with previous studies showing that collagens are very long-lived. As expected, we also found a large number of keratins. We identified numerous proteins that provide evidence of activation of the innate immunity system in two of the mummies, one of which also contained proteins indicating severe tissue inflammation, possibly indicative of an infection that we can speculate may have been related to the cause of death.This article is part of the themed issue 'Quantitative mass spectrometry'.
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Affiliation(s)
- Jana Jones
- Department of Ancient History, Macquarie University, North Ryde, NSW 2109, Australia
| | - Mehdi Mirzaei
- Department of Chemistry and Biomolecular Sciences, Macquarie University, North Ryde, NSW 2109, Australia
| | - Prathiba Ravishankar
- Department of Chemistry and Biomolecular Sciences, Macquarie University, North Ryde, NSW 2109, Australia
| | - Dylan Xavier
- Australian Proteome Analysis Facility, Macquarie University, North Ryde, NSW 2109, Australia
| | - Do Seon Lim
- Department of Dental Hygiene, College of Health Sciences, Eulji University, Sungnam, South Korea
| | - Dong Hoon Shin
- Department of Anatomy, Seoul National University, College of Medicine, Seoul, South Korea
| | - Raffaella Bianucci
- Department of Public Health and Paediatric Sciences, Legal Medicine Section, University of Turin, 10126 Turin, Italy UMR 7268, Laboratoire d'Anthropologie bio-culturelle, Droit, Étique and Santé (ADÉS), Faculté de Médecine de Marseille, 13344 Marseille, France
| | - Paul A Haynes
- Department of Chemistry and Biomolecular Sciences, Macquarie University, North Ryde, NSW 2109, Australia
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29
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Demarchi B, Hall S, Roncal-Herrero T, Freeman CL, Woolley J, Crisp MK, Wilson J, Fotakis A, Fischer R, Kessler BM, Rakownikow Jersie-Christensen R, Olsen JV, Haile J, Thomas J, Marean CW, Parkington J, Presslee S, Lee-Thorp J, Ditchfield P, Hamilton JF, Ward MW, Wang CM, Shaw MD, Harrison T, Domínguez-Rodrigo M, MacPhee RDE, Kwekason A, Ecker M, Kolska Horwitz L, Chazan M, Kröger R, Thomas-Oates J, Harding JH, Cappellini E, Penkman K, Collins MJ. Protein sequences bound to mineral surfaces persist into deep time. eLife 2016; 5. [PMID: 27668515 PMCID: PMC5039028 DOI: 10.7554/elife.17092] [Citation(s) in RCA: 101] [Impact Index Per Article: 12.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/21/2016] [Accepted: 08/17/2016] [Indexed: 12/14/2022] Open
Abstract
Proteins persist longer in the fossil record than DNA, but the longevity, survival mechanisms and substrates remain contested. Here, we demonstrate the role of mineral binding in preserving the protein sequence in ostrich (Struthionidae) eggshell, including from the palaeontological sites of Laetoli (3.8 Ma) and Olduvai Gorge (1.3 Ma) in Tanzania. By tracking protein diagenesis back in time we find consistent patterns of preservation, demonstrating authenticity of the surviving sequences. Molecular dynamics simulations of struthiocalcin-1 and -2, the dominant proteins within the eggshell, reveal that distinct domains bind to the mineral surface. It is the domain with the strongest calculated binding energy to the calcite surface that is selectively preserved. Thermal age calculations demonstrate that the Laetoli and Olduvai peptides are 50 times older than any previously authenticated sequence (equivalent to ~16 Ma at a constant 10°C). DOI:http://dx.doi.org/10.7554/eLife.17092.001 The pattern of chemical reactions that break down the molecules that make our bodies is still fairly mysterious. Archaeologists and geologists hope that dead organisms (or artefacts made from them) might not decay entirely, leaving behind clues to their lives. We know that some molecules are more resistant than others; for example, fats are tough and survive for a long time while DNA is degraded very rapidly. Proteins, which are made of chains of smaller molecules called amino acids, are usually sturdier than DNA. Since the amino acid sequence of a protein reflects the DNA sequence that encodes it, proteins in fossils can help researchers to reconstruct how extinct organisms are related in cases where DNA cannot be retrieved. Time, temperature, burial environment and the chemistry of the fossil all influence how quickly a protein decays. However, it is not clear what mechanisms slow down decay so that full protein sequences can be preserved and identified after millions of years. As a result, it is difficult to know where to look for these ancient sequences. In the womb of ostriches, several proteins are responsible for assembling the minerals that make up the ostrich eggshell. These proteins become trapped tightly within the mineral crystals themselves. In this situation, proteins can potentially be preserved over geological time. Demarchi et al. have now studied 3.8 million-year-old eggshells found close to the equator and, despite the extent to which the samples have degraded, discovered fully preserved protein sequences. Using a computer simulation method called molecular dynamics, Demarchi et al. calculated that the protein sequences that are able to survive the longest are stabilized by strong binding to the surface of the mineral crystals. The authenticity of these sequences was tested thoroughly using a combination of several approaches that Demarchi et al. recommend using as a standard for ancient protein studies. Overall, it appears that biominerals are an excellent source of ancient protein sequences because mineral binding ensures survival. A systematic survey of fossil biominerals from different environments is now needed to assess whether these biomolecules have the potential to act as barcodes for interpreting the evolution of organisms. DOI:http://dx.doi.org/10.7554/eLife.17092.002
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Affiliation(s)
- Beatrice Demarchi
- BioArCh, Department of Archaeology, University of York, York, United Kingdom
| | - Shaun Hall
- Department of Material Science and Engineering, University of Sheffield, Sheffield, United Kingdom
| | | | - Colin L Freeman
- Department of Material Science and Engineering, University of Sheffield, Sheffield, United Kingdom
| | - Jos Woolley
- BioArCh, Department of Archaeology, University of York, York, United Kingdom
| | - Molly K Crisp
- Department of Chemistry, University of York, York, United Kingdom
| | - Julie Wilson
- Department of Chemistry, University of York, York, United Kingdom.,Department of Mathematics, University of York, York, United Kingdom
| | - Anna Fotakis
- Centre for GeoGenetics, Natural History Museum of Denmark, University of Copenhagen, Copenhagen, Denmark
| | - Roman Fischer
- Advanced Proteomics Facility, Target Discovery Institute, Nuffield Department of Medicine, University of Oxford, Oxford, United Kingdom
| | - Benedikt M Kessler
- Advanced Proteomics Facility, Target Discovery Institute, Nuffield Department of Medicine, University of Oxford, Oxford, United Kingdom
| | | | - Jesper V Olsen
- Novo Nordisk Foundation Center for Protein Research, Faculty of Health Sciences, University of Copenhagen, Copenhagen, Denmark
| | - James Haile
- Research Laboratory for Archaeology and the History of Art, University of Oxford, Oxford, United Kingdom
| | - Jessica Thomas
- Centre for GeoGenetics, Natural History Museum of Denmark, University of Copenhagen, Copenhagen, Denmark.,Molecular Ecology and Fisheries Genetics Laboratory, School of Biological Sciences, Bangor University, Bangor, United Kingdom
| | - Curtis W Marean
- Institute of Human Origins, SHESC, Arizona State University, Tempe, United States.,Centre for Coastal Palaeoscience, Nelson Mandela Metropolitan University, Port Elizabeth, South Africa
| | - John Parkington
- Department of Archaeology, University of Cape Town, Cape Town, South Africa
| | - Samantha Presslee
- BioArCh, Department of Archaeology, University of York, York, United Kingdom
| | - Julia Lee-Thorp
- Research Laboratory for Archaeology and the History of Art, University of Oxford, Oxford, United Kingdom
| | - Peter Ditchfield
- Research Laboratory for Archaeology and the History of Art, University of Oxford, Oxford, United Kingdom
| | - Jacqueline F Hamilton
- Wolfson Atmospheric Chemistry Laboratories, Department of Chemistry, University of York, York, United Kingdom
| | - Martyn W Ward
- Wolfson Atmospheric Chemistry Laboratories, Department of Chemistry, University of York, York, United Kingdom
| | - Chunting Michelle Wang
- Wolfson Atmospheric Chemistry Laboratories, Department of Chemistry, University of York, York, United Kingdom
| | - Marvin D Shaw
- Wolfson Atmospheric Chemistry Laboratories, Department of Chemistry, University of York, York, United Kingdom
| | - Terry Harrison
- Center for the Study of Human Origins, Department of Anthropology, New York University, New York, United States
| | | | - Ross DE MacPhee
- Department of Mammalogy, American Museum of Natural History, New York, United States
| | | | - Michaela Ecker
- Research Laboratory for Archaeology and the History of Art, University of Oxford, Oxford, United Kingdom
| | - Liora Kolska Horwitz
- National Natural History Collections, Faculty of Life Sciences, The Hebrew University, Jerusalem, Israel
| | - Michael Chazan
- Department of Anthropology, University of Toronto, Toronto, Canada.,Evolutionary Studies Institute, University of the Witwatersrand, Braamfontein, South Africa
| | - Roland Kröger
- Department of Physics, University of York, York, United Kingdom
| | - Jane Thomas-Oates
- Department of Chemistry, University of York, York, United Kingdom.,Centre of Excellence in Mass Spectrometry, University of York, New York, United States
| | - John H Harding
- Department of Material Science and Engineering, University of Sheffield, Sheffield, United Kingdom
| | - Enrico Cappellini
- Centre for GeoGenetics, Natural History Museum of Denmark, University of Copenhagen, Copenhagen, Denmark
| | - Kirsty Penkman
- Department of Chemistry, University of York, York, United Kingdom
| | - Matthew J Collins
- BioArCh, Department of Archaeology, University of York, York, United Kingdom
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30
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Cleland TP, Schroeter ER, Schweitzer MH. Biologically and diagenetically derived peptide modifications in moa collagens. Proc Biol Sci 2016; 282:20150015. [PMID: 25972464 DOI: 10.1098/rspb.2015.0015] [Citation(s) in RCA: 59] [Impact Index Per Article: 7.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
Abstract
The modifications that occur on proteins in natural environments over time are not well studied, yet characterizing them is vital to correctly interpret sequence data recovered from fossils. The recently extinct moa (Dinornithidae) is an excellent candidate for investigating the preservation of proteins, their post-translational modifications (PTMs) and diagenetic alterations during degradation. Moa protein extracts were analysed using mass spectrometry, and peptides from collagen I, collagen II and collagen V were identified. We also identified biologically derived PTMs (i.e. methylation, di-methylation, alkylation, hydroxylation, fucosylation) on amino acids at locations consistent with extant proteins. In addition to these in vivo modifications, we detected novel modifications that are probably diagenetically derived. These include loss of hydroxylation/glutamic semialdehyde, carboxymethyllysine and peptide backbone cleavage, as well as previously noted deamidation. Moa collagen sequences and modifications provide a baseline by which to evaluate proteomic studies of other fossils, and a framework for defining the molecular relationship of moa to other closely related taxa.
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Affiliation(s)
- Timothy P Cleland
- Department of Biomedical Engineering, Rensselaer Polytechnic Institute, Troy, NY 12182, USA
| | - Elena R Schroeter
- Department of Biological Sciences, North Carolina State University, Raleigh, NC 27695, USA
| | - Mary H Schweitzer
- Department of Biological Sciences, North Carolina State University, Raleigh, NC 27695, USA North Carolina Museum of Natural Sciences, Raleigh, NC 27601, USA
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31
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Dallongeville S, Garnier N, Rolando C, Tokarski C. Proteins in Art, Archaeology, and Paleontology: From Detection to Identification. Chem Rev 2015; 116:2-79. [PMID: 26709533 DOI: 10.1021/acs.chemrev.5b00037] [Citation(s) in RCA: 80] [Impact Index Per Article: 8.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
Affiliation(s)
- Sophie Dallongeville
- Miniaturisation pour la Synthèse, l'Analyse & la Protéomique (MSAP), USR CNRS 3290, Université de Lille 1 Sciences et Technologies , 59655 Villeneuve d'Ascq Cedex, France
| | - Nicolas Garnier
- SARL Laboratoire Nicolas Garnier , 63270 Vic le Comte, France
| | - Christian Rolando
- Miniaturisation pour la Synthèse, l'Analyse & la Protéomique (MSAP), USR CNRS 3290, Université de Lille 1 Sciences et Technologies , 59655 Villeneuve d'Ascq Cedex, France
| | - Caroline Tokarski
- Miniaturisation pour la Synthèse, l'Analyse & la Protéomique (MSAP), USR CNRS 3290, Université de Lille 1 Sciences et Technologies , 59655 Villeneuve d'Ascq Cedex, France
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32
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Campbell K, Hofreiter M. Resurrecting phenotypes from ancient DNA sequences: promises and perspectives. CAN J ZOOL 2015. [DOI: 10.1139/cjz-2014-0337] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Abstract
Anatomical changes in extinct mammalian lineages over evolutionary time, such as the loss of fingers and teeth and the rapid increase in body size that accompanied the late Miocene dispersal of the progenitors of Steller’s sea cows (Hydrodamalis gigas (Zimmermann, 1780)) into North Pacific waters and the convergent development of a thick pelage and accompanying reductions in ear and tail surface area of woolly mammoths (Mammuthus primigenius (Blumenbach, 1799)) and woolly rhinoceros (Coelodonta antiquitatis (Blumenbach, 1799)), are prime examples of adaptive evolution underlying the exploitation of new habitats. It is likely, however, that biochemical specializations adopted during these evolutionary transitions were of similar or even greater biological importance. As these “living” processes do not fossilize, direct information regarding the physiological attributes of extinct species has largely remained beyond the range of scientific inquiry. However, the ability to retrieve genomic sequences from ancient DNA samples, combined with ectopic expression systems, now permit the evolutionary origins and structural and functional properties of authentic prehistoric proteins to be examined in great detail. Exponential technical advances in ancient DNA retrieval, enrichment, and sequencing will soon permit targeted generation of complete genomes from hundreds of extinct species across the last one million years that, in combination with emerging in vitro expression, genome engineering, and cell differentiation techniques, promises to herald an exciting new trajectory of evolutionary research at the interface of biochemistry, genomics, palaeontology, and cell biology.
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Affiliation(s)
- K.L. Campbell
- Department of Biological Sciences, University of Manitoba, Winnipeg, MB R3T 2N2, Canada
| | - M. Hofreiter
- Faculty of Mathematics and Life Sciences, Institute of Biochemistry and Biology, Unit of General Zoology–Evolutionary Adaptive Genomics, University of Potsdam, Karl-Liebknecht-Straße 24-25, 14476 Potsdam, Germany
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33
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Orlando L, Gilbert MTP, Willerslev E. Reconstructing ancient genomes and epigenomes. Nat Rev Genet 2015; 16:395-408. [PMID: 26055157 DOI: 10.1038/nrg3935] [Citation(s) in RCA: 113] [Impact Index Per Article: 12.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Abstract
Research involving ancient DNA (aDNA) has experienced a true technological revolution in recent years through advances in the recovery of aDNA and, particularly, through applications of high-throughput sequencing. Formerly restricted to the analysis of only limited amounts of genetic information, aDNA studies have now progressed to whole-genome sequencing for an increasing number of ancient individuals and extinct species, as well as to epigenomic characterization. Such advances have enabled the sequencing of specimens of up to 1 million years old, which, owing to their extensive DNA damage and contamination, were previously not amenable to genetic analyses. In this Review, we discuss these varied technical challenges and solutions for sequencing ancient genomes and epigenomes.
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Affiliation(s)
- Ludovic Orlando
- 1] Centre for GeoGenetics, Natural History Museum of Denmark, University of Copenhagen, Øster Voldgade 5-7, Copenhagen 1350C, Denmark. [2] Université de Toulouse, University Paul Sabatier (UPS), Laboratoire AMIS, CNRS UMR 5288, 37 allées Jules Guesde, 31000 Toulouse, France
| | - M Thomas P Gilbert
- 1] Centre for GeoGenetics, Natural History Museum of Denmark, University of Copenhagen, Øster Voldgade 5-7, Copenhagen 1350C, Denmark. [2] Trace and Environmental DNA Laboratory, Department of Environment and Agriculture, Curtin University, Perth, Western Australia 6102, Australia
| | - Eske Willerslev
- Centre for GeoGenetics, Natural History Museum of Denmark, University of Copenhagen, Øster Voldgade 5-7, Copenhagen 1350C, Denmark
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34
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Appels R, Nystrom J, Webster H, Keeble-Gagnere G. Discoveries and advances in plant and animal genomics. Funct Integr Genomics 2015; 15:121-9. [PMID: 25763751 PMCID: PMC4361718 DOI: 10.1007/s10142-015-0434-3] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/12/2015] [Revised: 02/17/2015] [Accepted: 02/19/2015] [Indexed: 12/04/2022]
Abstract
Plant and animal genomics is a broad area of research with respect to the biological issues covered because it continues to deal with the structure and function of genetic material underpinning all organisms. This mini-review utilizes the plenary lectures from the Plant and Animal Genome Conference as a basis for summarizing the trends in the genome-level studies of organisms.
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Affiliation(s)
- Rudi Appels
- School of Veterinary and Life Sciences, Murdoch University, 90 South Street, Murdoch, Perth, Australia, 6150,
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35
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Warinner C, Speller C, Collins MJ. A new era in palaeomicrobiology: prospects for ancient dental calculus as a long-term record of the human oral microbiome. Philos Trans R Soc Lond B Biol Sci 2015; 370:20130376. [PMID: 25487328 PMCID: PMC4275884 DOI: 10.1098/rstb.2013.0376] [Citation(s) in RCA: 110] [Impact Index Per Article: 12.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022] Open
Abstract
The field of palaeomicrobiology is dramatically expanding thanks to recent advances in high-throughput biomolecular sequencing, which allows unprecedented access to the evolutionary history and ecology of human-associated and environmental microbes. Recently, human dental calculus has been shown to be an abundant, nearly ubiquitous, and long-term reservoir of the ancient oral microbiome, preserving not only microbial and host biomolecules but also dietary and environmental debris. Modern investigations of native human microbiota have demonstrated that the human microbiome plays a central role in health and chronic disease, raising questions about changes in microbial ecology, diversity and function through time. This paper explores the current state of ancient oral microbiome research and discusses successful applications, methodological challenges and future possibilities in elucidating the intimate evolutionary relationship between humans and their microbes.
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36
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Der Sarkissian C, Allentoft ME, Ávila-Arcos MC, Barnett R, Campos PF, Cappellini E, Ermini L, Fernández R, da Fonseca R, Ginolhac A, Hansen AJ, Jónsson H, Korneliussen T, Margaryan A, Martin MD, Moreno-Mayar JV, Raghavan M, Rasmussen M, Velasco MS, Schroeder H, Schubert M, Seguin-Orlando A, Wales N, Gilbert MTP, Willerslev E, Orlando L. Ancient genomics. Philos Trans R Soc Lond B Biol Sci 2015; 370:20130387. [PMID: 25487338 PMCID: PMC4275894 DOI: 10.1098/rstb.2013.0387] [Citation(s) in RCA: 58] [Impact Index Per Article: 6.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
Abstract
The past decade has witnessed a revolution in ancient DNA (aDNA) research. Although the field's focus was previously limited to mitochondrial DNA and a few nuclear markers, whole genome sequences from the deep past can now be retrieved. This breakthrough is tightly connected to the massive sequence throughput of next generation sequencing platforms and the ability to target short and degraded DNA molecules. Many ancient specimens previously unsuitable for DNA analyses because of extensive degradation can now successfully be used as source materials. Additionally, the analytical power obtained by increasing the number of sequence reads to billions effectively means that contamination issues that have haunted aDNA research for decades, particularly in human studies, can now be efficiently and confidently quantified. At present, whole genomes have been sequenced from ancient anatomically modern humans, archaic hominins, ancient pathogens and megafaunal species. Those have revealed important functional and phenotypic information, as well as unexpected adaptation, migration and admixture patterns. As such, the field of aDNA has entered the new era of genomics and has provided valuable information when testing specific hypotheses related to the past.
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Affiliation(s)
- Clio Der Sarkissian
- Centre for GeoGenetics, Natural History Museum of Denmark, University of Copenhagen, Copenhagen, Denmark
| | - Morten E Allentoft
- Centre for GeoGenetics, Natural History Museum of Denmark, University of Copenhagen, Copenhagen, Denmark
| | - María C Ávila-Arcos
- Centre for GeoGenetics, Natural History Museum of Denmark, University of Copenhagen, Copenhagen, Denmark
| | - Ross Barnett
- Centre for GeoGenetics, Natural History Museum of Denmark, University of Copenhagen, Copenhagen, Denmark
| | - Paula F Campos
- Centre for GeoGenetics, Natural History Museum of Denmark, University of Copenhagen, Copenhagen, Denmark
| | - Enrico Cappellini
- Centre for GeoGenetics, Natural History Museum of Denmark, University of Copenhagen, Copenhagen, Denmark
| | - Luca Ermini
- Centre for GeoGenetics, Natural History Museum of Denmark, University of Copenhagen, Copenhagen, Denmark
| | - Ruth Fernández
- Centre for GeoGenetics, Natural History Museum of Denmark, University of Copenhagen, Copenhagen, Denmark
| | - Rute da Fonseca
- Centre for GeoGenetics, Natural History Museum of Denmark, University of Copenhagen, Copenhagen, Denmark
| | - Aurélien Ginolhac
- Centre for GeoGenetics, Natural History Museum of Denmark, University of Copenhagen, Copenhagen, Denmark
| | - Anders J Hansen
- Centre for GeoGenetics, Natural History Museum of Denmark, University of Copenhagen, Copenhagen, Denmark
| | - Hákon Jónsson
- Centre for GeoGenetics, Natural History Museum of Denmark, University of Copenhagen, Copenhagen, Denmark
| | - Thorfinn Korneliussen
- Centre for GeoGenetics, Natural History Museum of Denmark, University of Copenhagen, Copenhagen, Denmark
| | - Ashot Margaryan
- Centre for GeoGenetics, Natural History Museum of Denmark, University of Copenhagen, Copenhagen, Denmark
| | - Michael D Martin
- Centre for GeoGenetics, Natural History Museum of Denmark, University of Copenhagen, Copenhagen, Denmark
| | - J Víctor Moreno-Mayar
- Centre for GeoGenetics, Natural History Museum of Denmark, University of Copenhagen, Copenhagen, Denmark
| | - Maanasa Raghavan
- Centre for GeoGenetics, Natural History Museum of Denmark, University of Copenhagen, Copenhagen, Denmark
| | - Morten Rasmussen
- Centre for GeoGenetics, Natural History Museum of Denmark, University of Copenhagen, Copenhagen, Denmark
| | - Marcela Sandoval Velasco
- Centre for GeoGenetics, Natural History Museum of Denmark, University of Copenhagen, Copenhagen, Denmark
| | - Hannes Schroeder
- Centre for GeoGenetics, Natural History Museum of Denmark, University of Copenhagen, Copenhagen, Denmark
| | - Mikkel Schubert
- Centre for GeoGenetics, Natural History Museum of Denmark, University of Copenhagen, Copenhagen, Denmark
| | - Andaine Seguin-Orlando
- Centre for GeoGenetics, Natural History Museum of Denmark, University of Copenhagen, Copenhagen, Denmark
| | - Nathan Wales
- Centre for GeoGenetics, Natural History Museum of Denmark, University of Copenhagen, Copenhagen, Denmark
| | - M Thomas P Gilbert
- Centre for GeoGenetics, Natural History Museum of Denmark, University of Copenhagen, Copenhagen, Denmark
| | - Eske Willerslev
- Centre for GeoGenetics, Natural History Museum of Denmark, University of Copenhagen, Copenhagen, Denmark
| | - Ludovic Orlando
- Centre for GeoGenetics, Natural History Museum of Denmark, University of Copenhagen, Copenhagen, Denmark
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De Baets K, Littlewood DTJ. The Importance of Fossils in Understanding the Evolution of Parasites and Their Vectors. ADVANCES IN PARASITOLOGY 2015; 90:1-51. [PMID: 26597064 DOI: 10.1016/bs.apar.2015.07.001] [Citation(s) in RCA: 45] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/26/2022]
Abstract
Knowledge concerning the diversity of parasitism and its reach across our current understanding of the tree of life has benefitted considerably from novel molecular phylogenetic methods. However, the timing of events and the resolution of the nature of the intimate relationships between parasites and their hosts in deep time remain problematic. Despite its vagaries, the fossil record provides the only direct evidence of parasites and parasitism in the fossil record of extant and extinct lineages. Here, we demonstrate the potential of the fossil record and other lines of geological evidence to calibrate the origin and evolution of parasitism by combining different kinds of dating evidence with novel molecular clock methodologies. Other novel methods promise to provide additional evidence for the presence or the life habit of pathogens and their vectors, including the discovery and analysis of ancient DNA and other biomolecules, as well as computed tomographic methods.
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Major transitions in human evolution revisited: a tribute to ancient DNA. J Hum Evol 2014; 79:4-20. [PMID: 25532800 DOI: 10.1016/j.jhevol.2014.06.015] [Citation(s) in RCA: 32] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/14/2014] [Revised: 06/06/2014] [Accepted: 06/19/2014] [Indexed: 11/23/2022]
Abstract
The origin and diversification of modern humans have been characterized by major evolutionary transitions and demographic changes. Patterns of genetic variation within modern populations can help with reconstructing this ∼200 thousand year-long population history. However, by combining this information with genomic data from ancient remains, one can now directly access our evolutionary past and reveal our population history in much greater detail. This review outlines the main recent achievements in ancient DNA research and illustrates how the field recently moved from the polymerase chain reaction (PCR) amplification of short mitochondrial fragments to whole-genome sequencing and thereby revisited our own history. Ancient DNA research has revealed the routes that our ancestors took when colonizing the planet, whom they admixed with, how they domesticated plant and animal species, how they genetically responded to changes in lifestyle, and also, which pathogens decimated their populations. These approaches promise to soon solve many pending controversies about our own origins that are indecipherable from modern patterns of genetic variation alone, and therefore provide an extremely powerful toolkit for a new generation of molecular anthropologists.
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