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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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Hill RC, Wither MJ, Nemkov T, Barrett A, D'Alessandro A, Dzieciatkowska M, Hansen KC. Preserved Proteins from Extinct Bison latifrons Identified by Tandem Mass Spectrometry; Hydroxylysine Glycosides are a Common Feature of Ancient Collagen. Mol Cell Proteomics 2015; 14:1946-58. [PMID: 25948757 DOI: 10.1074/mcp.m114.047787] [Citation(s) in RCA: 66] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/22/2014] [Indexed: 11/06/2022] Open
Abstract
Bone samples from several vertebrates were collected from the Ziegler Reservoir fossil site, in Snowmass Village, Colorado, and processed for proteomics analysis. The specimens come from Pleistocene megafauna Bison latifrons, dating back ∼ 120,000 years. Proteomics analysis using a simplified sample preparation procedure and tandem mass spectrometry (MS/MS) was applied to obtain protein identifications. Several bioinformatics resources were used to obtain peptide identifications based on sequence homology to extant species with annotated genomes. With the exception of soil sample controls, all samples resulted in confident peptide identifications that mapped to type I collagen. In addition, we analyzed a specimen from the extinct B. latifrons that yielded peptide identifications mapping to over 33 bovine proteins. Our analysis resulted in extensive fibrillar collagen sequence coverage, including the identification of posttranslational modifications. Hydroxylysine glucosylgalactosylation, a modification thought to be involved in collagen fiber formation and bone mineralization, was identified for the first time in an ancient protein dataset. Meta-analysis of data from other studies indicates that this modification may be common in well-preserved prehistoric samples. Additional peptide sequences from extracellular matrix (ECM) and non-ECM proteins have also been identified for the first time in ancient tissue samples. These data provide a framework for analyzing ancient protein signatures in well-preserved fossil specimens, while also contributing novel insights into the molecular basis of organic matter preservation. As such, this analysis has unearthed common posttranslational modifications of collagen that may assist in its preservation over time. The data are available via ProteomeXchange with identifier PXD001827.
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Affiliation(s)
- Ryan C Hill
- From the ‡Department of Biochemistry and Molecular Genetics, University of Colorado Denver, Aurora, Colorado 80045, USA
| | - Matthew J Wither
- From the ‡Department of Biochemistry and Molecular Genetics, University of Colorado Denver, Aurora, Colorado 80045, USA
| | - Travis Nemkov
- From the ‡Department of Biochemistry and Molecular Genetics, University of Colorado Denver, Aurora, Colorado 80045, USA
| | - Alexander Barrett
- From the ‡Department of Biochemistry and Molecular Genetics, University of Colorado Denver, Aurora, Colorado 80045, USA
| | - Angelo D'Alessandro
- From the ‡Department of Biochemistry and Molecular Genetics, University of Colorado Denver, Aurora, Colorado 80045, USA
| | - Monika Dzieciatkowska
- From the ‡Department of Biochemistry and Molecular Genetics, University of Colorado Denver, Aurora, Colorado 80045, USA
| | - Kirk C Hansen
- From the ‡Department of Biochemistry and Molecular Genetics, University of Colorado Denver, Aurora, Colorado 80045, USA
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Poulakakis N, Kapli P, Lymberakis P, Trichas A, Vardinoyiannis K, Sfenthourakis S, Mylonas M. A review of phylogeographic analyses of animal taxa from the Aegean and surrounding regions. J ZOOL SYST EVOL RES 2014. [DOI: 10.1111/jzs.12071] [Citation(s) in RCA: 76] [Impact Index Per Article: 7.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Affiliation(s)
- Nikos Poulakakis
- Natural History Museum of Crete; University of Crete; Iraklion Greece
- Biology Department; University of Crete; Iraklion Greece
| | - Paschalia Kapli
- Natural History Museum of Crete; University of Crete; Iraklion Greece
- Biology Department; University of Crete; Iraklion Greece
| | - Petros Lymberakis
- Natural History Museum of Crete; University of Crete; Iraklion Greece
| | - Apostolos Trichas
- Natural History Museum of Crete; University of Crete; Iraklion Greece
| | | | | | - Moisis Mylonas
- Natural History Museum of Crete; University of Crete; Iraklion Greece
- Biology Department; University of Crete; Iraklion Greece
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Gold DA, Robinson J, Farrell AB, Harris JM, Thalmann O, Jacobs DK. Attempted DNA extraction from a Rancho La Brea Columbian mammoth (Mammuthus columbi): prospects for ancient DNA from asphalt deposits. Ecol Evol 2014; 4:329-36. [PMID: 24634719 PMCID: PMC3936381 DOI: 10.1002/ece3.928] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/27/2013] [Accepted: 12/01/2013] [Indexed: 11/30/2022] Open
Abstract
Fossil-bearing asphalt deposits are an understudied and potentially significant source of ancient DNA. Previous attempts to extract DNA from skeletons preserved at the Rancho La Brea tar pits in Los Angeles, California, have proven unsuccessful, but it is unclear whether this is due to a lack of endogenous DNA, or if the problem is caused by asphalt-mediated inhibition. In an attempt to test these hypotheses, a recently recovered Columbian mammoth (Mammuthus columbi) skeleton with an unusual pattern of asphalt impregnation was studied. Ultimately, none of the bone samples tested successfully amplified M. columbi DNA. Our work suggests that reagents typically used to remove asphalt from ancient samples also inhibit DNA extraction. Ultimately, we conclude that the probability of recovering ancient DNA from fossils in asphalt deposits is strongly (perhaps fatally) hindered by the organic compounds that permeate the bones and that at the Rancho La Brea tar pits, environmental conditions might not have been ideal for the general preservation of genetic material.
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Affiliation(s)
- David A Gold
- Department of Ecology and Evolutionary Biology, University of California Los Angeles, California 90095
| | - Jacqueline Robinson
- Department of Ecology and Evolutionary Biology, University of California Los Angeles, California 90095
| | - Aisling B Farrell
- The George C. Page Museum of La Brea Discoveries 5801 Wilshire Boulevard, Los Angeles, California 90036
| | - John M Harris
- The George C. Page Museum of La Brea Discoveries 5801 Wilshire Boulevard, Los Angeles, California 90036
| | - Olaf Thalmann
- Department of Biology, Division of Genetics and Physiology, University of Turku Itäinen Pitkäkatu 4, Turku 20014, Finland
| | - David K Jacobs
- Department of Ecology and Evolutionary Biology, University of California Los Angeles, California 90095
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Allentoft ME, Collins M, Harker D, Haile J, Oskam CL, Hale ML, Campos PF, Samaniego JA, Gilbert MTP, Willerslev E, Zhang G, Scofield RP, Holdaway RN, Bunce M. The half-life of DNA in bone: measuring decay kinetics in 158 dated fossils. Proc Biol Sci 2012; 279:4724-33. [PMID: 23055061 PMCID: PMC3497090 DOI: 10.1098/rspb.2012.1745] [Citation(s) in RCA: 274] [Impact Index Per Article: 22.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/26/2012] [Accepted: 09/14/2012] [Indexed: 12/26/2022] Open
Abstract
Claims of extreme survival of DNA have emphasized the need for reliable models of DNA degradation through time. By analysing mitochondrial DNA (mtDNA) from 158 radiocarbon-dated bones of the extinct New Zealand moa, we confirm empirically a long-hypothesized exponential decay relationship. The average DNA half-life within this geographically constrained fossil assemblage was estimated to be 521 years for a 242 bp mtDNA sequence, corresponding to a per nucleotide fragmentation rate (k) of 5.50 × 10(-6) per year. With an effective burial temperature of 13.1°C, the rate is almost 400 times slower than predicted from published kinetic data of in vitro DNA depurination at pH 5. Although best described by an exponential model (R(2) = 0.39), considerable sample-to-sample variance in DNA preservation could not be accounted for by geologic age. This variation likely derives from differences in taphonomy and bone diagenesis, which have confounded previous, less spatially constrained attempts to study DNA decay kinetics. Lastly, by calculating DNA fragmentation rates on Illumina HiSeq data, we show that nuclear DNA has degraded at least twice as fast as mtDNA. These results provide a baseline for predicting long-term DNA survival in bone.
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Affiliation(s)
- Morten E. Allentoft
- Ancient DNA Laboratory, School of Biological Sciences and Biotechnology, Murdoch University, 90 South Street, Perth, Western Australia 6150, Australia
- School of Biological Sciences, University of Canterbury, Private Bag 4800, Christchurch, New Zealand
- Centre for GeoGenetics, Natural History Museum of Denmark, University of Copenhagen, Øster Voldgade 5-7, 1350 Copenhagen K, Denmark
| | - Matthew Collins
- Department of Archaeology, University of York, PO Box 373, York, UK
| | - David Harker
- Department of Archaeology, University of York, PO Box 373, York, UK
| | - James Haile
- Ancient DNA Laboratory, School of Biological Sciences and Biotechnology, Murdoch University, 90 South Street, Perth, Western Australia 6150, Australia
| | - Charlotte L. Oskam
- Ancient DNA Laboratory, School of Biological Sciences and Biotechnology, Murdoch University, 90 South Street, Perth, Western Australia 6150, Australia
| | - Marie L. Hale
- School of Biological Sciences, University of Canterbury, Private Bag 4800, Christchurch, New Zealand
| | - Paula F. Campos
- Centre for GeoGenetics, Natural History Museum of Denmark, University of Copenhagen, Øster Voldgade 5-7, 1350 Copenhagen K, Denmark
- Museu da Ciência, University of Coimbra, Laboratorio Chimico, Largo Marquês de Pombal, 3000-272 Coimbra, Portugal
| | - Jose A. Samaniego
- Centre for GeoGenetics, Natural History Museum of Denmark, University of Copenhagen, Øster Voldgade 5-7, 1350 Copenhagen K, Denmark
| | - M. Thomas P. Gilbert
- Ancient DNA Laboratory, School of Biological Sciences and Biotechnology, Murdoch University, 90 South Street, Perth, Western Australia 6150, Australia
- Centre for GeoGenetics, Natural History Museum of Denmark, University of Copenhagen, Øster Voldgade 5-7, 1350 Copenhagen K, Denmark
| | - Eske Willerslev
- Centre for GeoGenetics, Natural History Museum of Denmark, University of Copenhagen, Øster Voldgade 5-7, 1350 Copenhagen K, Denmark
| | - Guojie Zhang
- Beijing Genomics Institute-Shenzhen, Shenzhen 518083, People's Republic of China
| | - R. Paul Scofield
- Canterbury Museum, Rolleston Avenue, Christchurch 8050, New Zealand
| | - Richard N. Holdaway
- School of Biological Sciences, University of Canterbury, Private Bag 4800, Christchurch, New Zealand
- Palaecol Research Ltd, 167 Springs Road, Hornby, Christchurch 8042, New Zealand
| | - Michael Bunce
- Ancient DNA Laboratory, School of Biological Sciences and Biotechnology, Murdoch University, 90 South Street, Perth, Western Australia 6150, Australia
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Rizzi E, Lari M, Gigli E, De Bellis G, Caramelli D. Ancient DNA studies: new perspectives on old samples. Genet Sel Evol 2012; 44:21. [PMID: 22697611 PMCID: PMC3390907 DOI: 10.1186/1297-9686-44-21] [Citation(s) in RCA: 129] [Impact Index Per Article: 10.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/06/2011] [Accepted: 06/14/2012] [Indexed: 11/24/2022] Open
Abstract
In spite of past controversies, the field of ancient DNA is now a reliable research area due to recent methodological improvements. A series of recent large-scale studies have revealed the true potential of ancient DNA samples to study the processes of evolution and to test models and assumptions commonly used to reconstruct patterns of evolution and to analyze population genetics and palaeoecological changes. Recent advances in DNA technologies, such as next-generation sequencing make it possible to recover DNA information from archaeological and paleontological remains allowing us to go back in time and study the genetic relationships between extinct organisms and their contemporary relatives. With the next-generation sequencing methodologies, DNA sequences can be retrieved even from samples (for example human remains) for which the technical pitfalls of classical methodologies required stringent criteria to guaranty the reliability of the results. In this paper, we review the methodologies applied to ancient DNA analysis and the perspectives that next-generation sequencing applications provide in this field.
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Affiliation(s)
- Ermanno Rizzi
- Institute for Biomedical Technologies, National Research Council, Via F.lli Cervi 93, Segrate, Milan 20090, Italy
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Abstract
The insular dwarfism seen in Pleistocene elephants has come to epitomize the island rule; yet our understanding of this phenomenon is hampered by poor taxonomy. For Mediterranean dwarf elephants, where the most extreme cases of insular dwarfism are observed, a key systematic question remains unresolved: are all taxa phyletic dwarfs of a single mainland species Palaeoloxodon antiquus (straight-tusked elephant), or are some referable to Mammuthus (mammoths)? Ancient DNA and geochronological evidence have been used to support a Mammuthus origin for the Cretan 'Palaeoloxodon' creticus, but these studies have been shown to be flawed. On the basis of existing collections and recent field discoveries, we present new, morphological evidence for the taxonomic status of 'P'. creticus, and show that it is indeed a mammoth, most probably derived from Early Pleistocene Mammuthus meridionalis or possibly Late Pliocene Mammuthus rumanus. We also show that Mammuthus creticus is smaller than other known insular dwarf mammoths, and is similar in size to the smallest dwarf Palaeoloxodon species from Sicily and Malta, making it the smallest mammoth species known to have existed. These findings indicate that extreme insular dwarfism has evolved to a similar degree independently in two elephant lineages.
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Affiliation(s)
- Victoria L Herridge
- Palaeontology Department, Natural History Museum, , Cromwell Road, London SW7 5BD, UK.
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Raines RT. Stronger and (now) longer synthetic collagen. ADVANCES IN EXPERIMENTAL MEDICINE AND BIOLOGY 2009; 611:xci-xcviii. [PMID: 19400067 PMCID: PMC2798061] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [MESH Headings] [Grants] [Subscribe] [Scholar Register] [Indexed: 05/27/2023]
Affiliation(s)
- Ronald T Raines
- Department of Biochemistry, University of Wisconsin-Madison, Madison, WI 53706, USA
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von Wurmb-Schwark N, Heinrich A, Freudenberg M, Gebühr M, Schwark T. The impact of DNA contamination of bone samples in forensic case analysis and anthropological research. Leg Med (Tokyo) 2008; 10:125-30. [DOI: 10.1016/j.legalmed.2007.10.001] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/08/2007] [Revised: 09/10/2007] [Accepted: 10/03/2007] [Indexed: 10/22/2022]
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Poulakakis N, Parmakelis A, Lymberakis P, Mylonas M, Zouros E, Reese DS, Glaberman S, Caccone A. It remains a mammoth DNA fragment. A reply to and. Biol Lett 2006. [DOI: 10.1098/rsbl.2006.0555] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
Affiliation(s)
- Nikos Poulakakis
- Natural History Museum of Crete, University of CretePO Box 2208, 71409 Heraklion Crete, Greece
- Department of Biology, University of CretePO Box 2208, 71409 Heraklion Crete, Greece
| | - Aris Parmakelis
- Natural History Museum of Crete, University of CretePO Box 2208, 71409 Heraklion Crete, Greece
- Department of Biology, University of CretePO Box 2208, 71409 Heraklion Crete, Greece
| | - Petros Lymberakis
- Natural History Museum of Crete, University of CretePO Box 2208, 71409 Heraklion Crete, Greece
| | - Moysis Mylonas
- Natural History Museum of Crete, University of CretePO Box 2208, 71409 Heraklion Crete, Greece
- Department of Biology, University of CretePO Box 2208, 71409 Heraklion Crete, Greece
| | - Eleftherios Zouros
- Department of Biology, University of CretePO Box 2208, 71409 Heraklion Crete, Greece
| | - David S Reese
- Peabody Museum of Natural History, Yale UniversityPO Box 208118, New Haven, CT 06520-8118, USA
| | - Scott Glaberman
- Department of Ecology and Evolutionary Biology and Yale Institute of Biospheric Studies, Yale UniversityPO Box 208118, New Haven, CT 06520-8118, USA
| | - Adalgisa Caccone
- Department of Ecology and Evolutionary Biology and Yale Institute of Biospheric Studies, Yale UniversityPO Box 208118, New Haven, CT 06520-8118, USA
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