Resolution of the type material of the Asian elephant,<i>Elephas maximus</i>Linnaeus, 1758 (Proboscidea, Elephantidae)

Cappellini, Enrico; Gentry, A. W.; Palkopoulou, Eleftheria; Ishida, Yasuko; Cram, David; Roos, Anna Marie; Watson, Michael; Johansson, Ulf S.; Fernholm, Bo; Agnelli, Paolo; Barbagli, Fausto; Littlewood, D. Timothy J.; Kelstrup, Christian D.; Olsen, Jesper V.; Lister, Adrian M.; Roca, Alfred L.; Dalén, Love; Gilbert, M. Thomas P.

doi:10.1111/zoj.12084

Cited by 32 publications

(12 citation statements)

References 27 publications

(29 reference statements)

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“…Proteins were extracted from powdered tooth samples (50 mg) using a modified filter-aided sample preparation (FASP) protocol as previously described (Cappellini et al, 2013, Warinner et al, 2014). Samples were digested using trypsin and analyzed by LC-MS/MS.…”

Section: Methodsmentioning

confidence: 99%

Neolithic and Medieval virus genomes reveal complex evolution of Hepatitis B

Krause‐Kyora

Susat

Key

et al. 2018

Preprint

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34The hepatitis B virus (HBV) is one of the most widespread human pathogens known today, 35 yet its origin and evolutionary history are still unclear and controversial. Here, we report the 36 analysis of three ancient HBV genomes recovered from human skeletons found at three 37 different archaeological sites in Germany. We reconstructed two Neolithic and one medieval 38 HBV genomes by de novo assembly from shotgun DNA sequencing data. Additionally, we 39 observed HBV-specific peptides using paleo-proteomics. Our results show that HBV 40 circulates in the European population for at least 7000 years. The Neolithic HBV genomes 41show a high genomic similarity to each other. In a phylogenetic network, they do not group 42 with any human-associated HBV genome and are most closely related to those infecting 43African non-human primates. These ancient virus forms appear to represent distinct lineages 44 that have no close relatives today and went possibly extinct. Our results reveal the great 45 potential of ancient DNA from human skeletons in order to study the long-time evolution of 46 blood borne viruses. 47 48 49

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Section: Methodsmentioning

confidence: 99%

Neolithic and Medieval virus genomes reveal complex evolution of Hepatitis B

Krause‐Kyora

Susat

Key

et al. 2018

Preprint

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“…Calculus deposits were weighed, and between 14–60 mg of calculus was included in the protein extraction (Supplementary Table 1). Proteins were extracted at BioArCh (University of York) using a filter-aided sample preparation method modified for ancient (Cappellini, et al, 2014) and mineralised samples (Warinner, et al, 2014a). LC-MS/MS was performed at the Mass Spectrometry Laboratory of the Target Discovery Institute, University of Oxford.…”

Section: Methodsmentioning

confidence: 99%

Preservation of the metaproteome: variability of protein preservation in ancient dental calculus

Mackie

Hendy

Lowe

et al. 2017

STAR: Science & Technology of Archaeological Research

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Proteomic analysis of dental calculus is emerging as a powerful tool for disease and dietary characterisation of archaeological populations. To better understand the variability in protein results from dental calculus, we analysed 21 samples from three Roman-period populations to compare: 1) the quantity of extracted protein; 2) the number of mass spectral queries; and 3) the number of peptide spectral matches and protein identifications. We found little correlation between the quantity of calculus analysed and total protein identifications, as well as no systematic trends between site location and protein preservation. We identified a wide range of individual variability, which may be associated with the mechanisms of calculus formation and/or post-depositional contamination, in addition to taphonomic factors. Our results suggest dental calculus is indeed a stable, long-term reservoir of proteins as previously reported, but further systematic studies are needed to identify mechanisms associated with protein entrapment and survival in dental calculus.

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“…Although the individual components of this method have been variously applied in previous palaeoproteomic studies (e.g. non-demineralizing buffer [13,18], FASP [19,20]), their combination and adaptation for humic removal has not yet been explored. We apply this combined method to a moa fossil [21] with humic content, from which preserved proteins were previously characterized by liquid chromatography–tandem mass spectrometry (LC–MS/MS) [22], to demonstrate its utility for preparing fossils samples for palaeoproteomic analyses.…”

Section: Introductionmentioning

confidence: 99%

Proteomic method to extract, concentrate, digest and enrich peptides from fossils with coloured (humic) substances for mass spectrometry analyses

et al. 2019

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Humic substances are breakdown products of decaying organic matter that co-extract with proteins from fossils. These substances are difficult to separate from proteins in solution and interfere with analyses of fossil proteomes. We introduce a method combining multiple recent advances in extraction protocols to both concentrate proteins from fossil specimens with high humic content and remove humics, producing clean samples easily analysed by mass spectrometry (MS). This method includes: (i) a non-demineralizing extraction buffer that eliminates protein loss during the demineralization step in routine methods; (ii) filter-aided sample preparation (FASP) of peptides, which concentrates and digests extracts in one filter, allowing the separation of large humics after digestion; (iii) centrifugal stage tipping, which further clarifies and concentrates samples in a uniform process performed simultaneously on multiple samples. We apply this method to a moa fossil (approx. 800–1000 years) dark with humic content, generating colourless samples and enabling the detection of more proteins with greater sequence coverage than previous MS analyses on this same specimen. This workflow allows analyses of low-abundance proteins in fossils containing humics and thus may widen the range of extinct organisms and regions of their proteomes we can explore with MS.

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Resolution of the type material of the Asian elephant,Elephas maximusLinnaeus, 1758 (Proboscidea, Elephantidae)

Cited by 32 publications

References 27 publications

Neolithic and Medieval virus genomes reveal complex evolution of Hepatitis B

Neolithic and Medieval virus genomes reveal complex evolution of Hepatitis B

Preservation of the metaproteome: variability of protein preservation in ancient dental calculus

Proteomic method to extract, concentrate, digest and enrich peptides from fossils with coloured (humic) substances for mass spectrometry analyses

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