PXD026042

PXD026042 is an original dataset announced via ProteomeXchange.

Title	Bone Diagenesis in Short Timescales: Insights from an Explor-atory Proteomic Analysis
Description	The evaluation of bone diagenetic phenomena in archaeological timescales has a long history, however little is known about the origins of the microbes driving bone diagenesis and on the ex-tent of bone diagenesis on short timeframes such as in forensic contexts. Previously, the analysis of non-collagenous proteins (NCPs) through bottom-up proteomics revealed the presence of potential biomarkers useful to estimate the postmortem interval (PMI). However, there is still a great need for enhancing the understanding of the diagenetic processes taking place in forensic timeframes, and to clarify if proteomic analyses can help to develop better models for estimating PMI reliably. To address these knowledge gaps, we designed an experiment based on whole rat carcasses, defleshed rat long bones and excised but still fleshed rat limbs that were either buried in soil or exposed on a clean plastic surface, left to decompose for 28 weeks and retrieved at different time intervals. This aimed to assess differences in bone protein relative abundances for the various deposition modalities and intervals. We further evaluated the effects that extrinsic factors, autol-ysis, and gut and soil bacteria had on bone diagenesis via bottom-up proteomics. Results showed six proteins whose abundance was significantly different between samples subjected to either mi-crobial decomposition (gut or soil bacteria) or to environmental factors. In particular, muscle and calcium-binding proteins were found to be more prone to degradation by bacterial attack where-as plasma and bone marrow proteins by the exposure to extrinsic agents. Results suggest that both gut and soil bacteria play a key role in bone diagenesis and protein decay on relatively short timescales and that bone proteomics is a proficient resource to identify microbially-driven versus extrinsically-driven diagenesis.
HostingRepository	PRIDE
AnnounceDate	2022-02-17
AnnouncementXML	Submission_2022-02-17_03:44:44.076.xml
DigitalObjectIdentifier
ReviewLevel	Peer-reviewed dataset
DatasetOrigin	Original dataset
RepositorySupport	Unsupported dataset by repository
PrimarySubmitter	Noemi Procopio
SpeciesList	scientific name: Rattus rattus (Black rat); NCBI TaxID: 10117;
ModificationList	monohydroxylated residue; iodoacetamide derivatized residue; deamidated residue
Instrument	Q Exactive HF

Revision	Datetime	Status	ChangeLog Entry
0	2021-05-17 03:18:46	ID requested
⏵ 1	2022-02-17 03:44:44	announced

Procopio N, Mein CA, Starace S, Bonicelli A, Williams A, Bone Diagenesis in Short Timescales: Insights from an Exploratory Proteomic Analysis. Biology (Basel), 10(6):(2021) [pubmed]

submitter keyword: taphonomy

bone proteomics

PMI

microbial decomposition

bioerosion

Noemi Procopio
contact affiliation	Ellison Place, Northumbria University Newcastle, NE18ST, Newcastle upon Tyne (UK)
contact email	noemi.procopio@norhumbria.ac.uk
lab head
Noemi Procopio
contact affiliation	Northumbria University
contact email	noemi.procopio@northumbria.ac.uk
dataset submitter

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PRIDE project URI

• PRIDE
  1. PXD026042
     1. Label: PRIDE project
     2. Name: Bone Diagenesis in Short Timescales: Insights from an Explor-atory Proteomic Analysis