Bone Diagenesis in Short Timescales: Insights from an Exploratory Proteomic Analysis.
Bone Diagenesis in Short Timescales: Insights from an Exploratory Proteomic Analysis.
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DOI：
10.3390/biology10060460
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发表时间：
2021-05-23
期刊：
影响因子：
4.2
通讯作者：
Williams A
中科院分区：
文献类型：
--
作者：
Procopio N;Mein CA;Starace S;Bonicelli A;Williams A
了解由细菌分解引起的骨骼退化的起源是至关重要的，这样可以创建更好的模型来估计死亡后的时间，用于法医案件工作，以及在时间过程中保存考古标本。在这项研究中，我们应用现代蛋白质组学技术，以评估在28周的时间里，分解大鼠骨骼中的蛋白质如何受到不同死后条件的影响，例如不同的沉积环境（埋藏的样本与暴露的样本）和不同的样本类型（完整的尸体、有肉的四肢和去皮的骨头）。我们发现特定蛋白质的丰度要么与微生物主导的分解类型有关，要么与特定的沉积后环境有关。总的来说，这项研究表明，蛋白质组学分析可以用于识别微生物与非微生物驱动的分解，并且特定蛋白质（如骨髓蛋白和血浆蛋白）比其他蛋白质更容易受到外部因素的影响，而钙结合蛋白似乎更容易受到微生物降解的影响。在考古时间尺度上对骨成岩现象的评价有着悠久的历史；然而，对驱动骨成岩作用的微生物的起源知之甚少，也不知道在短时间内骨成岩作用的程度-例如在法医环境中。此前，通过自下而上的蛋白质组学对非胶原蛋白（ncp）进行分析，发现存在潜在的生物标志物，可用于估计死后时间（PMI）。然而，仍然需要加强对法医时间框架内发生的成岩过程的理解，并澄清蛋白质组学分析是否有助于开发更好的模型来可靠地估计PMI。为了解决这些知识空白，我们设计了一个基于整只大鼠尸体、去皮的大鼠长骨和切除但仍有肉的大鼠四肢的实验，将它们埋在土壤中或暴露在干净的塑料表面上，让其分解28周，并在不同的时间间隔取出。本研究旨在评估不同沉积方式和沉积间隔下骨蛋白相对丰度的差异。我们通过自下而上的蛋白质组学进一步评估了外部因素、自溶、肠道和土壤细菌对骨成岩的影响。结果表明，6种蛋白质的丰度在微生物分解（肠道或土壤细菌）或环境因素下的样品之间存在显著差异。特别是，肌肉和钙结合蛋白被发现更容易被细菌攻击降解，而血浆和骨髓蛋白更容易暴露于外部介质。我们的研究结果表明，肠道和土壤细菌在相对较短的时间内对骨成岩作用和蛋白质衰变起关键作用，骨蛋白质组学是鉴定微生物驱动与外部驱动的成岩作用的熟练资源。
Understanding the origin of bone degradation led by bacterial decomposition is essential in order to allow for the creation of better models to estimate the time elapsed since death for forensic casework, as well as for the preservation of archaeological specimens over the course of time. Within this study we applied modern proteomic technologies in order to evaluate how proteins in decomposing rat bones are affected by different post-mortem conditions, such as different depositional environments (buried versus exposed samples) and different sample types (whole carcasses versus fleshed limbs versus defleshed bones), over a period of 28 weeks. We found that the abundance of specific proteins was associated either with a microbial-led type of decomposition or with a specific post-depositional environment. Overall, this study shows that proteomic analyses can be useful to identify microbially- versus non-microbially driven decomposition, and that specific proteins—such as bone marrow and plasma proteins—can be more affected than others by extrinsic agents, whereas calcium-binding proteins seem to be more affected by microbial degradation. 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, nor about the extent of bone diagenesis in 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 in estimating the post-mortem 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 whether 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 long rat bones, and excised but still-fleshed rat limbs, which 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 study aimed to assess differences in bone protein relative abundances for the various deposition modalities and intervals. We further evaluated the effects that extrinsic factors, autolysis, 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 microbial 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, whereas plasma and bone marrow proteins were more susceptible to exposure to extrinsic agents. Our results suggest that both gut and soil bacteria play key roles in bone diagenesis and protein decay in relatively short timescales, and that bone proteomics is a proficient resource with which to identify microbially-driven versus extrinsically-driven diagenesis.
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影响因子：
4.1
作者：
Genetos, Damian C.;Wong, Alice;Watari, Shinya;Yellowley, Clare E.
通讯作者：
Yellowley, Clare E.
影响因子：
3.7
作者：
Cobaugh KL;Schaeffer SM;DeBruyn JM
通讯作者：
DeBruyn JM
影响因子：
2.1
作者：
Hyde, Embriette R.;Haarmann, Daniel P.;Bucheli, Sibyl R.
通讯作者：
Bucheli, Sibyl R.
影响因子：
1.6
作者：
Damann, Franklin E.;Williams, Daniel E.;Layton, Alice C.
通讯作者：
Layton, Alice C.
DOI：
10.1016/j.palaeo.2014.06.026
发表时间：
2014-12-15
影响因子：
3
作者：
Buckley, M.;Wadsworth, C.
通讯作者：
Wadsworth, C.