Defining the Characteristics Essential for Biomolecular Preservation: A systematic Study of Bone Diagenesis

这一提议对古生物学研究有更广泛的影响。这是因为在这条调查路线中，成功的关键往往在于鉴定具有最佳保存的样品的能力。一个潜在的陷阱是，我们还远远没有理解限制古代生物分子生存的因素。这导致了为了破坏性分析而牺牲了大量化石。我们对骨成岩作用的系统研究的最终目标是重新定义骨骼遗骸选择任何种类正在进行的生物分子研究的方式。几封支持信表明，在发展他们对特定地点的古生态或化石特征的理解时，需要这些数据。该项目还与MJC目前正在进行的胶原蛋白研究和AC的其他DNA研究相吻合。每个PI教授各种相关课程，并将在他们的实验室接待本科生、研究生和博士后。这项建议着重于四个相关目标。第一个目的是确定一组按时间和沉积环境分层的样品中DNA和OC的生存极限。强调OC稳定性增强的数据（Collins et al., 2000; McNulty et al., in press）表明，它可能比DNA存活的时间更长，并可能提供一个深入时间的遗传窗口。第二个目标是将矿物特征（如孔隙度）与蛋白质和DNA的成岩状态（如OC和胶原浓度、OC衍生肽的丰度和类型、DNA的拷贝数和可扩增片段大小）联系起来。由于初步数据表明矿物特征与生物分子存活之间存在预测关系，因此第三个目标是建立一种可靠的筛选工具，根据矿物特征识别含有保存完好的生物分子的样品。OC， DNA和胶原蛋白的数据来源于我们的第二个目标。我们的分析通常需要20-500毫克的干净骨头，因此几乎不会造成破坏。第四个目标是应用DNA测序（线粒体基因组d环）和蛋白质测序来阐明古代muskoium （Euceratherium, preeovibos, Soergelia， Bootherium和Ovibos）的系统发育。尽管这一目标不是这项资助的主要焦点，但它反映了一种明智的策略，因为这些化石也将用于成岩研究。除了实现这些目标之外，该建议的智力价值部分源于使用新兴技术（例如MALDI-MS， SAXS）来解决长期存在的问题。古生物分子中心（AC）仍然处于古DNA测序新应用的前沿。质谱技术在古代蛋白质测序中的应用首次为53000年前的骨骼提供了完整的蛋白质序列。我们已经明确地表明，蛋白质和DNA序列可以来自同一化石。我们最近的论文（Nielsen-Marsh et al., 2002）得到了大量媒体的回应，这表明了公众对这项工作的广泛兴趣：例如，BBC、华盛顿邮报、探索频道、环球邮报、电讯报、新科学家和自然科学杂志。在我们对骨成岩作用的理解的基础上，开发一种筛选工具是许多古生态研究成功的基础，也是保护地球自然历史中不可替代的组成部分的必要条件。

EAR-0309467Peggy OstromABSTRACTThis proposal has broader impacts in paleontological inquiry. This is Because the key to success in this line of inquiry often lies in the ability to identify samples with optimal preservation. An underlying pitfall is that we are far from understanding factors that limit the survival of ancient biomolecules. This has led to the sacrifice of numerous fossils for destructive analysis. An ultimate goal of our systematic study of bone diagenesis to redefine the way skeletal remains are selected for any variety of on going biomolecular studies. Several letters of support indicate the need for this data in developing their understanding of the paleoecological or characteristics of fossils at a particular site. The project also parallels work currently being conducted on collagen by MJC and other DNA research by AC. Each of the PI's teach various related courses and will host undergraduates, graduates and post-doctoral fellows in their laboratories.This proposal focuses on four related objectives. The first objective is to determine the limit of survival of DNA and OC from a set of samples stratified by time and depositional environment. Data emphasizing the enhanced stability of OC (Collins et al., 2000; McNulty et al., in press) suggest that it is likely to survive longer than DNA and may offer a genetic window into deep time. The second objective is to relate mineral characteristics (e.g. porosity) to the diagenetic state of protein and DNA (e.g. OC and collagen concentrations, abundance and types of OC-derived peptides, and copy number and amplifiable fragment size for DNA). Because preliminary data suggest predictive relationships between mineral characteristics and biomolecular survival, the third objective is to establish a reliable screening tool that identifies samples containing well-preserved biomolecules, based on mineralogical characteristics. Data on OC, DNA and collagen derive from our second objective. Our analyses typically take 20-500 mg of clean bone and, thus, result in little destruction. The fourth objective is to apply DNA sequencing (D-loop of the mitochondrial genome) and protein sequencing to elucidate the phylogeny of ancient muskox (Euceratherium, Praeovibos, Soergelia, Bootherium and Ovibos). Although this objective is not a primary focus of this grant, it reflects an intelligent strategy because these fossils will also be used for diagenetic studies.In addition to fulfilling these objectives, the intellectual merit of this proposal in part stems from using emerging technology (e.g. MALDI-MS, SAXS) to long-standing issues. The Ancient Biomolecules Center (AC) remains on the forefront of new applications of ancient DNA sequencing. The application of mass spectrometric techniques to ancient protein sequencing has provided the first complete protein sequences for 53,000 yr BP bones. We have shown definitively that protein and DNA sequences can derive from the same fossils. The broad public interest in this work was demonstrated by an enormous press response to our recent paper (Nielsen-Marsh et al., 2002): e,g, the BBC, Washington Post, Discovery Channel, Globe and Mail, The Telegraph, New Scientist and Naturwissenschaften.Building on our understanding of bone diagenesis toward the development of a screening tool is fundamental to the success of numerous lines of paleoecological research and will be imperative for protecting an irreplaceable component of the Earth's natural history.