DiceCT applied to fossilized hard tissues: A preliminary case study using a miocene bird.

Iodine-based contrasting agents for computed tomography (CT) have been used for decades in medicine. Agents like Lugol's iodine enhance the contrasts between soft tissues and mineralized (skeletal) tissues. Because a recent study on extant avian heads showed that iodine-ethanol (I2 E) is a better contrast enhancer overall than the standard Lugol's iodine, here, we tested if I2 E could also enhance the CT contrasts of two fossilized skeletal tissues: bone and calcified cartilage. For this, we used a partial ankle joint from an extinct pheasant from the Late Miocene of Northwest China (Linxia Basin). The pre-staining CT scans showed no microstructural details of the sample. After being immersed into a solution of 1% I2 E for 8 days and scanned a second time, the contrasts were drastically enhanced between the mineralized tissues (bony trabeculae and calcified cartilage) and the sediments and minerals inside vascular spaces. After three other staining-scanning cycles in 2%, 3%, and 6% I2 E solutions, the best contrasts were obtained after immersion in 6% I2 E for 7 days. Energy Dispersive Spectroscopy showed that iodine was preferentially absorbed by the mineralized tissues and the minerals in the vascular spaces, but not by the sediments. This method not only effectively increased the contrasts of two different fossilized skeletal tissues, it was also non-destructive and reversible because part of the fossil was successfully de-stained after a few days in pure ethanol. These preliminary results indicate that iodine-ethanol has the potential to be used widely in vertebrate paleontology to improve CT imaging of fossilized tissues.

Genome-centric resolution of novel microbial lineages in an excavated Centrosaurus dinosaur fossil bone from the Late Cretaceous of North America.

BACKGROUND: Exceptional preservation of endogenous organics such as collagens and blood vessels has been frequently reported in Mesozoic dinosaur fossils. The persistence of these soft tissues in Mesozoic fossil bones has been challenged because of the susceptibility of proteins to degradation and because bone porosity allows microorganisms to colonize the inner microenvironments through geological time. Although protein lability has been studied extensively, the genomic diversity of microbiomes in dinosaur fossil bones and their potential roles in bone taphonomy remain underexplored. Genome-resolved metagenomics was performed, therefore, on the microbiomes recovered from a Late Cretaceous Centrosaurus bone and its encompassing mudstone in order to provide insight into the genomic potential for microbial alteration of fossil bone. RESULTS: Co-assembly and binning of metagenomic reads resulted in a total of 46 high-quality metagenome-assembled genomes (MAGs) affiliated to six bacterial phyla (Actinobacteria, Proteobacteria, Nitrospira, Acidobacteria, Gemmatimonadetes and Chloroflexi) and 1 archaeal phylum (Thaumarchaeota). The majority of the MAGs represented uncultivated, novel microbial lineages from class to species levels based on phylogenetics, phylogenomics and average amino acid identity. Several MAGs from the classes Nitriliruptoria, Deltaproteobacteria and Betaproteobacteria were highly enriched in the bone relative to the adjacent mudstone. Annotation of the MAGs revealed that the distinct putative metabolic functions of different taxonomic groups were linked to carbon, nitrogen, sulfur and iron metabolism. Metaproteomics revealed gene expression from many of the MAGs, but no endogenous collagen peptides were identified in the bone that could have been derived from the dinosaur. Estimated in situ replication rates among the bacterial MAGs suggested that most of the microbial populations in the bone might have been actively growing but at a slow rate. CONCLUSIONS: Our results indicate that excavated dinosaur bones are habitats for microorganisms including novel microbial lineages. The distinctive microhabitats and geochemistry of fossil bone interiors compared to that of the external sediment enrich a microbial biomass comprised of various novel taxa that harbor multiple gene sets related to interconnected biogeochemical processes. Therefore, the presence of these microbiomes in Mesozoic dinosaur fossils urges extra caution to be taken in the science of paleontology when hunting for endogenous biomolecules preserved from deep time.

Raman hyperspectral imaging as an effective and highly informative tool to study the diagenetic alteration of fossil bones.

Retrieving the pristine chemical or isotopic composition of archaeological bones is of great interest for many studies aiming to reconstruct the past life of ancient populations (i.e. diet, mobility, palaeoenvironment, age). However, from the death of the individual onwards, bones undergo several taphonomic and diagenetic processes that cause the alteration of their microstructure and composition. A detailed study on bone diagenesis has the double purpose to assess the preservation state of archaeological bones and to understand the alteration pathways, thus providing evidence that may contribute to evaluate the reliability of the retrieved information. On these bases, this research aims to explore the effectiveness of Raman hyperspectral imaging to detect types, extent and spatial distribution of diagenetic alteration at the micro-scale level. An early-Holocene bone sample from the Al Khiday cemetery (Khartoum, Sudan) was here analysed. Parameters related to the collagen content, bioapatite crystallinity and structural carbonate content, and to the occurrence of secondary mineral phases were calculated from Raman spectra. The acquired data provided spatially-resolved information on both the preservation state of bone constituents and the diagenetic processes occurring during burial. Given the minimal sample preparation, the easy and fast data acquisition and the improvement of system configurations, micro-Raman spectroscopy can be extensively applied as a screening method on a large set of samples in order to characterise the preservation state of archaeological bones. This technique can be effectively applied to identify suitable and well preserved portions of the analysed sample on which perform further analyses.

Na, K, Ca, Mg, and U-series in fossil bone and the proposal of a radial diffusion-adsorption model of uranium uptake.

Fossil bones are often the only materials available for chronological reconstruction of important archeological sites. However, since bone is an open system for uranium, it cannot be dated directly and therefore it is necessary to develop models for the U uptake. Hence, a radial diffusion-adsorption (RDA) model is described. Unlike the classic diffusion-adsorption (D-A) model, RDA uses a cylindrical geometry to describe the U uptake in fossil bones. The model was applied across a transverse section of a tibia of an extinct megamammal Macrauchenia patachonica from the La Paz Local Fauna, Montevideo State, Uruguay. Measurements of spatial distribution of Na, K, Ca, and Mg were also performed by neutron activation analysis (NAA). Gamma-ray spectrometric U-series dating was applied to determine the age of the bone sample. From U concentration profile, it was possible to observe the occurrence of a relatively slow and continuous uranium uptake under constant conditions that had not yet reached equilibrium, since the uranium distribution is a ∪-shaped closed-system. Predictions of the RDA model were obtained for a specific geochemical scenario, indicating that the effective diffusion coefficient D/R in this fossil bone is (2.4 ± 0.6)10(-12) cm(2)s(-1). Mean values of Na, K, Ca, and Mg contents along the radial line of the fossil tibia are consistent with the expected behavior for spatial distributions of these mineral elements across a modern bone section. This result indicates that the fossil tibia may have its mineral structure preserved.