Microscopic and immunohistochemical analyses of the claw of the nesting dinosaur, Citipati osmolskae

Preservation of proteins in the geosphere

Deep-time protein preservation has attracted increasing interest and rapid research activity within the palaeobiological community in recent years, but there are several different viewpoints without a cohesive framework for the interpretation of these proteins. Therefore, despite this activity, crucial gaps exist in the understanding of how proteins are preserved in the geological record and we believe it is vital to arrive at a synthesis of the various taphonomic pathways in order to proceed forward with their elucidation. Here we take a critical look at the state of knowledge regarding deep-time protein preservation and argue for the necessity of a more nuanced approach to understanding the molecular taphonomy of proteins through the lens of diagenetic pathways. We also propound an initial framework with which to comprehend the chemical changes undergone by proteins via the concept of 'proteagen'.

Chemistry and Analysis of Organic Compounds in Dinosaurs

This review provides an overview of organic compounds detected in non-avian dinosaur fossils to date. This was enabled by the development of sensitive analytical techniques. Non-destructive methods and procedures restricted to the sample surface, e.g., light and electron microscopy, infrared (IR) and Raman spectroscopy, as well as more invasive approaches including liquid chromatography coupled to tandem mass spectrometry (LC-MS/MS), time-of-flight secondary ion mass spectrometry, and immunological methods were employed. Organic compounds detected in samples of dinosaur fossils include pigments (heme, biliverdin, protoporphyrin IX, melanin), and proteins, such as collagens and keratins. The origin and nature of the observed protein signals is, however, in some cases, controversially discussed. Molecular taphonomy approaches can support the development of suitable analytical methods to confirm reported findings and to identify further organic compounds in dinosaur and other fossils in the future. The chemical properties of the various organic compounds detected in dinosaurs, and the techniques utilized for the identification and analysis of each of the compounds will be discussed.

Combining elemental and immunochemical analyses to characterize diagenetic alteration patterns in ancient skeletal remains

Bones and teeth are biological archives, but their structure and composition are subjected to alteration overtime due to biological and chemical degradation postmortem, influenced by burial environment and conditions. Nevertheless, organic fraction preservation is mandatory for several archeometric analyses and applications. The mutual protection between biomineral and organic fractions in bones and teeth may lead to a limited diagenetic alteration, promoting a better conservation of the organic fraction. However, the correlation between elemental variations and the presence of organic materials (e.g., collagen) in the same specimen is still unclear. To fill this gap, chemiluminescent (CL) immunochemical imaging analysis has been applied for the first time for collagen localization. Then, Laser Ablation-Inductively Coupled Plasma-Mass Spectrometry (LA-ICP-MS) and CL imaging were combined to investigate the correlation between elemental (i.e., REE, U, Sr, Ba) and collagen distribution. Teeth and bones from various archeological contexts, chronological periods, and characterized by different collagen content were analyzed. Immunochemical analysis revealed a heterogeneous distribution of collagen, especially in highly degraded samples. Subsequently, LA-ICP-MS showed a correlation between the presence of uranium and rare earth elements and areas with low amount of collagen. The innovative integration between the two methods permitted to clarify the mutual relation between elemental variation and collagen preservation overtime, thus contributing to unravel the effects of diagenetic alteration in bones and teeth.

Corneous beta proteins of the epidermal differentiation complex (EDC) form large part of the corneous material of claws and rhamphothecae in turtles

The presence of specific protein types in claws and beaks of turtles is poorly known. The present immunological study describes the localization of some of the main corneous beta proteins (CBPs) coded in the epidermal differentiation complex of turtles. Three antibodies here utilized revealed that glycine-, cysteine-, tyrosine-, and valine-rich CBPs are present in differentiating keratinocytes of the beak and of the dorsal (unguis) and ventral (sub-unguis) sides of the claw in different species, semi-aquatic and terrestrial. These proteins provide mechanical resilience to the horny material of claws and beaks through the formation of numerous -S-S- bonds and also hydrophobicity that contributes to preserve wearing of the horny material. The thicker corneous layer of the unguis is made of elongated and partially merged corneocytes, and no or few cells desquamate superficially. Unknown junctional proteins may contribute to maintain corneocytes connected one to another. In contrast, corneocytes of the sub-unguis show an elongated but lenticular shape and form a looser corneous layer whose cells remain separate and desquamate superficially. This suggests that other specific corneous proteins are present in the unguis in comparison with the sub-unguis to determine this different compaction. The wearing process present in the sub-unguis creates a loss of tissue that may favor the slow by continuous apical migration of corneocytes from the unguis into the initial part of the sub-unguis. Beak corneocytes form a compact corneous layer like the unguis but numerous superficial cells desquamate on both outer (epidermal) and inner (oral) sides.

Immunolocalization of corneous beta proteins of the Epidermal Differentiation Complex in the developing claw of the alligator

Knowledge on the sharpness, mechanical and hydration resistance of the corneous material of claws requires information on its constituent proteins. The present immunohistochemical study has localized some of the main corneous beta proteins (CBPs, formerly termed beta-keratins) indicated to be present in alligator claws only by genomic data. Using specific antibodies we show the immunolocalization of representative claws CBPs of the Epidermal Differentiation Complex (Beta A1 group) during late stages of claw development in alligator. Intense but asymmetric proliferation, revealed by 5BrdU-immunolabeling, determines the formation of a curved dorsal part (unguis) and a linear ventral part (sub-unguis). The large beta-cells generated in the unguis and their packing into a solid corneous layer occur before thinner beta-cells appear in the sub-unguis. In the latter, CBPs are also immune-detected but with less intensity compared to the unguis, and corneocytes remain separated and desquamate. It is suggested that at the tip of the developing claw beta-corneocytes move downward into the initial part of the sub-unguis. This circular movement contributes to sharpen the claw as these cells fully cornify and are desquamated from the sub-unguis. Corneocytes of the unguis contain 10-16 kDa proline-serine-rich proteins that also possess high percentages of glycine, cysteine, tyrosine, valine and leucine. Cysteines likely give rise to numerous SS bonds in the constituent hard horny material, tyrosine contribute to packing proteins into a dense horny material while glycine, valine and leucine increase the hydrophobic property of claws in these water-adapted predators.

Inferring lifestyle for Aves and Theropoda: A model based on curvatures of extant avian ungual bones

Claws are involved in a number of behaviours including locomotion and prey capture, and as a result animals evolve claw morphologies that enable these functions. Past authors have found geometry of the keratinous sheath of the claw to correlate with mode of life for extant birds and squamates; this relationship has frequently been cited to infer lifestyles for Mesozoic theropods including Archaeopteryx. However, many fossil claws lack keratinous sheaths and thus cannot be analysed using current methods. As the ungual phalanx within the claw is more commonly preserved in the fossil record, geometry of this bone may provide a more useful metric for paleontological analysis. In this study, ungual bones of 108 birds and 5 squamates were imaged using X-ray techniques and a relationship was found between curvatures of the ungual bone within the claw of pedal digit III and four modes of life; ground-dwelling, perching, predatory, and scansorial; using linear discriminant analysis with weighted accuracy equal to 0.79. Our model predicts arboreal lifestyles for Archaeopteryx and Microraptor and a predatory ecology for Confuciusornis. These findings demonstrate the utility of our model in answering questions of palaeoecology, the theropod-bird transition, and the evolution of avian flight. Though the metric exhibits a strong correlation with lifestyle, morphospaces for PD-III curvatures overlap and so this metric should be considered alongside additional evidence.

Proteomes of the past: the pursuit of proteins in paleontology

Introduction: Despite an extensive published literature, skepticism over the claim of original biochemicals including proteins preserved in the fossil record persists and the issue remains controversial. Workers using many different techniques including mass spectrometry, X-ray, electron microscopy and optical spectroscopic techniques, have attempted to verify proteinaceous or other biochemicals that appear endogenous to fossils found throughout the geologic column.Areas covered: This paper presents a review of the relevant literature published over the last 50 years. A comparative survey of the reported techniques used is also given.Expert opinion: Morphological and molecular investigations show that original biochemistry is geologically extensive, geographically global, and taxonomically wide-ranging. The survival of endogenous organics in fossils remains the subject of widespread and increasing research investigation.

The molecular evolution of feathers with direct evidence from fossils

Dinosaur fossils possessing integumentary appendages of various morphologies, interpreted as feathers, have greatly enhanced our understanding of the evolutionary link between birds and dinosaurs, as well as the origins of feathers and avian flight. In extant birds, the unique expression and amino acid composition of proteins in mature feathers have been shown to determine their biomechanical properties, such as hardness, resilience, and plasticity. Here, we provide molecular and ultrastructural evidence that the pennaceous feathers of the Jurassic nonavian dinosaur Anchiornis were composed of both feather β-keratins and α-keratins. This is significant, because mature feathers in extant birds are dominated by β-keratins, particularly in the barbs and barbules forming the vane. We confirm here that feathers were modified at both molecular and morphological levels to obtain the biomechanical properties for flight during the dinosaur-bird transition, and we show that the patterns and timing of adaptive change at the molecular level can be directly addressed in exceptionally preserved fossils in deep time.

Preservation potential of keratin in deep time

Multiple fossil discoveries and taphonomic experiments have established the durability of keratin. The utility and specificity of antibodies to identify keratin peptides has also been established, both in extant feathers under varying treatment conditions, and in feathers from extinct organisms. Here, we show localization of feather-keratin antibodies to control and heat-treated feathers, testifying to the repeatability of initial data supporting the preservation potential of keratin. We then show new data at higher resolution that demonstrates the specific response of these antibodies to the feather matrix, we support the presence of protein in heat-treated feathers using ToF-SIMS, and we apply these methods to a fossil feather preserved in the unusual environment of sinter hot springs. We stress the importance of employing realistic conditions such as sediment burial when designing experiments intended as proxies for taphonomic processes occurring in the fossil record. Our data support the hypothesis that keratin, particularly the β-keratin that comprises feathers, has potential to preserve in fossil remains.

Biochemistry and adaptive colouration of an exceptionally preserved juvenile fossil sea turtle

The holotype (MHM-K2) of the Eocene cheloniine Tasbacka danica is arguably one of the best preserved juvenile fossil sea turtles on record. Notwithstanding compactional flattening, the specimen is virtually intact, comprising a fully articulated skeleton exposed in dorsal view. MHM-K2 also preserves, with great fidelity, soft tissue traces visible as a sharply delineated carbon film around the bones and marginal scutes along the edge of the carapace. Here we show that the extraordinary preservation of the type of T. danica goes beyond gross morphology to include ultrastructural details and labile molecular components of the once-living animal. Haemoglobin-derived compounds, eumelanic pigments and proteinaceous materials retaining the immunological characteristics of sauropsid-specific β-keratin and tropomyosin were detected in tissues containing remnant melanosomes and decayed keratin plates. The preserved organics represent condensed remains of the cornified epidermis and, likely also, deeper anatomical features, and provide direct chemical evidence that adaptive melanism – a biological means used by extant sea turtle hatchlings to elevate metabolic and growth rates – had evolved 54 million years ago.

Disparities in correlating microstructural to nanostructural preservation of dinosaur femoral bones

Osteohistological researches on dinosaurs are well documented, but descriptions of direct correlations between the bone microstructure and corresponding nanostructure are currently lacking. By applying correlative microscopy, we aimed to verify that well-preserved osteohistological features correlate with pristine fossil bone nanostructures from the femoral bones of Koreanosaurus boseongensis. The quality of nanostructural preservation was evaluated based on the preferred orientation level of apatite crystals obtained from selected area electron diffraction (SAED) patterns and by measuring the "arcs" from the {100} and {002} diffraction rings. Unlike our expectations, our results revealed that well-preserved microstructures do not guarantee pristine nanostructures and vice versa. Structural preservation of bone from macro- to nanoscale primarily depends on original bioapatite density, and subsequent taphonomical factors such as effects from burial, pressure, influx of external elements and the rate of diagenetic alteration of apatite crystals. Our findings suggest that the efficient application of SAED analysis opens the opportunity for comprehensive nanostructural investigations of bone.