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

Fossilized anuran soft tissues reveal a new taphonomic model for the Eocene Geiseltal Konservat-Lagerstätte, Germany

The Eocene Geiseltal Konservat-Lagerstätte (Germany) is famous for reports of three dimensionally preserved soft tissues with sub-cellular detail. The proposed mode of preservation, direct replication in silica, is not known in other fossils and has not been verified using modern approaches. Here, we investigated the taphonomy of the Geiseltal anurans using diverse microbeam imaging and chemical analytical techniques. Our analyses confirm the preservation of soft tissues in all body regions but fail to yield evidence for silicified soft tissues. Instead, the anuran soft tissues are preserved as two layers that differ in microstructure and composition. Layer 1 comprises sulfur-rich carbonaceous microbodies interpreted as melanosomes. Layer 2 comprises the mid-dermal Eberth-Katschenko layer, preserved in calcium phosphate. In addition, patches of original aragonite crystals define the former position of the endolymphatic sac. The primary modes of soft tissue preservation are therefore sulfurization of melanosomes and phosphatization of more labile soft tissues, i.e., skin. This is consistent with the taphonomy of vertebrates in many other Konservat-Lagerstätten. These findings emphasize an emerging model for pervasive preservation of vertebrate soft tissues via melanosome films, particularly in stagnation-type deposits, with phosphatization of more labile tissues where tissue biochemistry is favorable.

Natural external plastron mold of the Triassic turtle Proterochersis: An unusual mode of preservation

Impressions of vertebrate bodies or their parts, such as trace fossils and natural molds of bones, are a valuable source of information about ancient faunas which may supplement the standard fossil record based on skeletal elements. Whereas trace fossils of animal activity are relatively common and actively studied within the field of ichnology, and natural impressions of internal or external surfaces are a frequent preservation mode in fossil invertebrates, natural molds of bones are comparatively rare and less extensively documented and discussed. Among them, internal molds (steinkerns) of turtle shells are a relatively well-known form of preservation, but the mechanisms and taphonomic prerequisites leading to their formation are poorly studied. External shell molds are even less represented in the literature. Herein, we describe a historic specimen of a natural external turtle plastron mold from the Triassic (Norian) Löwenstein Formation of Germany-a formation which also yielded a number of turtle steinkerns. The specimen is significant not only because it represents an unusual form of preservation, but also due to its remarkably large size and the presence of a potential shell pathology. Although it was initially interpreted as Proterochersis sp., the recent progress in the knowledge of proterochersid turtles leading to an increase in the number of known taxa within that group allows us to verify that assessment. We confirm that the specimen is morphologically consistent with the genus and tentatively identify it as Proterochersis robusta, the only representative of that genus from the Löwenstein Formation. We note, however, that its size exceeds the size observed thus far in Proterochersis robusta and fits within the range of Proterochersis porebensis from the Grabowa Formation of Poland. The marks interpreted as shell pathology are morphologically consistent with Karethraichnus lakkos-an ichnotaxon interpreted as a trace of ectoparasites, such as leeches. This may support the previously proposed interpretation of Proterochersis spp. as a semiaquatic turtle. Moreover, if the identification is correct, the specimen may represent a very rare case of a negative preservation of a named ichnotaxon. Finally, we discuss the taphonomy of the Löwenstein Formation turtles in comparison with other Triassic turtle-yielding formations which show no potential for the preservation of internal or external shell molds and propose a taphonomic model for the formation of such fossils.

Taphonomic experiments reveal authentic molecular signals for fossil melanins and verify preservation of phaeomelanin in fossils

Melanin pigments play a critical role in physiological processes and shaping animal behaviour. Fossil melanin is a unique resource for understanding the functional evolution of melanin but the impact of fossilisation on molecular signatures for eumelanin and, especially, phaeomelanin is not fully understood. Here we present a model for the chemical taphonomy of fossil eumelanin and phaeomelanin based on thermal maturation experiments using feathers from extant birds. Our results reveal which molecular signatures are authentic signals for thermally matured eumelanin and phaeomelanin, which signatures are artefacts derived from the maturation of non-melanin molecules, and how these chemical data are impacted by sample preparation. Our model correctly predicts the molecular composition of eumelanins in diverse vertebrate fossils from the Miocene and Cretaceous and, critically, identifies direct molecular evidence for phaeomelanin in these fossils. This taphonomic framework adds to the geochemical toolbox that underpins reconstructions of melanin evolution and of melanin-based coloration in fossil vertebrates.

Preservation of whole antibodies within ancient teeth

Archaeological remains can preserve some proteins into deep time, offering remarkable opportunities for probing past events in human history. Recovering functional proteins from skeletal tissues could uncover a molecular memory related to the life-history of the associated remains. We demonstrate affinity purification of whole antibody molecules from medieval human teeth, dating to the 13th-15th centuries, from skeletons with different putative pathologies. Purified antibodies are intact retaining disulphide-linkages, are amenable to primary sequences analysis, and demonstrate apparent immunoreactivity against contemporary EBV antigen on western blot. Our observations highlight the potential of ancient antibodies to provide insights into the long-term association between host immune factors and ancient microbes, and more broadly retain a molecular memory related to the natural history of human health and immunity.

Molecular Taphonomy of Heme: Chemical Degradation of Hemin under Presumed Fossilization Conditions

The metalloporphyrin heme acts as the oxygen-complexing prosthetic group of hemoglobin in blood. Heme has been noted to survive for many millions of years in fossils. Here, we investigate its stability and degradation under various conditions expected to occur during fossilization. Oxidative, reductive, aerobic, and anaerobic conditions were studied at neutral and alkaline pH values. Elevated temperatures were applied to accelerate degradation. High-performance liquid chromatography coupled to tandem mass spectrometry (HPLC-MS/MS) identified four main degradation products. The vinyl residues are oxidized to formyl and further to carboxylate groups. In the presence of air or H₂O₂, cleavage of the tetrapyrrole ring occurs, and hematinic acid is formed. The highest stability of heme was observed under anaerobic reductive conditions (half-life 9.5 days), while the lowest stability was found in the presence of H₂O₂ (half-life 1 min). We confirmed that the iron cation plays a crucial role in degradation, since protoporphyrin IX, lacking iron, remained significantly more stable. Under anaerobic, reductive conditions, the above-mentioned degradation products were not observed, suggesting a different degradation pathway. To our knowledge, this is the first molecular taphonomy study on heme, which will be useful for understanding its fate during fossilization.

An ancestral hard-shelled sea turtle with a mosaic of soft skin and scutes

The transition from terrestrial to marine environments by secondarily aquatic tetrapods necessitates a suite of adaptive changes associated with life in the sea, e.g., the scaleless skin in adult individuals of the extant leatherback turtle. A partial, yet exceptionally preserved hard-shelled (Pan-Cheloniidae) sea turtle with extensive soft-tissue remains, including epidermal scutes and a virtually complete flipper outline, was recently recovered from the Eocene Fur Formation of Denmark. Examination of the fossilized limb tissue revealed an originally soft, wrinkly skin devoid of scales, together with organic residues that contain remnant eumelanin pigment and inferred epidermal transformation products. Notably, this stem cheloniid-unlike its scaly living descendants-combined scaleless limbs with a bony carapace covered in scutes. Our findings show that the adaptive transition to neritic waters by the ancestral pan-chelonioids was more complex than hitherto appreciated, and included at least one evolutionary lineage with a mosaic of integumental features not seen in any living turtle.

Biomolecular histology as a novel proxy for ancient DNA and protein sequence preservation

Researchers' ability to accurately screen fossil and subfossil specimens for preservation of DNA and protein sequences remains limited. Thermal exposure and geologic age are usable proxies for sequence preservation on a broad scale but are of nominal use for specimens of similar depositional environments. Cell and tissue biomolecular histology is thus proposed as a novel proxy for determining sequence preservation potential of ancient specimens with improved accuracy. Biomolecular histology as a proxy is hypothesized to elucidate why fossils/subfossils of some depositional environments preserve sequences while others do not and to facilitate selection of ancient specimens for use in molecular studies.

Taphonomic and Diagenetic Pathways to Protein Preservation, Part II: The Case of Brachylophosaurus canadensis Specimen MOR 2598

Simple Summary

Reports of the recovery of proteins and other molecules from fossils have become so common over the last two decades that some paleontologists now focus almost entirely on studying how biologic molecules can persist in fossils. In this study, we explored the fossilization history of a specimen of the hadrosaurid dinosaur Brachylophosaurus which was previously shown to preserve original cells, tissues, and structural proteins. Trace element analyses of the tibia of this specimen revealed that after its bones were buried in a brackish estuarine channel, they fossilized under wet conditions which shifted in redox state multiple times. The successful recovery of proteins from this specimen, despite this complex history of chemical alterations, shows that the processes which bind and stabilize biologic molecules shortly after death provide them remarkable physical and chemical resiliency. By uniting our results with those of similar studies on other dinosaur fossils known to also preserve original proteins, we also conclude that exposure to oxidizing conditions in the initial ~48 h postmortem likely promotes molecular stabilization reactions, and the retention of early-diagenetic trace element signatures may be a useful proxy for molecular recovery potential.

Abstract

Recent recoveries of peptide sequences from two Cretaceous dinosaur bones require paleontologists to rethink traditional notions about how fossilization occurs. As part of this shifting paradigm, several research groups have recently begun attempting to characterize biomolecular decay and stabilization pathways in diverse paleoenvironmental and diagenetic settings. To advance these efforts, we assessed the taphonomic and geochemical history of Brachylophosaurus canadensis specimen MOR 2598, the left femur of which was previously found to retain endogenous cells, tissues, and structural proteins. Combined stratigraphic and trace element data show that after brief fluvial transport, this articulated hind limb was buried in a sandy, likely-brackish, estuarine channel. During early diagenesis, percolating groundwaters stagnated within the bones, forming reducing internal microenvironments. Recent exposure and weathering also caused the surficial leaching of trace elements from the specimen. Despite these shifting redox regimes, proteins within the bones were able to survive through diagenesis, attesting to their remarkable resiliency over geologic time. Synthesizing our findings with other recent studies reveals that oxidizing conditions in the initial ~48 h postmortem likely promote molecular stabilization reactions and that the retention of early-diagenetic trace element signatures may be a useful proxy for molecular recovery potential.

Detection of porphyrins in vertebrate fossils from the Messel and implications for organic preservation in the fossil record

Organic molecules preserved in fossils provide a wealth of new information about ancient life. The discovery of almost unaltered complex organic molecules in well-preserved fossils raise the question of how common such occurrences are in the fossil record, how to differentiate between endogenous and exogenous sources for the organic matter and what promotes such preservation. The aim of this study was the in-situ analysis of a well-preserved vertebrate fossil from 48 Ma Eocene sediments in the Messel pit, Germany for preservation of complex biomolecules. The fossil was characterized using a variety of techniques including time-of-flight secondary ion mass spectrometry (ToF-SIMS), scanning electron microscopy/energy dispersive x-ray spectroscopy (SEM/EDX), x-ray diffraction (XRD) and Raman spectroscopy. A suite of organic molecules was detected, including porphyrins, which given the context of the detected signal are most probably diagenetically altered heme originating from the fossil though a microbial contribution cannot be completely ruled out. Diagenetic changes to the porphyrin structure were observed that included the exchange of the central iron by nickel. Further analyses on the geochemistry of the fossil and surrounding sediments showed presence of pyrite and aluminosilicates, most likely clay. In addition, a carbonate and calcium phosphate dominated crust has formed around the fossil. This suggests that several different processes are involved in the preservation of the fossil and the organic molecules associated with it. Similar processes seem to have also been involved in preservation of heme in fossils from other localities.

Preservation and Taphonomy of Fossil Insects from the Earliest Eocene of Denmark

Simple Summary

Insect fossils dating 55 million-years-old from the Stolleklint Clay and Fur Formation of Denmark are known to preserve both fine morphological details and color patterns. To enhance our understanding on how such fragile animals are retained in the fossil record, we examined a pair of beetle elytra, a wasp and a damselfly using sensitive analytical techniques. In our paper, we demonstrate that all three insect fossils are composed of cuticular remains (that is, traces of the exoskeleton) that, in turn, are dominated by the natural pigment eumelanin. In addition, the beetle elytra show evidence of a delicate lamellar structure comparable to multilayered reflectors that produce metallic hues in modern insects. Our results contribute to improved knowledge on the process of fossilization of insect body fossils in marine environments.

Abstract

Marine sediments of the lowermost Eocene Stolleklint Clay and Fur Formation of north-western Denmark have yielded abundant well-preserved insects. However, despite a long history of research, in-depth information pertaining to preservational modes and taphonomic pathways of these exceptional animal fossils remains scarce. In this paper, we use a combination of scanning electron microscopy coupled with energy-dispersive X-ray spectroscopy (SEM-EDX), transmission electron microscopy (TEM) and time-of-flight secondary ion mass spectrometry (ToF-SIMS) to assess the ultrastructural and molecular composition of three insect fossils: a wasp (Hymenoptera), a damselfly (Odonata) and a pair of beetle elytra (Coleoptera). Our analyses show that all specimens are preserved as organic remnants that originate from the exoskeleton, with the elytra displaying a greater level of morphological fidelity than the other fossils. TEM analysis of the elytra revealed minute features, including a multilayered epicuticle comparable to those nanostructures that generate metallic colors in modern insects. Additionally, ToF-SIMS analyses provided spectral evidence for chemical residues of the pigment eumelanin as part of the cuticular remains. To the best of our knowledge, this is the first occasion where both structural colors and chemical traces of an endogenous pigment have been documented in a single fossil specimen. Overall, our results provide novel insights into the nature of insect body fossils and additionally shed light on exceptionally preserved terrestrial insect faunas found in marine paleoenvironments.

Taphonomic and Diagenetic Pathways to Protein Preservation, Part I: The Case of Tyrannosaurus rex Specimen MOR 1125

Many recent reports have demonstrated remarkable preservation of proteins in fossil bones dating back to the Permian. However, preservation mechanisms that foster the long-term stability of biomolecules and the taphonomic circumstances facilitating them remain largely unexplored. To address this, we examined the taphonomic and geochemical history of Tyrannosaurus rex specimen Museum of the Rockies (MOR) 1125, whose right femur and tibiae were previously shown to retain still-soft tissues and endogenous proteins. By combining taphonomic insights with trace element compositional data, we reconstruct the postmortem history of this famous specimen. Our data show that following prolonged, subaqueous decay in an estuarine channel, MOR 1125 was buried in a coarse sandstone wherein its bones fossilized while interacting with oxic and potentially brackish early-diagenetic groundwaters. Once its bones became stable fossils, they experienced minimal further chemical alteration. Comparisons with other recent studies reveal that oxidizing early-diagenetic microenvironments and diagenetic circumstances which restrict exposure to percolating pore fluids elevate biomolecular preservation potential by promoting molecular condensation reactions and hindering chemical alteration, respectively. Avoiding protracted interactions with late-diagenetic pore fluids is also likely crucial. Similar studies must be conducted on fossil bones preserved under diverse paleoenvironmental and diagenetic contexts to fully elucidate molecular preservation pathways.

Two turtles with soft tissue preservation from the platy limestones of Germany provide evidence for marine flipper adaptations in Late Jurassic thalassochelydians

Late Jurassic deposits across Europe have yielded a rich fauna of extinct turtles. Although many of these turtles are recovered from marine deposits, it is unclear which of these taxa are habitually marine and which may be riverine species washed into nearby basins, as adaptations to open marine conditions are yet to be found. Two new fossils from the Late Jurassic of Germany provide unusually strong evidence for open marine adaptations. The first specimen is a partial shell and articulated hind limb from the Late Jurassic (early Tithonian) platy limestones of Schernfeld near Eichstätt, which preserves the integument of the hind limb as an imprint. The skin is fully covered by flat, polygonal scales, which stiffen the pes into a paddle. Although taxonomic attribution is not possible, similarities are apparent with Thalassemys. The second specimen is a large, articulated skeleton with hypertrophied limbs referable to Thalassemys bruntrutana from the Late Jurassic (early Late Kimmeridgian) platy limestone of Wattendorf, near Bamberg. Even though the skin is preserved as a phosphatic film, the scales are not preserved. This specimen can nevertheless be inferred to have had paddles stiffened by scales based on the pose in which they are preserved, the presence of epibionts between the digits, and by full morphological correspondence to the specimen from Schernfeld. An analysis of scalation in extant turtles demonstrated that elongate flippers stiffed by scales are a marine adaptation, in contrast to the elongate but flexible flippers of riverine turtles. Phylogenetic analysis suggests that Thalassemys bruntrutana is referable to the mostly Late Jurassic turtle clade Thalassochelydia. The marine adapted flippers of this taxon therefore evolved convergently with those of later clades of marine turtles. Although thalassochelydian fossils are restricted to Europe, with one notable exception from Argentina, their open marine adaptations combined with the interconnectivity of Jurassic oceans predict that the clade must have been even more wide-spread during that time.

Chemistry of porphyrins in fossil plants and animals

Porphyrins are macrocyclic tetrapyrrole derivatives that are widely distributed in nature. They are often complexed with a metal ion located in the center of the ring system and may be modified by various substituents including additional rings, or by ring opening, which leads to a plethora of different functions. Due to their extended conjugated aromatic ring system, porphyrins absorb light in the visible range and therefore show characteristic colors. Well-known natural porphyrins include the red-colored heme present in hemoglobin, which is responsible for blood oxygen transport, and the chlorophylls in some bacteria and in plants which are utilized for photosynthesis. Porphyrins are mostly lipophilic pigments that display relatively high chemical stability. Therefore, they can even survive hundreds of millions of years. The present review article provides an overview of natural porphyrins, their chemical structures, and properties. A special focus is put on porphyrins discovered in the fossil record. Examples will be highlighted, and information on their chemical analysis will be provided. We anticipate that the development of novel analytical methods with increased sensitivity will prompt new discoveries of porphyrins in fossils.

Chemical Evaluation of Eumelanin Maturation by ToF-SIMS and Alkaline Peroxide Oxidation HPLC Analysis

Residual melanins have been detected in multimillion-year-old animal body fossils; however, confident identification and characterization of these natural pigments remain challenging due to loss of chemical signatures during diagenesis. Here, we simulate this post-burial process through artificial maturation experiments using three synthetic and one natural eumelanin exposed to mild (100 °C/100 bar) and harsh (250 °C/200 bar) environmental conditions, followed by chemical analysis employing alkaline hydrogen peroxide oxidation (AHPO) and time-of-flight secondary ion mass spectrometry (ToF-SIMS). Our results show that AHPO is sensitive to changes in the melanin molecular structure already during mild heat and pressure treatment (resulting, e.g., in increased C-C cross-linking), whereas harsh maturation leads to extensive loss of eumelanin-specific chemical markers. In contrast, negative-ion ToF-SIMS spectra are considerably less affected by mild maturation conditions, and eumelanin-specific features remain even after harsh treatment. Detailed analysis of ToF-SIMS spectra acquired prior to experimental treatment revealed significant differences between the investigated eumelanins. However, systematic spectral changes upon maturation reduced these dissimilarities, indicating that intense heat and pressure treatment leads to the formation of a common, partially degraded, eumelanin molecular structure. Our findings elucidate the complementary nature of AHPO and ToF-SIMS during chemical characterization of eumelanin traces in fossilized organismal remains.

Assessing ontogenetic maturity in extinct saurian reptiles

Morphology forms the most fundamental level of data in vertebrate palaeontology because it is through interpretations of morphology that taxa are identified, creating the basis for broad evolutionary and palaeobiological hypotheses. Assessing maturity is one of the most basic aspects of morphological interpretation and provides the means to study the evolution of ontogenetic changes, population structure and palaeoecology, life-history strategies, and heterochrony along evolutionary lineages that would otherwise be lost to time. Saurian reptiles (the least-inclusive clade containing Lepidosauria and Archosauria) have remained an incredibly diverse, numerous, and disparate clade through their ~260-million-year history. Because of the great disparity in this group, assessing maturity of saurian reptiles is difficult, fraught with methodological and terminological ambiguity. We compiled a novel database of literature, assembling >900 individual instances of saurian maturity assessment, to examine critically how saurian maturity has been diagnosed. We review the often inexact and inconsistent terminology used in saurian maturity assessment (e.g. 'juvenile', 'mature') and provide routes for better clarity and cross-study coherence. We describe the various methods that have been used to assess maturity in every major saurian group, integrating data from both extant and extinct taxa to give a full account of the current state of the field and providing method-specific pitfalls, best practices, and fruitful directions for future research. We recommend that a new standard subsection, 'Ontogenetic Assessment', be added to the Systematic Palaeontology portions of descriptive studies to provide explicit ontogenetic diagnoses with clear criteria. Because the utility of different ontogenetic criteria is highly subclade dependent among saurians, even for widely used methods (e.g. neurocentral suture fusion), we recommend that phylogenetic context, preferably in the form of a phylogenetic bracket, be used to justify the use of a maturity assessment method. Different methods should be used in conjunction as independent lines of evidence when assessing maturity, instead of an ontogenetic diagnosis resting entirely on a single criterion, which is common in the literature. Critically, there is a need for data from extant taxa with well-represented growth series to be integrated with the fossil record to ground maturity assessments of extinct taxa in well-constrained, empirically tested methods.

New preparation techniques for molecular and in-situ analysis of ancient organic micro- and nanostructures

Organic microfossils preserved in three dimensions in transparent mineral matrices such as cherts/quartzites, phosphates, or carbonates are best studied in petrographic thin sections. Moreover, microscale mass spectrometry techniques commonly require flat, polished surfaces to minimize analytical bias. However, contamination by epoxy resin in traditional petrographic sections is problematic for the geochemical study of the kerogen in these microfossils and more generally for the in situ analysis of fossil organic matter. Here, we show that epoxy contamination has a molecular signature that is difficult to distinguish from kerogen with time-of-flight secondary ion mass spectrometry (ToF-SIMS). This contamination appears pervasive in organic microstructures embedded in micro- to nano-crystalline carbonate. To solve this problem, a new semi-thin section preparation protocol without resin medium was developed for micro- to nanoscale in situ investigation of insoluble organic matter. We show that these sections are suited for microscopic observation of Proterozoic microfossils in cherts. ToF-SIMS reveals that these sections are free of pollution after final removal of a <10 nm layer of contamination using low-dose ion sputtering. ToF-SIMS maps of fragments from aliphatic and aromatic molecules and organic sulfur are correlated with the spatial distribution of organic microlaminae in a Jurassic stromatolite. Hydrocarbon-derived ions also appeared correlated with kerogenous microstructures in Archean cherts. These developments in analytical procedures should help future investigations of organic matter and in particular, microfossils, by allowing the spatial correlation of microscopy, spectroscopy, precise isotopic microanalyses, and novel molecular microanalyses such as ToF-SIMS.

Omega-3 Polyunsaturated Fatty Acids Decrease Aortic Valve Disease Through the Resolvin E1 and ChemR23 Axis

Supplemental Digital Content is available in the text.

Background:

Aortic valve stenosis (AVS), which is the most common valvular heart disease, causes a progressive narrowing of the aortic valve as a consequence of thickening and calcification of the aortic valve leaflets. The beneficial effects of omega-3 polyunsaturated fatty acids (n-3 PUFAs) in cardiovascular prevention have recently been demonstrated in a large randomized, controlled trial. In addition, n-3 PUFAs serve as the substrate for the synthesis of specialized proresolving mediators, which are known by their potent beneficial anti-inflammatory, proresolving, and tissue-modifying properties in cardiovascular disease. However, the effects of n-3 PUFA and specialized proresolving mediators on AVS have not yet been determined. The aim of this study was to identify the role of n-3 PUFA–derived specialized proresolving mediators in relation to the development of AVS.

Methods:

Lipidomic and transcriptomic analyses were performed in human tricuspid aortic valves. Apoe^−/− mice and wire injury in C57BL/6J mice were used as models for mechanistic studies.

Results:

We found that n-3 PUFA incorporation into human stenotic aortic valves was higher in noncalcified regions compared with calcified regions. Liquid chromatography tandem mass spectrometry–based lipid mediator lipidomics identified that the n-3 PUFA–derived specialized proresolving mediator resolvin E1 was dysregulated in calcified regions and acted as a calcification inhibitor. Apoe^−/− mice expressing the Caenorhabditis elegans Fat-1 transgene (Fat-1^tg×Apoe^−/−), which enables the endogenous synthesis of n-3 PUFA and increased valvular n-3 PUFA content, exhibited reduced valve calcification, lower aortic valve leaflet area, increased M2 macrophage polarization, and improved echocardiographic parameters. Finally, abrogation of the resolvin E1 receptor ChemR23 enhanced disease progression, and the beneficial effects of Fat-1^tg were abolished in the absence of ChemR23.

Conclusions:

n-3 PUFA-derived resolvin E1 and its receptor ChemR23 emerge as a key axis in the inhibition of AVS progression and may represent a novel potential therapeutic opportunity to be evaluated in patients with AVS.

Evidence of proteins, chromosomes and chemical markers of DNA in exceptionally preserved dinosaur cartilage

A histological ground-section from a duck-billed dinosaur nestling (Hypacrosaurus stebingeri) revealed microstructures morphologically consistent with nuclei and chromosomes in cells within calcified cartilage. We hypothesized that this exceptional cellular preservation extended to the molecular level and had molecular features in common with extant avian cartilage. Histochemical and immunological evidence supports in situ preservation of extracellular matrix components found in extant cartilage, including glycosaminoglycans and collagen type II. Furthermore, isolated Hypacrosaurus chondrocytes react positively with two DNA intercalating stains. Specific DNA staining is only observed inside the isolated cells, suggesting endogenous nuclear material survived fossilization. Our data support the hypothesis that calcified cartilage is preserved at the molecular level in this Mesozoic material, and suggest that remnants of once-living chondrocytes, including their DNA, may preserve for millions of years.

Taphonomic experiments resolve controls on the preservation of melanosomes and keratinous tissues in feathers

Fossils are a key source of data on the evolution of feather structure and function through deep time, but their ability to resolve macroevolutionary questions is compromised by an incomplete understanding of their taphonomy. Critically, the relative preservation potential of two key feather components, melanosomes and keratinous tissue, is not fully resolved. Recent studies suggesting that melanosomes are preferentially preserved conflict with observations that melanosomes preserve in fossil feathers as external moulds in an organic matrix. To date, there is no model to explain the latter mode of melanosome preservation. We addressed these issues by degrading feathers in systematic taphonomic experiments incorporating decay, maturation and oxidation in isolation and combination. Our results reveal that the production of mouldic melanosomes requires interactions with an oxidant and is most likely to occur prior to substantial maturation. This constrains the taphonomic conditions under which melanosomes are likely to be fossilized. Critically, our experiments also confirm that keratinous feather structures have a higher preservation potential than melanosomes under a range of diagenetic conditions, supporting hitherto controversial hypotheses that fossil feathers can retain degraded keratinous structures.

Applications of chemical imaging techniques in paleontology

Chemical imaging techniques, based on a combination of microscopy and spectroscopy, are designed to analyse the composition and spatial distribution of heterogeneous chemical complexes within a sample. Over the last few decades, it has become an increasingly popular tool for characterizing trace elements, isotopic information and organic biomarkers (molecular biosignatures) found in fossils. Here, we introduce the analytical principle of each technique and the interpretation of the chemical signals, followed by a review of the main applications of these techniques in paleontology. We also demonstrate that each technique is associated with pros and cons, and the current limitations and obstacles associated with the use of each specific technique should be taken into account before being applied to fossil samples. Finally, we propose that, due to the rapid advances in the available technology and overall trends towards more multi-disciplinary studies in paleontology, chemical imaging techniques can be expected to have broader applications in paleontology in the near future.

Dinosaur paleohistology: review, trends and new avenues of investigation

In the mid-19th century, the discovery that bone microstructure in fossils could be preserved with fidelity provided a new avenue for understanding the evolution, function, and physiology of long extinct organisms. This resulted in the establishment of paleohistology as a subdiscipline of vertebrate paleontology, which has contributed greatly to our current understanding of dinosaurs as living organisms. Dinosaurs are part of a larger group of reptiles, the Archosauria, of which there are only two surviving lineages, crocodilians and birds. The goal of this review is to document progress in the field of archosaur paleohistology, focusing in particular on the Dinosauria. We briefly review the "growth age" of dinosaur histology, which has encompassed new and varied directions since its emergence in the 1950s, resulting in a shift in the scientific perception of non-avian dinosaurs from "sluggish" reptiles to fast-growing animals with relatively high metabolic rates. However, fundamental changes in growth occurred within the sister clade Aves, and we discuss this major evolutionary transition as elucidated by histology. We then review recent innovations in the field, demonstrating how paleohistology has changed and expanded to address a diversity of non-growth related questions. For example, dinosaur skull histology has elucidated the formation of curious cranial tissues (e.g., "metaplastic" tissues), and helped to clarify the evolution and function of oral adaptations, such as the dental batteries of duck-billed dinosaurs. Lastly, we discuss the development of novel techniques with which to investigate not only the skeletal tissues of dinosaurs, but also less-studied soft-tissues, through molecular paleontology and paleohistochemistry-recently developed branches of paleohistology-and the future potential of these methods to further explore fossilized tissues. We suggest that the combination of histological and molecular methods holds great potential for examining the preserved tissues of dinosaurs, basal birds, and their extant relatives. This review demonstrates the importance of traditional bone paleohistology, but also highlights the need for innovation and new analytical directions to improve and broaden the utility of paleohistology, in the pursuit of more diverse, highly specific, and sensitive methods with which to further investigate important paleontological questions.

Tissue-specific geometry and chemistry of modern and fossilized melanosomes reveal internal anatomy of extinct vertebrates

Recent reports of nonintegumentary melanosomes in fossils hint at functions for melanin beyond color production, but the biology and evolution of internal melanins are poorly understood. Our results show that internal melanosomes are widespread in diverse fossil and modern vertebrates and have tissue-specific geometries and metal chemistries. Tissue-specific chemical signatures can persist in fossils despite some diagenetic overprint, allowing the reconstruction of internal soft-tissue anatomy in fossil vertebrates, and suggest that links between melanin and metal regulation have deep evolutionary origins in vertebrates.

Recent discoveries of nonintegumentary melanosomes in extant and fossil amphibians offer potential insights into the physiological functions of melanin not directly related to color production, but the phylogenetic distribution and evolutionary history of these internal melanosomes has not been characterized systematically. Here, we present a holistic method to discriminate among melanized tissues by analyzing the anatomical distribution, morphology, and chemistry of melanosomes in various tissues in a phylogenetically broad sample of extant and fossil vertebrates. Our results show that internal melanosomes in all extant vertebrates analyzed have tissue-specific geometries and elemental signatures. Similar distinct populations of preserved melanosomes in phylogenetically diverse vertebrate fossils often map onto specific anatomical features. This approach also reveals the presence of various melanosome-rich internal tissues in fossils, providing a mechanism for the interpretation of the internal anatomy of ancient vertebrates. Collectively, these data indicate that vertebrate melanins share fundamental physiological roles in homeostasis via the scavenging and sequestering of metals and suggest that intimate links between melanin and metal metabolism in vertebrates have deep evolutionary origins.

Paleoproteomics of Mesozoic Dinosaurs and Other Mesozoic Fossils

Molecular studies have contributed greatly to our understanding of evolutionary processes that act upon virtually every aspect of living organisms. However, these studies are limited with regard to extinct organisms, particularly those from the Mesozoic because fossils pose unique challenges to molecular workflows, and because prevailing wisdom suggests no endogenous molecular components can persist into deep time. Here, the power and potential of a molecular approach to Mesozoic fossils is discussed. Molecular methods that have been applied to Mesozoic fossils-including iconic, non-avian dinosaurs- and the challenges inherent in such analyses, are compared and evaluated. Taphonomic processes resulting in the transition of living organisms from the biosphere into the fossil record are reviewed, and the possible effects of taphonomic alteration on downstream analyses that can be problematic for very old material (e.g., molecular modifications, limitations of on comparative databases) are addressed. Molecular studies applied to ancient remains are placed in historical context, and past and current studies are evaluated with respect to producing phylogenetically and/or evolutionarily significant data. Finally, some criteria for assessing the presence of endogenous biomolecules in very ancient fossil remains are suggested as a starting framework for such studies.

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.

Analysis of the Myc-induced pancreatic β cell islet tumor microenvironment using imaging ToF-SIMS

Solid tumors are a structurally complex system, composed of many different cell types. The tumor microenvironment includes nonmalignant cell types that participate in complex interactions with tumor cells. The cross talk between tumor and normal cells is implicated in regulating cell growth, metastatic potential, and chemotherapeutic drug resistance. A new approach is required to interrogate and quantitatively characterize cell to cell interactions in this complex environment. Here, the authors have applied time-of-flight secondary ion mass spectrometry (ToF-SIMS) to analyze Myc-induced pancreatic β cell islet tumors. The high mass resolution and micron spatial resolution of ToF-SIMS allows detection of metabolic intermediates such as lipids and amino acids. Employing multivariate analysis, specifically, principal component analysis, the authors show that it is possible to chemically distinguish cancerous islets from normal tissue, in addition to intratumor heterogeneity. These heterogeneities can then be imaged and investigated using another modality such as sum harmonic generation microscopy. Using these techniques with a specialized mouse model, the authors found significant metabolic changes occurring within β cell tumors and the surrounding tissues. Specific alterations of the lipid, amino acid, and nucleotide metabolism were observed, demonstrating that ToF-SIMS can be utilized to identify large-scale changes that occur in the tumor microenvironment and could thereby increase the understanding of tumor progression and the tumor microenvironment.

A new species of Peritresius Leidy, 1856 (Testudines: Pan-Cheloniidae) from the Late Cretaceous (Campanian) of Alabama, USA, and the occurrence of the genus within the Mississippi Embayment of North America

Late Cretaceous members of Peritresius belong to a diverse clade of marine adapted turtles currently thought to be some of the earliest representatives of the lineage leading to modern hard-shelled sea turtles (Pan-Cheloniidae). Prior studies have suggested that Peritresius was monospecific, with a distribution restricted to Maastrichtian deposits in North America. However, new Peritresius specimens identified from Alabama and Mississippi, USA, show that the genus contains two taxa, Peritresius ornatus, and a new species Peritresius martini sp. nov. These two taxa are characterized by the presence of a generally cordiform carapace with moderately serrated peripherals, well-developed ventral flanges beginning at the third peripheral, squarish umbilical and lateral plastral fontanelles, and a narrow bridge formed by the contact between the hyoplastron and hypoplastron. Peritresius martini sp. nov. can be distinguished by its lack of dermal ornamentation and the presence of a 'rib-free' 10th peripheral. These new specimens represent the first occurrences of Peritresius from the Late Cretaceous Mississippi Embayment and extend the temporal range of this genus back to the early Campanian. When tested within a global phylogenetic context, Peritresius is placed on the stem of Cheloniidae (Pan-Cheloniidae) along with Ctenochelys and Allopleuron hofmanni. The heavily vascularized and uniquely sculptured dermal elements of P. ornatus are interpreted here as potentially relating to thermoregulation and therefore may have been one of the key factors contributing to the survival of Peritresius into the Maastrichtian, a period of cooling when other lineages of Campanian marine turtles (e.g., Protostegids, Toxochelys, and Ctenochelys) went extinct.