Analyses of soft tissue from Tyrannosaurus rex suggest the presence of protein

Latest Advances in Structural Insights and Quantification Techniques for Type I Collagen Biomarkers: A path toward standardization?

With an aging population, the demand for sensitive and specific biomarkers to assess bone turnover has surged. Bone turnover involves 2 key processes: bone formation, during which Type I procollagen is cleaved into Type I collagen and subsequently mineralized into bone, and bone resorption, during which Type I collagen is demineralized and degraded into peptides by cathepsin K. To identify biomarkers that accurately reflect these processes, extensive efforts have been made to characterize the peptides generated during both formation and resorption. Over the years, numerous biomarkers have been discovered for various disorders. However, despite their clinical utility, many of these markers lack specificity. This is due to factors such as the degradation of trimers into monomers, the coexistence of multiple peptide species arising from the unpredictable cleavage of Type I collagen/procollagen by cathepsin K and metalloproteinases, and the lack of assay standardization. Standardization is further hindered by the incomplete characterization of many of these peptides. For accurate assay development, a gold-standard technique like LC-MS/MS is essential, requiring full peptide characterization during method development. This review aims to present recent advances in the characterization of Type I collagen-derived peptides, providing a foundation for improved biomarker standardization and application in clinical practice.

Evidence for Endogenous Collagen in Edmontosaurus Fossil Bone

Reports of proteins in fossilized bones have been a subject of controversy in the scientific literature because it is assumed that fossilization results in the destruction of all organic components. In this paper, a novel combination of analytical techniques is used to address this question for an exceptionally well-preserved Edmontosaurus sacrum excavated from the Upper Cretaceous strata of the South Dakota Hell Creek Formation. Cross-polarized light microscopy (XPol) shows birefringence consistent with collagen presence. Tandem LC-MS unambiguously identified, and for the first time quantified, hydroxyproline, a unique collagen-indicator amino acid, in acid-digested samples from the Edmontosaurus. LC-MS/MS bottom-up proteomics shows identical collagen peptide sequences previously identified and reported for another hadrosaur and a T. rex sample.

Pauli Exclusion by n→π* Interactions: Implications for Paleobiology

Proteins have evolved to function in an aqueous environment. Collagen, which provides the bodily scaffold for animals, has a special need to retain its integrity. This need was addressed early on, as intact collagen has been detected in dinosaur fossils, even though peptide bonds have a half-life of only ∼500 years in a neutral aqueous solution. We sought to discover the physicochemical basis for this remarkable resistance to hydrolysis. Using experimental and computational methods, we found that a main-chain acyl group can be protected from hydrolysis by an O···C=O n→π* interaction with a neighboring acyl group. These interactions engage virtually every peptide bond in a collagen triple helix. This protection, which arises from the Pauli exclusion principle, could underlie the preservation of ancient collagen.

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'.

The diagenetic fate of collagen as revealed by analytical pyrolysis of fossil fish scales from deep time

The mechanism of protein degradation has remained a topic of debate (specifically concerning their preservation in deep time), which has recently been invigorated due to multiple published reports of preservation ranging from Miocene to the Triassic that potentially challenge the convention that protein preservation beyond the Cenozoic is extremely uncommon or is expected to be absent altogether, and thus have attracted skepticism. In this paper, we analyze fossil fish scales from the Cretaceous, Jurassic, and Triassic using comprehensive pyrolysis gas chromatography coupled with time-of-flight mass spectrometry and compare the pyrolytic products so obtained with a well-preserved fish scale from Late Pliocene, in an attempt to better understand the effects of diagenesis on protein degradation at the molecular level through deep time. We find that the Pliocene fish scale displays a large number of N-bearing pyrolytic products, including abundant substituted cyclic 2,5-diketopiperazines (2,5-DKPs) which are diagnostic products of peptide and amino acid pyrolysis. We identify N-bearing compounds in the Mesozoic fish scales-however, among the 2,5-DKPs that were identified in the Pliocene scale, only diketodipyrrole (or cyclo (Pyr-Pyr)) is present in the Mesozoic scales. We discuss the implications of N-bearing pyrolytic products with emphasis on 2,5-DKPs in geological samples and conclude that the discrepancy in abundance and variety of N-bearing products between Pliocene and Mesozoic scales indicates that the protein component in the latter has been extensively diagenetically altered, while a suite of DKPs such as in the former would imply stronger evidence to indicate preservation of protein. We conclude that analytical pyrolysis is an effective tool for detecting preservation of intact proteins, as well as for providing insights into their degradation mechanisms, and can potentially be utilized to assign proteinaceous origin to a fossil sample of unknown affinity.

Independent Evidence for the Preservation of Endogenous Bone Biochemistry in a Specimen of Tyrannosaurus rex

Biomolecules preserved in deep time have potential to shed light on major evolutionary questions, driving the search for new and more rigorous methods to detect them. Despite the increasing body of evidence from a wide variety of new, high resolution/high sensitivity analytical techniques, this research is commonly met with skepticism, as the long standing dogma persists that such preservation in very deep time (>1 Ma) is unlikely. The Late Cretaceous dinosaur Tyrannosaurus rex (MOR 1125) has been shown, through multiple biochemical studies, to preserve original bone chemistry. Here, we provide additional, independent support that deep time bimolecular preservation is possible. We use synchrotron X-ray fluorescence imaging (XRF) and X-ray absorption spectroscopy (XAS) to investigate a section from the femur of this dinosaur, and demonstrate preservation of elements (S, Ca, and Zn) associated with bone remodeling and redeposition. We then compare these data to the bone of an extant dinosaur (bird), as well as a second non-avian dinosaur, Tenontosaurus tilletti (OMNH 34784) that did not preserve any sign of original biochemistry. Our data indicate that MOR 1125 bone cortices have similar bone elemental distributions to that of an extant bird, which supports preservation of original endogenous chemistry in this specimen.

Collagen Derived from Fish Industry Waste: Progresses and Challenges

Fish collagen garnered significant academic and commercial focus in the last decades featuring prospective applications in a variety of health-related industries, including food, medicine, pharmaceutics, and cosmetics. Due to its distinct advantages over mammalian-based collagen, including the reduced zoonosis transmission risk, the absence of cultural-religious limitations, the cost-effectiveness of manufacturing process, and its superior bioavailability, the use of collagen derived from fish wastes (i.e., skin, scales) quickly expanded. Moreover, by-products are low cost and the need to minimize fish industry waste's environmental impact paved the way for the use of discards in the development of collagen-based products with remarkable added value. This review summarizes the recent advances in the valorization of fish industry wastes for the extraction of collagen used in several applications. Issues related to processing and characterization of collagen were presented. Moreover, an overview of the most relevant applications in food industry, nutraceutical, cosmetics, tissue engineering, and food packaging of the last three years was introduced. Lastly, the fish-collagen market and the open technological challenges to a reliable recovery and exploitation of this biopolymer were discussed.

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.

Preparation and Use of Decellularized Extracellular Matrix for Tissue Engineering

The multidisciplinary fields of tissue engineering and regenerative medicine have the potential to revolutionize the practise of medicine through the abilities to repair, regenerate, or replace tissues and organs with functional engineered constructs. To this end, tissue engineering combines scaffolding materials with cells and biologically active molecules into constructs with the appropriate structures and properties for tissue/organ regeneration, where scaffolding materials and biomolecules are the keys to mimic the native extracellular matrix (ECM). For this, one emerging way is to decellularize the native ECM into the materials suitable for, directly or in combination with other materials, creating functional constructs. Over the past decade, decellularized ECM (or dECM) has greatly facilitated the advance of tissue engineering and regenerative medicine, while being challenged in many ways. This article reviews the recent development of dECM for tissue engineering and regenerative medicine, with a focus on the preparation of dECM along with its influence on cell culture, the modification of dECM for use as a scaffolding material, and the novel techniques and emerging trends in processing dECM into functional constructs. We highlight the success of dECM and constructs in the in vitro, in vivo, and clinical applications and further identify the key issues and challenges involved, along with a discussion of future research directions.

Using Macro- and Microscale Preservation in Vertebrate Fossils as Predictors for Molecular Preservation in Fluvial Environments

Exceptionally preserved fossils retain soft tissues and often the biomolecules that were present in an animal during its life. The majority of terrestrial vertebrate fossils are not traditionally considered exceptionally preserved, with fossils falling on a spectrum ranging from very well-preserved to poorly preserved when considering completeness, morphology and the presence of microstructures. Within this variability of anatomical preservation, high-quality macro-scale preservation (e.g., articulated skeletons) may not be reflected in molecular-scale preservation (i.e., biomolecules). Excavation of the Hayden Quarry (HQ; Chinle Formation, Ghost Ranch, NM, USA) has resulted in the recovery of thousands of fossilized vertebrate specimens. This has contributed greatly to our knowledge of early dinosaur evolution and paleoenvironmental conditions during the Late Triassic Period (~212 Ma). The number of specimens, completeness of skeletons and fidelity of osteohistological microstructures preserved in the bone all demonstrate the remarkable quality of the fossils preserved at this locality. Because the Hayden Quarry is an excellent example of good preservation in a fluvial environment, we have tested different fossil types (i.e., bone, tooth, coprolite) to examine the molecular preservation and overall taphonomy of the HQ to determine how different scales of preservation vary within a single locality. We used multiple high-resolution mass spectrometry techniques (TOF-SIMS, GC-MS, FT-ICR MS) to compare the fossils to unaltered bone from extant vertebrates, experimentally matured bone, and younger dinosaurian skeletal material from other fluvial environments. FT-ICR MS provides detailed molecular information about complex mixtures, and TOF-SIMS has high elemental spatial sensitivity. Using these techniques, we did not find convincing evidence of a molecular signal that can be confidently interpreted as endogenous, indicating that very good macro- and microscale preservation are not necessarily good predictors of molecular preservation.

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.

Soft Tissue and Biomolecular Preservation in Vertebrate Fossils from Glauconitic, Shallow Marine Sediments of the Hornerstown Formation, Edelman Fossil Park, New Jersey

Endogenous biomolecules and soft tissues are known to persist in the fossil record. To date, these discoveries derive from a limited number of preservational environments, (e.g., fluvial channels and floodplains), and fossils from less common depositional environments have been largely unexplored. We conducted paleomolecular analyses of shallow marine vertebrate fossils from the Cretaceous–Paleogene Hornerstown Formation, an 80–90% glauconitic greensand from Jean and Ric Edelman Fossil Park in Mantua Township, NJ. Twelve samples were demineralized and found to yield products morphologically consistent with vertebrate osteocytes, blood vessels, and bone matrix. Specimens from these deposits that are dark in color exhibit excellent histological preservation and yielded a greater recovery of cells and soft tissues, whereas lighter-colored specimens exhibit poor histology and few to no cells/soft tissues. Additionally, a well-preserved femur of the marine crocodilian Thoracosaurus was found to have retained endogenous collagen I by immunofluorescence and enzyme-linked immunosorbent assays. Our results thus not only corroborate previous findings that soft tissue and biomolecular recovery from fossils preserved in marine environments are possible but also expand the range of depositional environments documented to preserve endogenous biomolecules, thus broadening the suite of geologic strata that may be fruitful to examine in future paleomolecular studies.

Synthesis and characterization of stimuli-responsive hydrogels: evaluation of external stimuli influence on L929 fibroblast viability

In this study, poly(2-hydroxyethyl methacrylate) [p(HEMA)] based hydrogels responsive to the pH, temperature and magnetic field were synthesized. The surface properties of p(HEMA) were improved by designing the stimuli-responsive hydrogels made of MAGA, NIPAAm and methacrylate-decorated magnetite nanoparticles as a function of pH-, thermo- and magnetic responsive cell culture surfaces. These materials were then modified an abundant extracellular matrix component, type I collagen, which has been considered as a biorecognition element to increase the applicability of hydrogels to cell viability. Based on results from scanning electron microscopy (SEM) and thermal gravimetric analysis (TGA), stimuli-responsive hydrogel demonstrated improved non-porous structures and thermal stability with a high degree of cross-linking. Mechanical analyses of the hydrogels also showed that stimuli-responsive hydrogels are more elastomeric due to the polymeric chains and heterogeneous amorphous segments compared to plain hydrogels. Furthermore, surface modification of hydrogels with collagen provided better biocompatibility, which was confirmed with L929 fibroblast cell adhesion. Produced stimuli-responsive hydrogels modulated cellular viability by changing pH and magnetic field.

Biofinder detects biological remains in Green River fish fossils from Eocene epoch at video speed

The “Search for life”, which may be extinct or extant on other planetary bodies is one of the major goals of NASA planetary exploration missions. Finding such evidence of biological residue in a vast planetary landscape is an enormous challenge. We have developed a highly sensitive instrument, the “Compact Color Biofinder”, which can locate minute amounts of biological material in a large area at video speed from a standoff distance. Here we demonstrate the efficacy of the Biofinder to detect fossils that still possess strong bio-fluorescence signals from a collection of samples. Fluorescence images taken by the Biofinder instrument show that all Knightia spp. fish fossils analysed from the Green River formation (Eocene, 56.0–33.9 Mya) still contain considerable amounts of biological residues. The biofluorescence images support the fact that organic matter has been well preserved in the Green River formation, and thus, not diagenetically replaced (replaced by minerals) over such a significant timescale. We further corroborated results from the Biofinder fluorescence imagery through Raman and attenuated total reflection Fourier-transform infrared (ATR-FTIR) spectroscopies, scanning electron microscopy, energy dispersive X-ray spectroscopy (SEM–EDS), and fluorescence lifetime imaging microscopy (FLIM). Our findings confirm once more that biological residues can survive millions of years, and that using biofluorescence imaging effectively detects these trace residues in real time. We anticipate that fluorescence imaging will be critical in future NASA missions to detect organics and the existence of life on other planetary bodies.

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.

Deep Time Paleoproteomics: Looking Forward

The goal of paleoproteomics is to characterize proteins from specimens that have been subjected to the degrading and obscuring effects of time, thus obtaining biological information about tissues or organisms both unobservable in the present and unobtainable through morphological study. Although the description of sequences from Tyrannosaurus rex and Brachylophosaurus canadensis suggested that proteins may persist over tens of millions of years, the majority of paleoproteomic analyses have focused on historical, archeological, or relatively young paleontological samples that rarely exceed 1 million years in age. However, recent advances in methodology and analyses of diverse tissues types (e.g., fossil eggshell, dental enamel) have begun closing the large window of time that remains unexplored in the fossil history of the Cenozoic. In this perspective, we discuss the history and current state of deep time paleoproteomics (DTPp), here defined as paleoproteomic study of samples ∼1 million years (1 Ma) or more in age. We then discuss the future of DTPp research, including what we see as critical ways the field can expand, advancements in technology that can be utilized, and the types of questions DTPp can address if such a future is realized.

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.

Forensic proteomics

Protein is a major component of all biological evidence, often the matrix that embeds other biomolecules such as polynucleotides, lipids, carbohydrates, and small molecules. The proteins in a sample reflect the transcriptional and translational program of the originating cell types. Because of this, proteins can be used to identify body fluids and tissues, as well as convey genetic information in the form of single amino acid polymorphisms, the result of non-synonymous SNPs. This review explores the application and potential of forensic proteomics. The historical role that protein analysis played in the development of forensic science is examined. This review details how innovations in proteomic mass spectrometry have addressed many of the historical limitations of forensic protein science, and how the application of forensic proteomics differs from proteomics in the life sciences. Two more developed applications of forensic proteomics are examined in detail: body fluid and tissue identification, and proteomic genotyping. The review then highlights developing areas of proteomics that have the potential to impact forensic science in the near future: fingermark analysis, species identification, peptide toxicology, proteomic sex estimation, and estimation of post-mortem intervals. Finally, the review highlights some of the newer innovations in proteomics that may drive further development of the field. In addition to potential impact, this review also attempts to evaluate the stage of each application in the development, validation and implementation process. This review is targeted at investigators who are interested in learning about proteomics in a forensic context and expanding the amount of information they can extract from biological evidence.

Molecular preservation in mammoth bone and variation based on burial environment

Biomolecules preserved in fossils are expanding our understanding of the biology and evolution of ancient animals. Molecular taphonomy seeks to understand how these biomolecules are preserved and how they can be interpreted. So far, few studies on molecular preservation have considered burial context to understand its impact on preservation or the potentially complementary information from multiple biomolecular classes. Here, we use mass spectrometry and other analytical techniques to detect the remains of proteins and lipids within intact fossil mammoth bones of different ages and varied depositional setting. By combining these approaches, we demonstrate that endogenous amino acids, amides and lipids can preserve well in fossil bone. Additionally, these techniques enable us to examine variation in preservation based on location within the bone, finding dense cortical bone better preserves biomolecules, both by slowing the rate of degradation and limiting the extent of exogenous contamination. Our dataset demonstrates that biomolecule loss begins early, is impacted by burial environment and temperature, and that both exogenous and endogenous molecular signals can be both present and informative in a single fossil.

Recycling of Chrome-Tanned Leather and Its Utilization as Polymeric Materials and in Polymer-Based Composites: A Review

Tanneries generate large amounts of solid and liquid wastes, which contain harmful chemical compounds in the environment, such as chromium, that is used in the tanning process. Until now, they have been almost completely dumped in landfills. Thus, finding eco-sustainable and innovative alternatives for the management and disposal of these wastes is becoming a huge challenge for tanneries and researchers around the world. In particular, the scientific and industrial communities have started using wastes to produce new materials exploiting the characteristics of leather, which are strongly connected with the macromolecular structure of its main component, collagen. None of the reviews on leather waste management actually present in the scientific literature report in detail the use of leather to make composite materials and the mechanical properties of the materials obtained, which are of fundamental importance for an effective industrial exploitation of leather scraps. This comprehensive review reports for the first time the state of the art of the strategies related to the recovery and valorization of both hydrolyzed collagen and leather waste for the realization of composite materials, reporting in detail the properties and the industrial applications of the materials obtained. In the conclusion section, the authors provide practical implications for industry in relation to sustainability and identify research gaps that can guide future authors and industries in their work.

Molecular tests support the viability of rare earth elements as proxies for fossil biomolecule preservation

The rare earth element (REE) composition of a fossil bone reflects its chemical alteration during diagenesis. Consequently, fossils presenting low REE concentrations and/or REE profiles indicative of simple diffusion, signifying minimal alteration, have been proposed as ideal candidates for paleomolecular investigation. We directly tested this prediction by conducting multiple biomolecular assays on a well-preserved fibula of the dinosaur Edmontosaurus from the Cretaceous Hell Creek Formation previously found to exhibit low REE concentrations and steeply-declining REE profiles. Gel electrophoresis identified the presence of organic material in this specimen, and subsequent immunofluorescence and enzyme-linked immunosorbant assays identified preservation of epitopes of the structural protein collagen I. Our results thereby support the utility of REE profiles as proxies for soft tissue and biomolecular preservation in fossil bones. Based on considerations of trace element taphonomy, we also draw predictions as to the biomolecular recovery potential of additional REE profile types exhibited by fossil bones.

Sea Cucumber Derived Type I Collagen: A Comprehensive Review

Collagen is the major fibrillar protein in most living organisms. Among the different types of collagen, type I collagen is the most abundant one in tissues of marine invertebrates. Due to the health-related risk factors and religious constraints, use of mammalian derived collagen has been limited. This triggers the search for alternative sources of collagen for both food and non-food applications. In this regard, numerous studies have been conducted on maximizing the utilization of seafood processing by-products and address the need for collagen. However, less attention has been given to marine invertebrates and their by-products. The present review has focused on identifying sea cucumber as a potential source of collagen and discusses the general scope of collagen extraction, isolation, characterization, and physicochemical properties along with opportunities and challenges for utilizing marine-derived collagen.

Confirmation of ovarian follicles in an enantiornithine (Aves) from the Jehol biota using soft tissue analyses

The remains of ovarian follicles reported in nine specimens of basal birds represents one of the most remarkable examples of soft-tissue preservation in the Early Cretaceous Jehol Biota. This discovery was immediately contested and the structures alternatively interpreted as ingested seeds. Fragments of the purported follicles preserved in an enantiornithine (STM10-12) were extracted and subjected to multiple high-resolution analyses. The structures in STM10-12 possess the histological and histochemical characteristics of smooth muscles fibers intertwined together with collagen fibers, resembling the contractile structure in the perifollicular membrane (PFM) of living birds. Fossilized blood vessels, very abundant in extant PFMs, are also preserved. Energy Dispersive Spectroscopy shows the preserved tissues primarily underwent alumino-silicification, with minor mineralization via iron oxides. No evidence of plant tissue was found. These results confirm the original interpretation as follicles within the left ovary, supporting the interpretation that the right ovary was functionally lost early in avian evolution.

Bailleul et al. employ histology, histochemistry and Energy Dispersive Spectroscopy to confirm the presence of disputed ovarian follicles in a specimen of fossil Cretaceous bird. These findings have implications for the evolution of the avian breeding system seen in birds today.

Ambiguity Coding Allows Accurate Inference of Evolutionary Parameters from Alignments in an Aggregated State-Space

How can we best learn the history of a protein’s evolution? Ideally, a model of sequence evolution should capture both the process that generates genetic variation and the functional constraints determining which changes are fixed. However, in practical terms the most suitable approach may simply be the one that combines the convenience of easily available input data with the ability to return useful parameter estimates. For example, we might be interested in a measure of the strength of selection (typically obtained using a codon model) or an ancestral structure (obtained using structural modeling based on inferred amino acid sequence and side chain configuration).

But what if data in the relevant state-space are not readily available? We show that it is possible to obtain accurate estimates of the outputs of interest using an established method for handling missing data. Encoding observed characters in an alignment as ambiguous representations of characters in a larger state-space allows the application of models with the desired features to data that lack the resolution that is normally required. This strategy is viable because the evolutionary path taken through the observed space contains information about states that were likely visited in the “unseen” state-space. To illustrate this, we consider two examples with amino acid sequences as input. We show that \documentclass[12pt]{minimal} \usepackage{amsmath} \usepackage{wasysym} \usepackage{amsfonts} \usepackage{amssymb} \usepackage{amsbsy} \usepackage{upgreek} \usepackage{mathrsfs} \setlength{\oddsidemargin}{-69pt} \begin{document} }{}$$\omega$$\end{document}, a parameter describing the relative strength of selection on nonsynonymous and synonymous changes, can be estimated in an unbiased manner using an adapted version of a standard 61-state codon model. Using simulated and empirical data, we find that ancestral amino acid side chain configuration can be inferred by applying a 55-state empirical model to 20-state amino acid data. Where feasible, combining inputs from both ambiguity-coded and fully resolved data improves accuracy. Adding structural information to as few as 12.5% of the sequences in an amino acid alignment results in remarkable ancestral reconstruction performance compared to a benchmark that considers the full rotamer state information. These examples show that our methods permit the recovery of evolutionary information from sequences where it has previously been inaccessible. [Ancestral reconstruction; natural selection; protein structure; state-spaces; substitution models.]

Ancient dental pulp: Masterpiece tissue for paleomicrobiology

Introduction

Dental pulp with special structure has become a good reference sample in paleomicrobiology‐related blood‐borne diseases, many pathogens were detected by different methods based on the diagnosis of nucleic acids and proteins.

Objectives

This review aims to propose the preparation process from ancient teeth collection to organic molecule extraction of dental pulp and summary, analyze the methods that have been applied to detect septicemic pathogens through ancient dental pulps during the past 20 years following the first detection of an ancient microbe.

Methods

The papers used in this review with two main objectives were obtained from PubMed and Google scholar with combining keywords: “ancient,” “dental pulp,” “teeth,” “anatomy,” “structure,” “collection,” “preservation,” “selection,” “photography,” “radiography,” “contamination,” “decontamination,” “DNA,” “protein,” “extraction,” “bone,” “paleomicrobiology,” “bacteria,” “virus,” “pathogen,” “molecular biology,” “proteomics,” “PCR,” “MALDI‐TOF,” “LC/MS,” “ELISA,” “immunology,” “immunochromatography,” “genome,” “microbiome,” “metagenomics.”

Results

The analysis of ancient dental pulp should have a careful preparation process with many different steps to give highly accurate results, each step complies with the rules in archaeology and paleomicrobiology. After the collection of organic molecules from dental pulp, they were investigated for pathogen identification based on the analysis of DNA and protein. Actually, DNA approach takes a principal role in diagnosis while the protein approach is more and more used. A total of seven techniques was used and ten bacteria (Yersinia pestis, Bartonella quintana, Salmonella enterica serovar Typhi, Salmonella enterica serovar Paratyphi C, Mycobacterium leprae, Mycobacterium tuberculosis, Rickettsia prowazeki, Staphylococcus aureus, Borrelia recurrentis, Bartonella henselae) and one virus (Anelloviridae) were identified. Y. pestis had the most published in quantity and all methods were investigated for this pathogen, S. aureus and B. recurrentis were identified by three different methods and others only by one. The combining methods interestingly increase the positive rate with ELISA, PCR and iPCR in Yersinia pestis diagnosis. Twenty‐seven ancient genomes of Y. pestis and one ancient genome of B. recurrentis were reconstructed. Comparing to the ancient bone, ancient teeth showed more advantage in septicemic diagnosis. Beside pathogen identification, ancient pulp help to distinguish species.

Conclusions

Dental pulp with specific tissue is a suitable sample for detection of the blood infection in the past through DNA and protein identification with the correct preparation process, furthermore, it helps to more understand the pathogens of historic diseases and epidemics.

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.

Comparison of structure and composition of a fossil Champsosaurus vertebra with modern Crocodylidae vertebrae: A multi-instrumental approach

Information on the adaptation of bone structures during evolution is rare since histological data are limited. Micro- and nano-computed tomography of a fossilized vertebra from Champsosaurus sp., which has an estimated age of 70-73 million years, revealed lower porosity and higher bone density compared to modern Crocodylidae vertebrae. Mid-infrared reflectance and energy dispersive X-ray mapping excluded a petrification process, and demonstrated a typical carbonate apatite distribution, confirming histology in light- and electron microscopy of the preserved vertebra. As a consequence of this evolutionary process, the two vertebrae of modern Crocodylidae show reduced overall stiffness in the finite element analysis simulation compared to the fossilized Champsosaurus sp. vertebra, with predominant stiffness along the longitudinal z-axes.

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.

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.

Determination of scoring functions for protein damage susceptibility

Protein damage (partly followed by protein aggregation) plays a significant role in ageing, cancer and in neurodegenerative and other diseases. It is known that the proteinogenic amino acids differ in their susceptibility to non-enzymatic modification, such as hydroxylation, peroxidation, chlorination etc. In a novel bioinformatics approach, we introduce measures to quantify the susceptibility of the 20 standard proteinogenic amino acids to such modification. Based on these amino acid scores, we calculated different susceptibilities for 116,387 proteins, testing various scoring approaches. These approaches are based on review articles, text mining and a combination of both. We also show an application by combining the score information with a tool for visualization.

Early Pleistocene enamel proteome from Dmanisi resolves Stephanorhinus phylogeny

Ancient DNA (aDNA) sequencing has enabled reconstruction of speciation, migration, and admixture events for extinct taxa¹. Outside the permafrost, however, irreversible aDNA post-mortem degradation² has so far limited aDNA recovery to the past ~0.5 million years (Ma)³. Contrarily, tandem mass spectrometry (MS) allowed sequencing ~1.5 million year (Ma) old collagen type I (COL1)⁴ and suggested the presence of protein residues in Cretaceous fossil remains⁵, although with limited phylogenetic use⁶. In the absence of molecular evidence, the speciation of several Early and Middle Pleistocene extinct species remain contentious. In this study, we address the phylogenetic relationships of the Eurasian Pleistocene Rhinocerotidae^7–9 using a ~1.77 Ma old dental enamel proteome of a Stephanorhinus specimen from the Dmanisi archaeological site in Georgia (South Caucasus)¹⁰. Molecular phylogenetic analyses place the Dmanisi Stephanorhinus as a sister group to the woolly (Coelodonta antiquitatis) and Merck’s rhinoceros (S. kirchbergensis) clade. We show that Coelodonta evolved from an early Stephanorhinus lineage and that the latter includes at least two distinct evolutionary lines. As such, the genus Stephanorhinus is currently paraphyletic and its systematic revision is therefore needed. We demonstrate that Early Pleistocene dental enamel proteome sequencing overcomes the limits of ancient collagen- and aDNA-based phylogenetic inference. It also provides additional information about the sex and taxonomic assignment of the specimens analysed. Dental enamel, the hardest tissue in vertebrates¹¹, is highly abundant in the fossil record. Our findings reveal that palaeoproteomic investigation of this material can push biomolecular investigation further back into the Early Pleistocene.

Collagen-Based Tissue Engineering Strategies for Vascular Medicine

Cardiovascular diseases (CVDs) account for the 31% of total death per year, making them the first cause of death in the world. Atherosclerosis is at the root of the most life-threatening CVDs. Vascular bypass/replacement surgery is the primary therapy for patients with atherosclerosis. The use of polymeric grafts for this application is still burdened by high-rate failure, mostly caused by thrombosis and neointima hyperplasia at the implantation site. As a solution for these problems, the fast re-establishment of a functional endothelial cell (EC) layer has been proposed, representing a strategy of crucial importance to reduce these adverse outcomes. Implant modifications using molecules and growth factors with the aim of speeding up the re-endothelialization process has been proposed over the last years. Collagen, by virtue of several favorable properties, has been widely studied for its application in vascular graft enrichment, mainly as a coating for vascular graft luminal surface and as a drug delivery system for the release of pro-endothelialization factors. Collagen coatings provide receptor-ligand binding sites for ECs on the graft surface and, at the same time, act as biological sealants, effectively reducing graft porosity. The development of collagen-based drug delivery systems, in which small-molecule and protein-based drugs are immobilized within a collagen scaffold in order to control their release for biomedical applications, has been widely explored. These systems help in protecting the biological activity of the loaded molecules while slowing their diffusion from collagen scaffolds, providing optimal effects on the targeted vascular cells. Moreover, collagen-based vascular tissue engineering substitutes, despite not showing yet optimal mechanical properties for their use in the therapy, have shown a high potential as physiologically relevant models for the study of cardiovascular therapeutic drugs and diseases. In this review, the current state of the art about the use of collagen-based strategies, mainly as a coating material for the functionalization of vascular graft luminal surface, as a drug delivery system for the release of pro-endothelialization factors, and as physiologically relevant in vitro vascular models, and the future trend in this field of research will be presented and discussed.

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.

Cretaceous dinosaur bone contains recent organic material and provides an environment conducive to microbial communities

Fossils were thought to lack original organic molecules, but chemical analyses show that some can survive. Dinosaur bone has been proposed to preserve collagen, osteocytes, and blood vessels. However, proteins and labile lipids are diagenetically unstable, and bone is a porous open system, allowing microbial/molecular flux. These 'soft tissues' have been reinterpreted as biofilms. Organic preservation versus contamination of dinosaur bone was examined by freshly excavating, with aseptic protocols, fossils and sedimentary matrix, and chemically/biologically analyzing them. Fossil 'soft tissues' differed from collagen chemically and structurally; while degradation would be expected, the patterns observed did not support this. 16S rRNA amplicon sequencing revealed that dinosaur bone hosted an abundant microbial community different from lesser abundant communities of surrounding sediment. Subsurface dinosaur bone is a relatively fertile habitat, attracting microbes that likely utilize inorganic nutrients and complicate identification of original organic material. There exists potential post-burial taphonomic roles for subsurface microorganisms.

The Collagen Suprafamily: From Biosynthesis to Advanced Biomaterial Development

Collagen is the oldest and most abundant extracellular matrix protein that has found many applications in food, cosmetic, pharmaceutical, and biomedical industries. First, an overview of the family of collagens and their respective structures, conformation, and biosynthesis is provided. The advances and shortfalls of various collagen preparations (e.g., mammalian/marine extracted collagen, cell-produced collagens, recombinant collagens, and collagen-like peptides) and crosslinking technologies (e.g., chemical, physical, and biological) are then critically discussed. Subsequently, an array of structural, thermal, mechanical, biochemical, and biological assays is examined, which are developed to analyze and characterize collagenous structures. Lastly, a comprehensive review is provided on how advances in engineering, chemistry, and biology have enabled the development of bioactive, 3D structures (e.g., tissue grafts, biomaterials, cell-assembled tissue equivalents) that closely imitate native supramolecular assemblies and have the capacity to deliver in a localized and sustained manner viable cell populations and/or bioactive/therapeutic molecules. Clearly, collagens have a long history in both evolution and biotechnology and continue to offer both challenges and exciting opportunities in regenerative medicine as nature's biomaterial of choice.

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.

Plant Tissue Decay in Long-Term Experiments with Microbial Mats

The sequence of decay in fern pinnules was tracked using the species Davallia canariensis. Taphonomic alterations in the sediment–water interface (control tanks) and in subaqueous conditions with microbial mats were compared. The decay sequences were similar in control and mat tanks; in both cases, pinnules preserved the shape throughout the four-month experience. However, the quality and integrity of tissues were greater in mats. In control tanks, in which we detected anoxic and neutral acid conditions, the appearance of a fungal–bacterial biofilm promoted mechanical (cell breakage and tissue distortions) and geochemical changes (infrequent mineralizations) on the external and internal pinnule tissues. In mats, characterized by stable dissolved oxygen and basic pH, pinnules became progressively entombed. These settings, together with the products derived from mat metabolisms (exopolymeric substances, proteins, and rich-Ca nucleation), promoted the integrity of external and internal tissues, and favored massive and diverse mineralization processes. The experience validates that the patterns of taphonomic alterations may be applied in fossil plants.

A Comparison of Common Mass Spectrometry Approaches for Paleoproteomics

The last two decades have seen a broad diversity of methods used to identify and/or characterize proteins in the archeological and paleontological record. Of these, mass spectrometry has opened an unprecedented window into the proteomes of the past, providing protein sequence data from long extinct animals as well as historical and prehistorical artifacts. Thus, application of mass spectrometry to fossil remains has become an attractive source for ancient molecular sequences with which to conduct evolutionary studies, particularly in specimens older than the proposed limit of amplifiable DNA detection. However, "mass spectrometry" covers a range of mass-based proteomic approaches, each of which utilize different technology and physical principles to generate unique types of data, with their own strengths and challenges. Here, we discuss a variety of mass spectrometry techniques that have or may be used to detect and characterize archeological and paleontological proteins, with a particular focus on MALDI-MS, LC-MS/MS, TOF-SIMS, and MSi. The main differences in their functionality, the types of data they produce, and the potential effects of diagenesis on their results are considered.

Palaeobiology of red and white blood cell-like structures, collagen and cholesterol in an ichthyosaur bone

Carbonate concretions are known to contain well-preserved fossils and soft tissues. Recently, biomolecules (e.g. cholesterol) and molecular fossils (biomarkers) were also discovered in a 380 million-year-old concretion, revealing their importance in exceptional preservation of biosignatures. Here, we used a range of microanalytical techniques, biomarkers and compound specific isotope analyses to report the presence of red and white blood cell-like structures as well as platelet-like structures, collagen and cholesterol in an ichthyosaur bone encapsulated in a carbonate concretion from the Early Jurassic (~182.7 Ma). The red blood cell-like structures are four to five times smaller than those identified in modern organisms. Transmission electron microscopy (TEM) analysis revealed that the red blood cell-like structures are organic in composition. We propose that the small size of the blood cell-like structures results from an evolutionary adaptation to the prolonged low oxygen atmospheric levels prevailing during the 70 Ma when ichthyosaurs thrived. The δ¹³C of the ichthyosaur bone cholesterol indicates that it largely derives from a higher level in the food chain and is consistent with a fish and cephalopod diet. The combined findings above demonstrate that carbonate concretions create isolated environments that promote exceptional preservation of fragile tissues and biomolecules.

Cellular preservation of musculoskeletal specializations in the Cretaceous bird Confuciusornis

The hindlimb of theropod dinosaurs changed appreciably in the lineage leading to extant birds, becoming more ‘crouched' in association with changes to body shape and gait dynamics. This postural evolution included anatomical changes of the foot and ankle, altering the moment arms and control of the muscles that manipulated the tarsometatarsus and digits, but the timing of these changes is unknown. Here, we report cellular-level preservation of tendon- and cartilage-like tissues from the lower hindlimb of Early Cretaceous Confuciusornis. The digital flexor tendons passed through cartilages, cartilaginous cristae and ridges on the plantar side of the distal tibiotarsus and proximal tarsometatarsus, as in extant birds. In particular, fibrocartilaginous and cartilaginous structures on the plantar surface of the ankle joint of Confuciusornis may indicate a more crouched hindlimb posture. Recognition of these specialized soft tissues in Confuciusornis is enabled by our combination of imaging and chemical analyses applied to an exceptionally preserved fossil.

Birds have a more crouched posture compared to their theropod dinosaur ancestors. Here, Jiang and colleagues describe a lower hindlimb of the Early Cretaceous bird Confuciusornis with soft tissues apparently preserved even as molecules, indicating a somewhat more modern posture in ancient birds.

Expansion for the Brachylophosaurus canadensis Collagen I Sequence and Additional Evidence of the Preservation of Cretaceous Protein

Sequence data from biomolecules such as DNA and proteins, which provide critical information for evolutionary studies, have been assumed to be forever outside the reach of dinosaur paleontology. Proteins, which are predicted to have greater longevity than DNA, have been recovered from two nonavian dinosaurs, but these results remain controversial. For proteomic data derived from extinct Mesozoic organisms to reach their greatest potential for investigating questions of phylogeny and paleobiology, it must be shown that peptide sequences can be reliably and reproducibly obtained from fossils and that fragmentary sequences for ancient proteins can be increasingly expanded. To test the hypothesis that peptides can be repeatedly detected and validated from fossil tissues many millions of years old, we applied updated extraction methodology, high-resolution mass spectrometry, and bioinformatics analyses on a Brachylophosaurus canadensis specimen (MOR 2598) from which collagen I peptides were recovered in 2009. We recovered eight peptide sequences of collagen I: two identical to peptides recovered in 2009 and six new peptides. Phylogenetic analyses place the recovered sequences within basal archosauria. When only the new sequences are considered, B. canadensis is grouped more closely to crocodylians, but when all sequences (current and those reported in 2009) are analyzed, B. canadensis is placed more closely to basal birds. The data robustly support the hypothesis of an endogenous origin for these peptides, confirm the idea that peptides can survive in specimens tens of millions of years old, and bolster the validity of the 2009 study. Furthermore, the new data expand the coverage of B. canadensis collagen I (a 33.6% increase in collagen I alpha 1 and 116.7% in alpha 2). Finally, this study demonstrates the importance of reexamining previously studied specimens with updated methods and instrumentation, as we obtained roughly the same amount of sequence data as the previous study with substantially less sample material. Data are available via ProteomeXchange with identifier PXD005087.

Evidence of preserved collagen in an Early Jurassic sauropodomorph dinosaur revealed by synchrotron FTIR microspectroscopy

Fossilized organic remains are important sources of information because they provide a unique form of biological and evolutionary information, and have the long-term potential for genomic explorations. Here we report evidence of protein preservation in a terrestrial vertebrate found inside the vascular canals of a rib of a 195-million-year-old sauropodomorph dinosaur, where blood vessels and nerves would normally have been present in the living organism. The in situ synchrotron radiation-based Fourier transform infrared (SR-FTIR) spectra exhibit the characteristic infrared absorption bands for amide A and B, amide I, II and III of collagen. Aggregated haematite particles (α-Fe2O3) about 6∼8 μm in diameter are also identified inside the vascular canals using confocal Raman microscopy, where the organic remains were preserved. We propose that these particles likely had a crucial role in the preservation of the proteins, and may be remnants partially contributed from haemoglobin and other iron-rich proteins from the original blood.

Identification of proteins from 4200-year-old skin and muscle tissue biopsies from ancient Egyptian mummies of the first intermediate period shows evidence of acute inflammation and severe immune response

We performed proteomics analysis on four skin and one muscle tissue samples taken from three ancient Egyptian mummies of the first intermediate period, approximately 4200 years old. The mummies were first dated by radiocarbon dating of the accompany-\break ing textiles, and morphologically examined by scanning electron microscopy of additional skin samples. Proteins were extracted, separated on SDS-PAGE (sodium dodecyl sulfate polyacrylamide gel electrophoresis) gels, and in-gel digested with trypsin. The resulting peptides were analysed using nanoflow high-performance liquid chromatography-mass spectrometry. We identified a total of 230 unique proteins from the five samples, which consisted of 132 unique protein identifications. We found a large number of collagens, which was confirmed by our microscopy data, and is in agreement with previous studies showing that collagens are very long-lived. As expected, we also found a large number of keratins. We identified numerous proteins that provide evidence of activation of the innate immunity system in two of the mummies, one of which also contained proteins indicating severe tissue inflammation, possibly indicative of an infection that we can speculate may have been related to the cause of death.This article is part of the themed issue 'Quantitative mass spectrometry'.

Bone protein "extractomics": comparing the efficiency of bone protein extractions of Gallus gallus in tandem mass spectrometry, with an eye towards paleoproteomics

Proteomic studies of bone require specialized extraction protocols to demineralize and solubilize proteins from within the bone matrix. Although various protocols exist for bone protein recovery, little is known about how discrete steps in each protocol affect the subset of the bone proteome recovered by mass spectrometry (MS) analyses. Characterizing these different “extractomes” will provide critical data for development of novel and more efficient protein extraction methodologies for fossils. Here, we analyze 22 unique sub-extractions of chicken bone and directly compare individual extraction components for their total protein yield and diversity and coverage of bone proteins identified by MS. We extracted proteins using different combinations and ratios of demineralizing reagents, protein-solubilizing reagents, and post-extraction buffer removal methods, then evaluated tryptic digests from 20 µg aliquots of each fraction by tandem MS/MS on a 12T FT-ICR mass spectrometer. We compared total numbers of peptide spectral matches, peptides, and proteins identified from each fraction, the redundancy of protein identifications between discrete steps of extraction methods, and the sequence coverage obtained for select, abundant proteins. Although both alpha chains of collagen I (the most abundant protein in bone) were found in all fractions, other collagenous and non-collagenous proteins (e.g., apolipoprotein, osteonectin, hemoglobin) were differentially identified. We found that when a standardized amount of extracted proteins was analyzed, extraction steps that yielded the most protein (by weight) from bone were often not the ones that produced the greatest diversity of bone proteins, or the highest degree of protein coverage. Generally, the highest degrees of diversity and coverage were obtained from demineralization fractions, and the proteins found in the subsequent solubilization fractions were highly redundant with those in the previous fraction. Based on these data, we identify future directions and parameters to consider (e.g., proteins targeted, amount of sample required) when applying discrete parts of these protocols to fossils.

Influence of carboxylation on osteocalcin detection by mass spectrometry

RATIONALE

Osteocalcin is a small, abundant bone protein that is difficult to detect using high-throughput tandem mass spectrometry (MS/MS) proteomic approaches from bone protein extracts, and is predominantly detected by non-MS immunological methods. Here, we analyze bovine osteocalcin and its post-translational modifications to determine why a protein of this size goes undetected.

METHODS

Osteocalcin was purified from cow bone using well-established methods. Intact osteocalcin or trypsin-digested osteocalcin were separated using an Agilent 1200 series high-performance liquid chromatography (HPLC) system and analyzed using a ThermoScientific LTQ-Orbitrap XL after fragmentation with higher-energy collision dissociation. Data were analyzed using Mascot or Prosight Lite.

RESULTS

Our results support previous findings that the cow osteocalcin has up to three carboxylations using both intact osteocalcin and digested forms. Using Mascot, we were able to detect osteocalcin peptides, but no fragments that localized the carboxylations. Full annotation using Prosight Lite of the intact (three carboxylations), N-terminal peptide (one carboxylation), and middle peptide (two carboxylations) showed complete fragmentation was present, but complete neutral loss was observed.

CONCLUSIONS

Osteocalcin carboxylation, and its associated neutral losses, makes high-throughput detection of this protein challenging; however, alternative fragmentation or limited purification can overcome these challenges. Copyright © 2016 John Wiley & Sons, Ltd.

Chemistry supports the identification of gender-specific reproductive tissue in Tyrannosaurus rex

Medullary bone (MB), an estrogen-dependent reproductive tissue present in extant gravid birds, is texturally, histologically and compositionally distinct from other bone types. Phylogenetic proximity led to the proposal that MB would be present in non-avian dinosaurs, and recent studies have used microscopic, morphological, and regional homologies to identify this reproductive tissue in both theropod and ornithischian dinosaurs. Here, we capitalize on the unique chemical and histological fingerprint of MB in birds to characterize, at the molecular level, MB in the non-avian theropod Tyrannosaurus rex (MOR 1125), and show that the retention of original molecular components in fossils allows deeper physiological and evolutionary questions to be addressed.