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

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.

Monolithic DNApatite: An Elastic Apatite with Sub-Nanometer Scale Organo-Inorganic Structures

Hydroxyapatite (HA) exhibits outstanding biocompatibility, bioactivity, osteoconductivity, and natural anti-inflammatory properties. Pure HA, ion-doped HA, and HA-polymer composites are investigated, but critical limitations such as brittleness remain; numerous efforts are being made to address them. Herein, the novel self-crystallization of a polymeric single-stranded deoxyribonucleic acid (ssDNA) without additional phosphate ions for synthesizing deoxyribonucleic apatite (DNApatite) is presented. The synthesized DNApatite, DNA1Ca2.2(PO4)1.3OH2.1, has a repetitive dual phase of inorganic HA crystals and amorphous organic ssDNA at the sub-nm scale, forming nanorods. Its mechanical properties, including toughness and elasticity, are significantly enhanced compared with those of HA nanorod, with a Young's modulus similar to that of natural bone.

Parental feeding in the dinosaur Lufengosaurus revealed through multidisciplinary comparisons with altricial and precocious birds

Previous studies arguing for parental care in dinosaurs have been primarily based on fossil accumulations of adults and hatchlings, perinatal and post-hatchlings in nests and nest areas, and evidence of brooding, the majority of which date to the Late Cretaceous. Similarly, the general body proportions of preserved embryonic skeletons of the much older Early Jurassic Massospondylus have been used to suggest that hatchlings were unable to forage for themselves. Here, we approach the question of parental care in dinosaurs by using a combined morphological, chemical, and biomechanical approach to compare early embryonic and hatchling bones of the Early Jurassic sauropodomorph Lufengosaurus with those of extant avian taxa with known levels of parental care. We compare femora, the main weight-bearing limb bone, at various embryonic and post-embryonic stages in a precocious and an altricial extant avian dinosaur with those of embryonic and hatchling Lufengosaurus, and find that the rate and degree of bone development in Lufengosaurus is closer to that of the highly altricial Columba (pigeon) than the precocious Gallus (chicken), providing strong support for the hypothesis that Lufengosaurus was fully altricial. We suggest that the limb bones of Lufengosaurus hatchlings were not strong enough to forage for themselves and would likely need parental feeding.

An evaluation of the effect of hydrofluoric acid (HF) treatment on keratins

Hydrofluoric acid (HF) is commonly used in geological and paleontological research to extract organic fossils for morphological and chemical studies. However, during HF treatment, organic matter can also be altered, which raises concerns that HF-treated organic matter may not be representative of the original organic matter. To provide reference data for protein studies on fossils, herein, we use Fourier transform infrared (FTIR) spectroscopy to investigate the effect of HF (21.3 M) treatment on keratins, with treatment durations ranging from 2 to 48 h. Results show that the FTIR spectra of HF-treated samples are overall similar to that of the untreated sample, while curve fitting shows that HF treatment has led to alteration of the secondary structure in all the HF-treated samples and the effect is time-dependent. The 2- and 4-h treatment mainly reduced the content of the random coils, α-helix, and intermolecular β-sheet. From 8h onwards, the content of random coils greatly increased at the expense of other structures. Our results imply that for protein detection in fossils using FTIR spectroscopy, the negative effect of HF treatment is not substantial, as the bands characteristic of proteins, that is, amide A, amide B, amide I, amide II, and amide III, are still present after the 48-h treatment. If the target is a secondary structure, the effect of HF treatment should be considered. When HF treatment is necessary, limiting the treatment duration to less than 4h may be a choice.

Organic preservation of vase-shaped microfossils from the late Tonian Chuar Group, Grand Canyon, Arizona, USA

Vase-shaped microfossils (VSMs) are found globally in middle Neoproterozoic (800-730 Ma) marine strata and represent the earliest evidence for testate (shell-forming) amoebozoans. VSM tests are hypothesized to have been originally organic in life but are most commonly preserved as secondary mineralized casts and molds. A few reports, however, suggest possible organic preservation. Here, we test the hypothesis that VSMs from shales of the lower Walcott Member of the Chuar Group, Grand Canyon, Arizona, contain original organic material, as reported by B. Bloeser in her pioneering studies of Chuar VSMs. We identified VSMs from two thin section samples of Walcott Member black shales in transmitted light microscopy and used scanning electron microscopy to image VSMs. Carbonaceous material is found within the internal cavity of all VSM tests from both samples and is interpreted as bitumen mobilized from Walcott shales likely during the Cretaceous. Energy dispersive X-ray spectroscopy (EDS) and wavelength dispersive X-ray spectroscopy (WDS) reveal that VSM test walls contain mostly carbon, iron, and sulfur, while silica is present only in the surrounding matrix. Raman spectroscopy was used to compare the thermal maturity of carbonaceous material within the samples and indicated the presence of pyrite and jarosite within fossil material. X-ray absorption spectroscopy revealed the presence of reduced organic sulfur species within the carbonaceous test walls, the carbonaceous material found within test cavities, and in the sedimentary matrix, suggesting that organic matter sulfurization occurred within the Walcott shales. Our suite of spectroscopic analyses reveals that Walcott VSM test walls are organic and sometimes secondarily pyritized (with the pyrite variably oxidized to jarosite). Both preservation modes can occur at a millimeter spatial scale within sample material, and at times even within a single specimen. We propose that sulfurization within the Walcott Shales promoted organic preservation, and furthermore, the ratio of iron to labile VSM organic material controlled the extent of pyrite replacement. Based on our evidence, we conclude that the VSMs are preserved with original organic test material, and speculate that organic VSMs may often go unrecognized, given their light-colored, translucent appearance in transmitted light.

Attenuated Total Reflection Fourier Transform Infrared (ATR FT-IR) Spectroscopy Sensitivity to the Thermal Decay of Bone Collagen

The analysis of collagen stability is of interest in forensics, archaeology, and molecular paleontology. Collagen decay rates are often measured by thermal kinetic studies that employ liquid chromatography mass spectrometry (LC-MS) to assay collagen quantities. However, these kinetic studies generally focus on measuring the decreasing levels of collagen instead of an exact molecular concentration of each sample. Thus, attenuated total reflection Fourier transform infrared (ATR FT-IR) spectroscopy can offer a simpler and less expensive alternative to LC-MS. The application of a new protocol to determine decreasing amounts of bone collagen in artificially decayed porcine and bovine bone was assessed. The protocol uses a forensic application of ATR FT-IR spectroscopy on size-restricted bone powder from three uniformly high temperature conditions. Also, for the first time, collagen-specific second-harmonic generation (SHG) imaging was also applied to artificially aged bone to add an independent, qualitative perspective to parallel FT-IR assessments. SHG images and ATR FT-IR spectra together reveal the same orderly bone collagen decay as found in previous thermal kinetic studies. Resulting Arrhenius plots with r² values > 0.95 suggest that the ATR FT-IR-based protocol has potential as a precise and simple tool for measuring bone collagen decay rates. The results are significant for applications of thermal kinetic studies, and our protocol can serve as an inexpensive, precise, and pragmatic means of evaluating bone collagen stability within an array of conditions.

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.

Raman Spectra and Ancient Life: Vibrational ID Profiles of Fossilized (Bone) Tissues

Raman micro-spectroscopy is a non-destructive and non-contact analytical technique that combines microscopy and spectroscopy, thus providing a potential for non-invasive and in situ molecular identification, even over heterogeneous and rare samples such as fossilized tissues. Recently, chemical imaging techniques have become an increasingly popular tool for characterizing trace elements, isotopic information, and organic markers in fossils. Raman spectroscopy also shows a growing potential in understanding bone microstructure, chemical composition, and mineral assemblance affected by diagenetic processes. In our lab, we have investigated a wide range of different fossil tissues, mainly of Mesozoic vertebrates (from Jurassic through Cretaceous). Besides standard spectra of sedimentary rocks, including pigment contamination, our Raman spectra also exhibit interesting spectral features in the 1200-1800 cm-1 spectral range, where Raman bands of proteins, nucleic acids, and other organic molecules can be identified. In the present study, we discuss both a possible origin of the observed bands of ancient organic residues and difficulties with definition of the specific spectral markers in fossilized soft and hard tissues.

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.

Soft-Tissue, Rare Earth Element, and Molecular Analyses of Dreadnoughtus schrani, an Exceptionally Complete Titanosaur from Argentina

Evidence that organic material preserves in deep time (>1 Ma) has been reported using a wide variety of analytical techniques. However, the comprehensive geochemical data that could aid in building robust hypotheses for how soft-tissues persist over millions of years are lacking from most paleomolecular reports. Here, we analyze the molecular preservation and taphonomic history of the Dreadnougtus schrani holotype (MPM-PV 1156) at both macroscopic and microscopic levels. We review the stratigraphy, depositional setting, and physical taphonomy of the D. schrani skeletal assemblage, and extensively characterize the preservation and taphonomic history of the humerus at a micro-scale via: (1) histological analysis (structural integrity) and X-ray diffraction (exogenous mineral content); (2) laser ablation-inductively coupled plasma mass spectrometry (analyses of rare earth element content throughout cortex); (3) demineralization and optical microscopy (soft-tissue microstructures); (4) in situ and in-solution immunological assays (presence of endogenous protein). Our data show the D. schrani holotype preserves soft-tissue microstructures and remnants of endogenous bone protein. Further, it was exposed to LREE-enriched groundwaters and weakly-oxidizing conditions after burial, but experienced negligible further chemical alteration after early-diagenetic fossilization. These findings support previous hypotheses that fossils that display low trace element uptake are favorable targets for paleomolecular analyses.

Proteins, possibly human, found in World War II concentration camp artifact

Museums displaying artifacts of the human struggle against oppression are often caught in their own internal struggle between presenting factual and unbiased descriptions of their collections, or relying on testament of survivors. Often this quandary is resolved in favor of what can be verified, not what is remembered. However, with improving instrumentation, methods and informatic approaches, science can help uncover evidence able to reconcile memory and facts. Following World War II, thousands of small, cement-like disks with numbers impressed on one side were found at concentration camps throughout Europe. Survivors claimed these disks were made of human cremains; museums erred on the side of caution—without documentation of the claims, was it justifiable to present them as fact? The ability to detect species relevant biological material in these disks could help resolve this question. Proteomic mass spectrometry of five disks revealed all contained proteins, including collagens and hemoglobins, suggesting they were made, at least in part, of animal remains. A new protein/informatics approach to species identification showed that while human was not always identified as the top contributor, human was the most likely explanation for one disk. To our knowledge, this is the first demonstration of protein recovery from cremains. Data are available via ProteomeXchange with identifier PXD035267.

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.

Analysis and comparison of protein secondary structures in the rachis of avian flight feathers

Avians have evolved many different modes of flying as well as various types of feathers for adapting to varied environments. However, the protein content and ratio of protein secondary structures (PSSs) in mature flight feathers are less understood. Further research is needed to understand the proportions of PSSs in feather shafts adapted to various flight modes in different avian species. Flight feathers were analyzed in chicken, mallard, sacred ibis, crested goshawk, collared scops owl, budgie, and zebra finch to investigate the PSSs that have evolved in the feather cortex and medulla by using nondestructive attenuated total reflection Fourier transform infrared spectroscopy (ATR-FTIR). In addition, synchrotron radiation-based, Fourier transform infrared microspectroscopy (SR-FTIRM) was utilized to measure and analyze cross-sections of the feather shafts of seven bird species at a high lateral resolution to resolve the composition of proteins distributed within the sampled area of interest. In this study, significant amounts of α-keratin and collagen components were observed in flight feather shafts, suggesting that these proteins play significant roles in the mechanical strength of flight feathers. This investigation increases our understanding of adaptations to flight by elucidating the structural and mechanistic basis of the feather composition.

Putative fossil blood cells reinterpreted as diagenetic structures

Red to red-orange spheres in the vascular canals of fossil bone thin sections have been repeatedly reported using light microscopy. Some of these have been interpreted as the fossilized remains of blood cells or, alternatively, pyrite framboids. Here, we assess claims of blood cell preservation within bones of the therizinosauroid theropod Beipiaosaurus inexpectus from the Jehol Lagerstätte. Using Raman spectroscopy, Energy Dispersive X-ray Spectrometry, and Time of Flight Secondary Ion Mass Spectroscopy, we found evidence of high taphonomic alteration of the bone. We also found that the vascular canals in the bone, once purported to contain fossil red blood cell, are filled with a mix of clay minerals and carbonaceous compounds. The spheres could not be analyzed in isolation, but we did not find any evidence of pyrite or heme compounds in the vessels, surrounding bone, or matrix. However, we did observe similar spheres under light microscopy in petrified wood found in proximity to the dinosaur. Consequently, we conclude that the red spheres are most likely diagenetic structures replicated by the clay minerals present throughout the vascular canals.

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.

Diagnosis of liver cancer by FTIR spectra of serum

Liver cancer is the most common fatal malignant tumor in the world. Early diagnosis of liver cancer can improve the survival rate of the patients with liver disease. In this paper, Fourier transform infrared (FTIR) spectroscopy combined with curve fitting and chemometrics was used to distinguish the serum from patients from that of healthy people. The curve fitting results in protein range of 1700-1600 cm^-1 showed that there were differences in the secondary structure of protein in serum between the patients with liver cancer and healthy people. Principal component analysis (PCA) in lipid range of 2900-2800 cm^-1 could distinguish the serum of patients with liver cancer from that of healthy people. The first two principal components PC1 and PC2 explained 95% of the total data variance. The sensitivity and specificity of partial least squares discriminant analysis (PLS-DA) in lipid range of 2900-2800 cm^-1 reached 92.85% and 95.23% respectively. It is shown that FTIR spectroscopy might be developed as an effective method for the diagnosis of liver cancer.

The diet of early birds based on modern and fossil evidence and a new framework for its reconstruction

Birds are some of the most diverse organisms on Earth, with species inhabiting a wide variety of niches across every major biome. As such, birds are vital to our understanding of modern ecosystems. Unfortunately, our understanding of the evolutionary history of modern ecosystems is hampered by knowledge gaps in the origin of modern bird diversity and ecosystem ecology. A crucial part of addressing these shortcomings is improving our understanding of the earliest birds, the non-avian avialans (i.e. non-crown birds), particularly of their diet. The diet of non-avian avialans has been a matter of debate, in large part because of the ambiguous qualitative approaches that have been used to reconstruct it. Here we review methods for determining diet in modern and fossil avians (i.e. crown birds) as well as non-avian theropods, and comment on their usefulness when applied to non-avian avialans. We use this to propose a set of comparable, quantitative approaches to ascertain fossil bird diet and on this basis provide a consensus of what we currently know about fossil bird diet. While no single approach can precisely predict diet in birds, each can exclude some diets and narrow the dietary possibilities. We recommend combining (i) dental microwear, (ii) landmark-based muscular reconstruction, (iii) stable isotope geochemistry, (iv) body mass estimations, (v) traditional and/or geometric morphometric analysis, (vi) lever modelling, and (vii) finite element analysis to reconstruct fossil bird diet accurately. Our review provides specific methodologies to implement each approach and discusses complications future researchers should keep in mind. We note that current forms of assessment of dental mesowear, skull traditional morphometrics, geometric morphometrics, and certain stable isotope systems have yet to be proven effective at discerning fossil bird diet. On this basis we report the current state of knowledge of non-avian avialan diet which remains very incomplete. The ancestral dietary condition in non-avian avialans remains unclear due to scarce data and contradictory evidence in Archaeopteryx. Among early non-avian pygostylians, Confuciusornis has finite element analysis and mechanical advantage evidence pointing to herbivory, whilst Sapeornis only has mechanical advantage evidence indicating granivory, agreeing with fossilised ingested material known for this taxon. The enantiornithine ornithothoracine Shenqiornis has mechanical advantage and pedal morphometric evidence pointing to carnivory. In the hongshanornithid ornithuromorph Hongshanornis only mechanical advantage evidence indicates granivory, but this agrees with evidence of gastrolith ingestion in this taxon. Mechanical advantage and ingested fish support carnivory in the songlingornithid ornithuromorph Yanornis. Due to the sparsity of robust dietary assignments, no clear trends in non-avian avialan dietary evolution have yet emerged. Dietary diversity seems to increase through time, but this is a preservational bias associated with a predominance of data from the Early Cretaceous Jehol Lagerstätte. With this new framework and our synthesis of the current knowledge of non-avian avialan diet, we expect dietary knowledge and evolutionary trends to become much clearer in the coming years, especially as fossils from other locations and climates are found. This will allow for a deeper and more robust understanding of the role birds played in Mesozoic ecosystems and how this developed into their pivotal role in modern ecosystems.

Systematic changes of bone hydroxyapatite along a charring temperature gradient: An integrative study with dissolution behavior

The applicability of bone char as a long-term phosphorus nutrient source was assessed by integrating their mineral transformation and physicochemical properties with their dissolution behavior. We have explored synchrotron-based spectroscopic and imaging techniques (FTIR, XRD, and TXM) to investigate the physicochemical changes of bone and bone char along a charring temperature gradient (300-1200 °C) and used a lab incubation experiment to study their dissolution behaviors in solutions of different pH (4, 6, and 6.9). The thermal decomposition of inorganic carbonate (CO₃^2-) and the loss of organic components rendered a crystallographic rearrangement (blueshift of the PO₄^3- peak) and mineral transformation with increasing temperatures. The mineral transformation from B-type to AB- and A-type carbonate substitution occurred mainly at <700 °C, while the transformation from carbonated hydroxyapatite (CHAp) to more mineralogically and chemically stable HAp occurred at >800 °C. The loss of inorganic carbonate and the increase of structural OH^- with increasing temperatures explained the change of pH buffering capacity and increase of pH and their dissolution behaviors. The higher peak area ratios of phosphate to carbonate and phosphate to amide I band with increasing temperatures corroborated the higher stability and resistivity to acidic dissolution by bone chars made at higher temperatures. Our findings suggest that bone char made at low to intermediate temperatures can be a substantial source of phosphorus for soil fertility via waste management and recycling. The bone char made at 500 °C exhibited a high pH buffering capacity in acidic and near-neutral solutions. The 700 °C bone char was proposed as a suitable liming agent for raising the soil pH and abating soil acidity. Our study has underpinned the systematic changes of bone char and interlinked the charring effect with their dissolution behavior, providing a scientific base for understanding the applicability of different bone chars as suitable P-fertilizers.

Comparison of different protocols for demineralization of cortical bone

Bone is a biological composite material consisting of two main components: collagen and mineral. Collagen is the most abundant protein in vertebrates, which makes it of high clinical and scientific interest. In this paper, we compare the composition and structure of cortical bone demineralized using several protocols: ethylene-diamine-tetraacetic acid (EDTA), formic acid (CH₂O₂), hydrochloric acid (HCl), and HCl/EDTA mixture. The efficiencies of these four agents were investigated by assessing the remaining mineral quantities and collagen integrity with various experimental techniques. Raman spectroscopy results show that the bone demineralized by the CH₂O₂ agent has highest collagen quality parameter. The HCl/EDTA mixture removes the most mineral, but it affects the collagen secondary structure as amide II bands are shifted as observed by Fourier transform infrared spectroscopy. Thermogravimetric analysis reveals that HCl and EDTA are most effective in removing the mineral with bulk measurements. In summary, we conclude that HCl best demineralizes bone, leaving the well-preserved collagen structure in the shortest time. These findings guide on the best demineralization protocol to obtain high-quality collagen from bone for clinical and scientific applications.

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.

Recent developments in using the molecular decay dating method: a review

The dating of organic findings is a fundamental task for many scientific fields. Radiocarbon dating is currently the most commonly used method. For wood, dendrochronology is another state‐of‐the‐art method. Both methods suffer from systematic restrictions, leading to samples that have not yet been able to be dated. Molecular changes over time are reported for many materials under different preservation conditions. Many of them are intrinsically monotonous. These monotonous molecular decay (MD) patterns can be understood as clocks that start at the time when a given molecule was formed. Factors that influence these clocks include input material composition and preservation conditions. Different wood species, degrees of pyrolysis, and pretreatments lead to different prediction models. Preservation conditions might change the speed of a given clock and lead to different prediction models. Currently published models for predicting the age of wood, paper, and parchment depend on infrared spectroscopy. In contrast to radiocarbon dating, dating via MD does not comprise a single methodology. Some clocks may deliver less precise results than the others. Ultimately, developing a completely different, new dating strategy‐such as MD dating–will help to bring to light a treasure trove of information hidden in the darkness of organic findings.

Linking structural and compositional changes in archaeological human bone collagen: an FTIR-ATR approach

Collagen is the main structural and most abundant protein in the human body, and it is routinely extracted and analysed in scientific archaeology. Its degree of preservation is, therefore, crucial and several approaches are used to determine it. Spectroscopic techniques provide a cost-effective, non-destructive method to investigate the molecular structure, especially when combined with multivariate statistics (chemometric approach). In this study, we used FTIR-ATR spectroscopy to characterise collagen extracted from skeletons recovered from necropoleis in NW Spain spanning from the Bronze Age to eighteenth century AD. Principal components analysis was performed on a selection of bands and structural equation models (SEM) were developed to relate the collagen quality indicators to collagen structural change. Four principal components represented: (i) Cp1, transformations of the backbone protein with a residual increase in proteoglycans; (ii) Cp2, protein transformations not accompanied by changes in proteoglycans abundance; (iii) Cp3, variations in aliphatic side chains and (iv) Cp4, absorption of the OH of carbohydrates and amide. Highly explanatory SEM models were obtained for the traditional collagen quality indicators (collagen yield, C, N, C:N), but no relationship was found between quality and δ¹³C and δ¹⁵N ratios. The observed decrease in C and N content and increase in C:N ratios is controlled by the degradation of protein backbone components and the relative preservation of carbon-rich compounds, proteoglycans and, to a lesser extent, aliphatic moieties. Our results suggest that FTIR-ATR is an ideal technique for collagen characterization/pre-screening for palaeodiet, mobility and radiocarbon research.

Assessment of different screening methods for selecting palaeontological bone samples for peptide sequencing

Ancient proteomics is being applied to samples dating further and further back in time, with many palaeontological specimens providing protein sequence data for phylogenetic analysis as well as protein degradation studies. However, fossils are a precious material and proteomic analysis is destructive and costly. In this paper we consider three different techniques (ATR-FTIR, MALDI-ToF MS and chiral AA analysis) to screen fossil material for potential protein preservation, aiming to maximise the proteomic information recovered and saving costly time consuming analyses which may produce low quality results. It was found that splitting factor and C/P indices from ATR-FTIR were not a reliable indicator of protein survival as they are confounded by secondary mineralisation of the fossil material. Both MALDI-ToF MS and chiral AA analysis results were able to successfully identify samples with surviving proteins, and it is suggested that one or both of these analyses be used for screening palaeontological specimens. SIGNIFICANCE: This study has shown both chiral amino acid analysis and MALDI-ToF MS are reliable screening methods for predicting protein survival in fossils. Both these methods are quick, cheap, minimally destructive (1 mg and 15 mg respectively) and can provide crucial additional information about the endogeneity of the surviving proteins. It is hoped that the use of these screening methods will encourage the examination of a wide range of palaeontological specimens for potential proteomic analysis. This in turn will give us a better understanding of protein survival far back in time and under different environmental conditions.

In-place molecular preservation of cellulose in 5,000-year-old archaeological textiles

The understanding of fossilization mechanisms at the nanoscale remains extremely challenging despite its fundamental interest and its implications for paleontology, archaeology, geoscience, and environmental and material sciences. The mineralization mechanism by which cellulosic, keratinous, and silk tissues fossilize in the vicinity of archaeological metal artifacts offers the most exquisite preservation through a mechanism unexplored on the nanoscale. It is at the center of the vast majority of ancient textiles preserved under nonextreme conditions, known through extremely valuable fragments. Here we show the reconstruction of the nanoscale mechanism leading to the preservation of an exceptional collection of ancient cellulosic textiles recovered in the ancient Near East (4,000 to 5,000 years ago). We demonstrate that even the most mineralized fibers, which contain inorganic compounds throughout their histology, enclose preserved cellulosic remains in place. We evidence a process that combines the three steps of water transport of biocidal metal cations and soil solutes, degradation and loss of crystallinity of cellulosic polysaccharides, and silicification.

Exceptionally preserved 'skin' in an Early Cretaceous fish from Colombia

Studies of soft tissue, cells and original biomolecular constituents preserved in fossil vertebrates have increased greatly in recent years. Here we report preservation of 'skin' with chemical and molecular characterization from a three-dimensionally preserved caudal portion of an aspidorhynchid Cretaceous fish from the equatorial Barremian of Colombia, increasing the number of localities for which exceptional preservation is known. We applied several analytical techniques including SEM-EDS, FTIR and ToF-SIMS to characterize the micromorphology and molecular and elemental composition of this fossil. Here, we show that the fossilized 'skin' exhibits similarities with those from extant fish, including the wrinkles after suffering compression stress and flexibility, as well as architectural and tissue aspects of the two main layers (epidermis and dermis). This similarity extends also to the molecular level, with the demonstrated preservation of potential residues of original proteins not consistent with a bacterial source. Our results show a potential preservation mechanism where scales may have acted as an external barrier and together with an internal phosphate layer resulting from the degradation of the dermis itself creating an encapsulated environment for the integument.

Chitosan-glucan complex hollow fibers reinforced collagen wound dressing embedded with aloe vera. II. Multifunctional properties to promote cutaneous wound healing

This study presents an innovative multifunctional system in fabricating new functional wound dressing (FWD) products that could be used for skin regeneration, especially in cases of infected chronic wounds and ulcers. The innovation is based on the extraction, characterization, and application of collagen (CO)/chitosan-glucan complex hollow fibers (CSGC)/aloe vera (AV) as a novel FWS. For the first time, specific hollow fibers were extracted with controlled inner (500-900 nm)/outer (2-3 µm) diameters from mycelium of Schizophyllum commune. Further on, research and evaluation of morphology, hydrolytic stability, and swelling characteristics of CO/CSGC@AV were carried out. The obtained FWS showed high hydrolytic stability with enhanced swelling characteristics compared to native collagen. The hemostatic effect of FWS increased significantly in the presence of CSGC, compared to native CO and displayed excellent biocompatibility which was tested by using normal human dermal fibroblast (NHDF). The FWS showed high antibacterial activity against different types of bacteria (positive/negative grams). From in vivo measurements, the novel FWS increased the percentage of wound closure after one week of treatment. All these results imply that the new CO/CSGC@AV-FWD has the potential for clinical skin regeneration and applying for controlled drug release.

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.

Fluoridation of a lizard bone embedded in Dominican amber suggests open-system behavior

Vertebrate fossils embedded in amber represent a particularly valuable paleobiological record as amber is supposed to be a barrier to the environment, precluding significant alteration of the animals' body over geological time. The mode and processes of amber preservation are still under debate, and it is questionable to what extent original material may be preserved. Due to their high value, vertebrates in amber have never been examined with analytical methods, which means that the composition of bone tissue in amber is unknown. Here, we report our results of a study on a left forelimb from a fossil Anolis sp. indet. (Squamata) that was fully embedded in Miocene Dominican amber. Our results show a transformation of the bioapatite to fluorapatite associated with a severe alteration of the collagen phase and the formation of an unidentified carbonate. These findings argue for a poor survival potential of macromolecules in Dominican amber fossils.

Molecular identification of fungi microfossils in a Neoproterozoic shale rock

Precambrian fossils of fungi are sparse, and the knowledge of their early evolution and the role they played in the colonization of land surface are limited. Here, we report the discovery of fungi fossils in a 810 to 715 million year old dolomitic shale from the Mbuji-Mayi Supergroup, Democratic Republic of Congo. Syngenetically preserved in a transitional, subaerially exposed paleoenvironment, these carbonaceous filaments of ~5 μm in width exhibit low-frequency septation (pseudosepta) and high-angle branching that can form dense interconnected mycelium-like structures. Using an array of microscopic (SEM, TEM, and confocal laser scanning fluorescence microscopy) and spectroscopic techniques (Raman, FTIR, and XANES), we demonstrated the presence of vestigial chitin in these fossil filaments and document the eukaryotic nature of their precursor. Based on those combined evidences, these fossil filaments and mycelium-like structures are identified as remnants of fungal networks and represent the oldest, molecularly identified remains of Fungi.

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.

Mechanisms of soft tissue and protein preservation in Tyrannosaurus rex

The idea that original soft tissue structures and the native structural proteins comprising them can persist across geological time is controversial, in part because rigorous and testable mechanisms that can occur under natural conditions, resulting in such preservation, have not been well defined. Here, we evaluate two non-enzymatic structural protein crosslinking mechanisms, Fenton chemistry and glycation, for their possible contribution to the preservation of blood vessel structures recovered from the cortical bone of a Tyrannosaurus rex (USNM 555000 [formerly, MOR 555]). We demonstrate the endogeneity of the fossil vessel tissues, as well as the presence of type I collagen in the outermost vessel layers, using imaging, diffraction, spectroscopy, and immunohistochemistry. Then, we use data derived from synchrotron FTIR studies of the T. rex vessels to analyse their crosslink character, with comparison against two non-enzymatic Fenton chemistry- and glycation-treated extant chicken samples. We also provide supporting X-ray microprobe analyses of the chemical state of these fossil tissues to support our conclusion that non-enzymatic crosslinking pathways likely contributed to stabilizing, and thus preserving, these T. rex vessels. Finally, we propose that these stabilizing crosslinks could play a crucial role in the preservation of other microvascular tissues in skeletal elements from the Mesozoic.

Highly fluorescent Ti3C2 MXene quantum dots for macrophage labeling and Cu2+ ion sensing

Quantum dots, derived from two-dimensional (2D) materials, have shown promise in bioimaging, sensing and photothermal applications, and in white light emitting devices (WLEDs). Herein, nitrogen and phosphorus functionalized Ti3C2 MXene based quantum dots (N,P-MQDs) were successfully prepared through a top-bottom hydrothermal method. This type of photoluminescent quantum dots has realized green fluorescence for the first time at around 560 nm with a photoluminescence quantum yield (PLQY) of 20.1%, the highest ever reported; meanwhile, it also exhibits excellent photostability and pH resistance capacities. Comprehensive characterization and well-resolved density functional theory (DFT) calculation were implemented to determine the mechanism of fluorescence shift and enhancement. Furthermore, the N,P-MQDs have been proved to efficiently act as fluorescent probes for macrophage labeling. In addition, the high sensitivity of the N,P-MQDs toward Cu2+ ions made them a low cost, sensitive, environment-friendly, and label-free fluorescence platform for Cu2+ detection. The outstanding performance of Ti3C2 MXene based quantum dots has demonstrated their great potential to be used as promising fluorescent probes in the fields of biological imaging, optical sensing, photoelectric conversion, etc.

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.

Different Molecular Interaction between Collagen and α- or β-Chitin in Mechanically Improved Electrospun Composite

Although collagens from vertebrates are mainly used in regenerative medicine, the most elusive issue in the collagen-based biomedical scaffolds is its insufficient mechanical strength. To solve this problem, electrospun collagen composites with chitins were prepared and molecular interactions which are the cause of the mechanical improvement in the composites were investigated by two-dimensional correlation spectroscopy (2DCOS). The electrospun collagen is composed of two kinds of polymorphs, α- and β-chitin, showing different mechanical enhancement and molecular interactions due to different inherent configurations in the crystal structure, resulting in solvent and polymer susceptibility. The collagen/α-chitin has two distinctive phases in the composite, but β-chitin composite has a relatively homogeneous phase. The β-chitin composite showed better tensile strength with ~41% and ~14% higher strength compared to collagen and α-chitin composites, respectively, due to a favorable secondary interaction, i.e., inter- rather than intra-molecular hydrogen bonds. The revealed molecular interaction indicates that β-chitin prefers to form inter-molecular hydrogen bonds with collagen by rearranging their uncrumpled crystalline regions, unlike α-chitin.

Fossilised Biomolecules and Biomarkers in Carbonate Concretions from Konservat-Lagerstätten

In the vast majority of fossils, the organic matter is degraded with only an impression or cast of the organism remaining. In rare cases, ideal burial conditions result in a rapid fossilisation with an exceptional preservation of soft tissues and occasionally organic matter. Such deposits are known as Lagerstätten and have been found throughout the geological record. Exceptional preservation is often associated with finely crystalline quartz (e.g., cherts), fine sediments (e.g., muds) or volcanic ashes. Other mechanisms include burial in anoxic/euxinic sediments and in the absence of turbidity or scavenging. Exceptional preservation can also occur when an organism is encapsulated in carbonate cement, forming a concretion. This mechanism involves complex microbial processes, resulting in a supersaturation in carbonate, with microbial sulfate reduction and methane cycling the most commonly suggested processes. In addition, conditions of photic zone euxinia are often found to occur during concretion formation in marine environments. Concretions are ideal for the study of ancient and long-extinct organisms, through both imaging techniques and biomolecular approaches. These studies have provided valuable insights into the evolution of organisms and their environments through the Phanerozoic and have contributed to increasing interest in fields including chemotaxonomy, palaeobiology, palaeoecology and palaeophysiology.

The slow rise of complex life as revealed through biomarker genetics

Organic molecules preserved in ancient rocks can function as 'biomarkers', providing a unique window into the evolution of life. While biomarkers demonstrate intriguing patterns through the Neoproterozoic, it can be difficult to constrain particular biomarkers to specific organisms. The goal of the present paper is to demonstrate the utility of biomarkers when we focus less on which organisms produce them, and more on how their underlying genetic pathways evolved. Using this approach, it becomes clear that there are discrepancies between the biomarker, fossil, and molecular records. However, these discrepancies probably represent long time periods between the diversification of eukaryotic groups through the Neoproterozoic and their eventual rise to ecological significance. This 'long fuse' hypothesis contrasts with the adaptive radiations often associated with the development of complex life.

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.

Second-harmonic generation imaging of collagen in ancient bone

Second-harmonic generation imaging (SHG) captures triple helical collagen molecules near tissue surfaces. Biomedical research routinely utilizes various imaging software packages to quantify SHG signals for collagen content and distribution estimates in modern tissue samples including bone. For the first time using SHG, samples of modern, medieval, and ice age bones were imaged to test the applicability of SHG to ancient bone from a variety of ages, settings, and taxa. Four independent techniques including Raman spectroscopy, FTIR spectroscopy, radiocarbon dating protocols, and mass spectrometry-based protein sequencing, confirm the presence of protein, consistent with the hypothesis that SHG imaging detects ancient bone collagen. These results suggest that future studies have the potential to use SHG imaging to provide new insights into the composition of ancient bone, to characterize ancient bone disorders, to investigate collagen preservation within and between various taxa, and to monitor collagen decay regimes in different depositional environments.

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Second-Harmonic Generation (SHG) confocal laser scanning microscopy is used to investigate collagen remnants in ancient bone.

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Four independent techniques confirm the presence of collagen remnants in ancient bone samples with SHG-detected collagen.

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SHG imaging can visualise collagen remnants in ancient bone of various taxa, ages, and settings.

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.

Inhabited or Uninhabited? Pitfalls in the Interpretation of Possible Chemical Signatures of Extraterrestrial Life

The "Rare Earth" hypothesis-put forward by Ward and Brownlee in their 2000 book of the same title-states that prokaryote-type organisms may be common in the universe but animals and higher plants are exceedingly rare. If this idea is correct, the search for extraterrestrial life is essentially the search for microorganisms. Various indicators may be used to detect extant or extinct microbial life beyond Earth. Among them are chemical biosignatures, such as biomolecules and stable isotope ratios. The present minireview focuses on the major problems associated with the identification of chemical biosignatures. Two main types of misinterpretation are distinguished, namely false positive and false negative results. The former can be caused by terrestrial biogenic contaminants or by abiotic products. Terrestrial contamination is a common problem in space missions that search for biosignatures on other planets and moons. Abiotic organics can lead to false positive results if erroneously interpreted as biomolecules, but also to false negatives, for example when an abiotic source obscures a less productive biological one. In principle, all types of putative chemical biosignatures are prone to misinterpretation. Some, however, are more reliable ("stronger") than others. These include: (i) homochiral polymers of defined length and sequence, comparable to proteins and polynucleotides; (ii) enantiopure compounds; (iii) the existence of only a subset of molecules when abiotic syntheses would produce a continuous range of molecules; the proteinogenic amino acids constitute such a subset. These considerations are particularly important for life detection missions to solar system bodies such as Mars, Europa, and Enceladus.