Pheomelanin pigment remnants mapped in fossils of an extinct mammal

Nanoscopic imaging of ancient protein and vasculature offers insight into soft tissue and biomolecule fossilization

Fossil bones have been studied by paleontologists for centuries. Despite this, empirical knowledge regarding the progression of biomolecular (soft) tissue diagenesis within ancient bone is limited; this is particularly the case for specimens spanning Pleistocene directly into pre-Ice Age strata. A nanoscopic approach is reported herein that facilitates direct imaging, and thus empirical observation, of soft tissue preservation state. Presented data include the first extensive nanoscopic (up to 150,000× magnification), three-dimensional (3D) images of ancient bone protein and vasculature; chemical signals consistent with collagen protein and membrane lipids, respectively, are also localized to these structures. These findings support the analyzed permafrost bones are not fully fossilized but rather represent subfossil bone tissue as they preserve an underlying collagen framework. Extension of these methods to specimens spanning the geologic record will help reveal changes biomolecular tissues undergo during fossilization and is a potential proxy approach for screening specimen suitability for molecular sequencing.

Bio-molecular analyses enable new insights into the taphonomy of feathers

Exceptionally preserved feathers from the Mesozoic era have provided valuable insights into the early evolution of feathers and enabled color reconstruction of extinct dinosaurs, including early birds. Mounting chemical evidence for the two key components of feathers-keratins and melanins-in fossil feathers has demonstrated that exceptional preservation can be traced down to the molecular level. However, the chemical changes that keratin and eumelanin undergo during fossilization are still not fully understood, introducing uncertainty in the identification of these two molecules in fossil feathers. To address this issue, we need to examine their taphonomic process. In this study, we analyzed the structural and chemical composition of fossil feathers from the Jehol Biota and compared them with the structural and chemical changes observed in modern feathers during the process of biodegradation and thermal degradation, as well as the structural and chemical characteristics of a Cenozoic fossil feather. Our results suggest that the taphonomic process of feathers from the Cretaceous Jehol Biota is mainly controlled by the process of thermal degradation. The Cretaceous fossil feathers studied exhibited minimal keratin preservation but retained strong melanin signals, attributed to melanin's higher thermal stability. Low-maturity carbonaceous fossils can indeed preserve biosignals, especially signals from molecules with high resistance to thermal degradation. These findings provide clues about the preservation potential of keratin and melanin, and serve as a reference for searching for those two biomolecules in different geological periods and environments.

A new non-destructive method to decipher the origin of organic matter in fossils using Raman spectroscopy

Ancient biomolecules provide a unique perspective on the past but are underutilized in paleontology because of challenges in interpreting the chemistry of fossils. Most organically preserved soft tissues in fossils have been altered by thermal maturation during the fossilization process, obscuring original chemistry. Here, we use a comprehensive program of thermal maturation experiments on soft tissues from diverse extant organisms to systematically test whether thermally altered biosignatures can be discriminated using Raman spectroscopy. All experimentally matured samples show chemical signatures that are superficially similar. Comparative analysis of Raman spectra following peak deconvolution, however, reveals strong tissue-specific signals. Application of this approach to fossils from the Bolca (49 Ma) and Libros (10 Ma) Konservat-Lagerstätten successfully discriminates fossil vertebrate soft tissue from that of fossil plants. Critically, our data confirm that a robust interrogation of Raman spectra coupled with multivariate analysis is a powerful tool to shed light on the taxonomic origins of thermally matured fossil soft tissues.

Reduction of oxidative rancidification of fungal melanin-coated films in pork lard preservation in trading

Storage of meat has always been challenging due to its deterioration caused by oxidative rancidity and microbial activity, especially in trading. The melanin-coated film acts as a potent antioxidant, prevents the oxidation of fatty acids, and neutralizes the reactive oxygen species (ROS) helping to withstand or perpetuate the oxidative stress of meat. This study emphasizes the production of fungal melanin extracted from Curvularia lunata and the preparation of two different melanin film combinations of gelatin/melanin and agar/melanin at 0.1% and 0.5% formulation for rancidity stability of coated pork lard. Interpretations revealed the delayed rancidity in both peroxide and acid values with 5.76% in 0.5% agar-coated melanin up to the 11th day which was supported by arithmetical analysis showing p < 0.05 are statistically significant. Further, upon testing the brine shrimp assay for melanin toxicity, 7% were in a mortal state at 1000 µg/mL concentration, considered zero lethality. This result implies that modified coatings, particularly when trading meats, that include fungal melanin can effectively prevent the oxidation of pork lard.

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

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

Melanin: insights into structure, analysis, and biological activities for future development

Melanin, a widely distributed pigment found in various organisms, possesses distinct structures that can be classified into five main types: eumelanin (found in animals and plants), pheomelanin (found in animals and plants), allomelanin (found in plants), neuromelanin (found in animals), and pyomelanin (found in fungi and bacteria). In this review, we present an overview of the structure and composition of melanin, as well as the various spectroscopic identification methods that can be used, such as Fourier transform infrared (FTIR) spectroscopy, electron spin resonance (ESR) spectroscopy, and thermogravimetric analysis (TGA). We also provide a summary of the extraction methods of melanin and its diverse biological activities, including antibacterial properties, anti-radiation effects, and photothermal effects. The current state of research on natural melanin and its potential for further development is discussed. In particular, the review provides a comprehensive summary of the analysis methods used to determine melanin species, offering valuable insights and references for future research. Overall, this review aims to provide a thorough understanding of the concept and classification of melanin, its structure, physicochemical properties, and structural identification methods, as well as its various applications in the field of biology.

Melanin biopolymers from microbial world with future perspectives-a review

Melanin is an amorphous polymer made of heterogeneous functional groups synthesized by diverse organisms including fungi, bacteria, animals, and plants. It was widely acknowledged for its biological processes and its key role in the protection of organisms from environmental stress. Recently, melanin clutches attention in the field of nanobiotechnology, drug delivery, organic semiconductors and bioelectronics, environmental bioremediation, photoprotection, etc., Furthermore, melanin from natural sources like microbial community shows antimicrobial, fighting cancer, radical scavenging, cosmeceuticals, and many therapeutic areas as well. Though the multipotentiality nature of melanin has been put forth, real-world applications still flag fall behind, which might be anticipated to the inadequate and high price essence of natural melanin. However, current bioprocess technologies have paved for the large-scale or industrial production of microbial melanin, which could help in the replacement of synthetic melanin. Thus, this review emphasizes the various sources for melanin, i.e., types-based on its pathways and its chemical structures, functional efficiency, physical properties, and conventional and modern methods of both extraction and characterization. Moreover, an outlook on how it works in the field of medicine, bioremediation, and other related areas provides perspectives on the complete exploitation of melanin in practical applications of medicine and the environment.

Recent Advances in Characterization of Melanin Pigments in Biological Samples

The melanin pigments eumelanin (EM) and pheomelanin (PM), which are dark brown to black and yellow to reddish-brown, respectively, are widely found among vertebrates. They are produced in melanocytes in the epidermis, hair follicles, the choroid, the iris, the inner ear, and other tissues. The diversity of colors in animals is mainly caused by the quantity and quality of their melanin, such as by the ratios of EM versus PM. We have developed micro-analytical methods to simultaneously measure EM and PM and used these to study the biochemical and genetic fundamentals of pigmentation. The photoreactivity of melanin has become a major focus of research because of the postulated relevance of EM and PM for the risk of UVA-induced melanoma. Our biochemical methods have found application in many clinical studies on genetic conditions associated with alterations in pigmentation. Recently, besides chemical degradative methods, other methods have been developed for the characterization of melanin, and these are also discussed here.

Trace Impurities Identified as Forensic Signatures in CMX-5 Fuel Pellets Using X-ray Spectroscopic Techniques

Small-particle analysis is a highly promising emerging forensic tool for analysis of interdicted special nuclear materials. Integration of microstructural, morphological, compositional, and molecular impurity signatures could provide significant advancements in forensic capabilities. We have applied rapid, high-sensitivity, hard X-ray synchrotron chemical imaging to analyze impurity signatures in two differently fabricated fuel pellets from the 5th Collaborative Materials Exercise (CMX5) of the IAEA Nuclear Forensics International Working Group. The spatial distributions, chemical compositions, and morphological and molecular characteristics of impurities were evaluated using X-ray absorption near-edge structure (XANES) and X-ray fluorescence chemical imaging to discover principal impurities, their granularity, particle sizes, modes of occurrence (distinct grains vs incorporation in the UO₂ lattice), and sources and mechanisms of incorporation. Differences in UO_2+x stoichiometry were detected at the microscale in nominally identical UO₂ ceramics (CMX5-A and CMX5-B), implying the presence of multiple UO₂ host phases with characteristic microstructures and feedstock compositions. Al, Fe, Ni, W, and Zr impurities and integrated impurity signature analysis identified distinctly different pellet synthesis and processing methods. For example, two different Al, W, and Zr populations in the CMX5-B sample indicated a more complex processing history than the CMX5-A sample. K-edge XANES measurements reveal both metallic and oxide forms of Fe and Ni but with different proportions between each sample. Altogether, these observations suggest multiple sources of impurities, including fabrication (e.g., force-sieving) and feedstock (mineral oxides). This study demonstrates the potential of synchrotron techniques to integrate different signatures across length scales (angstrom to micrometer) to detect and differentiate between contrasting UO₂ fuel fabrication techniques.

The mucin protein MUCL1 regulates melanogenesis and melanoma genes in a manner dependent on threonine content

Background

The regulation of melanogenesis has been investigated as a long‐held aim for pharmaceutical manipulations with denotations for malignancy of melanoma. Mucins have a protective function in epithelial organs; however, in the most outer organ, the skin, the role of mucins has not been studied enough.

Objectives

Our initial hypothesis developed from the identification of correlations between pigmentation and expressions of skin mucins, particularly those existing in skin tissue. We aimed to investigate the action of mucins in human melanocytic cells.

Materials and methods

The expression of mucin proteins in human skin was investigated using microarray data from the Human Protein Atlas consortium (HPA) and the Genotype‐Tissue Expression consortium (GTEx) database. Mucin expression was measured at RNA and protein levels in melanoma cells. The findings were further validated and confirmed by analysis of independent experiments.

Results

We found that the several mucin proteins showed expression in human skin cells and among these, mucin‐like protein 1 (MUCL1) showed the highest expression and also clear negative correlation with melanogenesis in epidermal melanocytes. We confirmed the correlations between melanogenesis and MUCL1 by revealing negative correlations in melanocytes with different melanin production, resulting from increased composition of threonine, mucin‐conforming amino acid, and increased autophagy‐related forkhead‐box O signalling. Furthermore, threonine itself affects melanogenesis and metastatic activity in melanoma cells.

Conclusions

We identified a significant association between MUCL1 and threonine with melanogenesis and metastasis‐related genes in melanoma cells. Our results define a novel mechanism of mucin regulation, suggesting diagnostic and preventive roles of MUCL1 in cutaneous melanoma.

Whatis already known about this topic?

Despite considerable advances in radioactive therapeutics or chemotherapeutic approaches for the treatment of abnormal melanogenesis, there are still many caveats to delivery, effectiveness and safety, thus leaving a necessity for more immediate pharmaceutical targets.

Mucins have protective and chemical barrier functions in epithelial organs; however, in the skin, mucin has scarce expression and is known only as a diagnostic aid in skin disorders such as mucinosis.

Whatdoes this study add?

We provide detailed analysis demonstrating the potential of mucin‐like protein 1 (MUCL1), which showed negative correlations in melanocytes with different melanin production, resulting from increased composition of threonine and increased autophagy‐related forkhead‐box O signalling in epidermal melanocytes and melanoma cells.

We established that through an alternative pathway for MUCL1 biosynthesis, threonine supplementation recovers MUCL1 levels in melanoma. Changes, brought on by the essential amino acid threonine, resulted in substantial modulations in melanogenesis and reduced metastasis‐related genes.

Whatis the translational message?

This study demonstrates for the first time that the mucin protein of skin cells is compounded by distorted mucin homeostasis, with major effects on melanogenesis and metastasis‐related genes in melanoma.

We anticipate that these novel findings will be of keen interest to the community of scientists and medical practitioners examining skin dysfunction.

Linked Comment: C. Casalou and D.J. Tobin. Br J Dermatol 2022; 186:388–389.

Plain language summary available online

Unraveling the Structure and Function of Melanin through Synthesis

Melanin is ubiquitous in living organisms across different biological kingdoms of life, making it an important, natural biomaterial. Its presence in nature from microorganisms to higher animals and plants is attributed to the many functions of melanin, including pigmentation, radical scavenging, radiation protection, and thermal regulation. Generally, melanin is classified into five types-eumelanin, pheomelanin, neuromelanin, allomelanin, and pyomelanin-based on the various chemical precursors used in their biosynthesis. Despite its long history of study, the exact chemical makeup of melanin remains unclear, and it moreover has an inherent diversity and complexity of chemical structure, likely including many functions and properties that remain to be identified. Synthetic mimics have begun to play a broader role in unraveling structure and function relationships of natural melanins. In the past decade, polydopamine, which has served as the conventional form of synthetic eumelanin, has dominated the literature on melanin-based materials, while the synthetic analogues of other melanins have received far less attention. In this perspective, we will discuss the synthesis of melanin materials with a special focus beyond polydopamine. We will emphasize efforts to elucidate biosynthetic pathways and structural characterization approaches that can be harnessed to interrogate specific structure-function relationships, including electron paramagnetic resonance (EPR) and solid-state nuclear magnetic resonance (ssNMR) spectroscopy. We believe that this timely Perspective will introduce this class of biopolymer to the broader chemistry community, where we hope to stimulate new opportunities in novel, melanin-based poly-functional synthetic materials.

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

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

Transcriptomic and genomic changes associated with radioadaptation in Exophiala dermatitidis

Melanized fungi have been isolated from some of the harshest radioactive environments, and their ability to thrive in these locations is in part due to the pigment melanin. Melanin imparts a selective advantage to fungi by providing a physical shield, a chemical shield, and possibly a signaling mechanism. In previous work we demonstrated that protracted exposure of the melanized yeast Exophiala dermatitidis to mixed alpha-, beta-, and gamma-emitting radiation resulted in an adapted strain able to mount a unique response to ionizing radiation in the environment in a melanin-dependent fashion. By exploring the genome and transcriptome of this adapted melanized strain relative to a non-irradiated control we determined the altered response was transcriptomic in nature, as whole genome sequencing revealed limited variation. Transcriptomic analysis indicated that of the adapted isolates analyzed, two lineages existed: one like the naïve, non-adapted strain, and one with a unique transcriptomic signature that exhibited downregulation of metabolic processes, and upregulation of translation-associated genes. Analysis of differential gene expression in the adapted strain showed an overlap in response between the control conditions and reactive oxygen species conditions, whereas exposure to an alpha particle source resulted in a robust downregulation of metabolic processes and upregulation of DNA replication and repair genes, and RNA metabolic processes. This suggest previous exposure to radiation primes the fungus to respond to subsequent exposures in a unique way. By exploring this unique response, we have expanded our knowledge of how melanized fungi interact with and respond to ionizing radiation in their environment.

Hierarchical biota-level and taxonomic controls on the chemistry of fossil melanosomes revealed using synchrotron X-ray fluorescence

Fossil melanosomes, micron-sized granules rich in melanin in vivo, provide key information for investigations of the original coloration, taxonomy and internal anatomy of fossil vertebrates. Such studies rely, in part, on analysis of the inorganic chemistry of preserved melanosomes and an understanding of melanosome chemical taphonomy. The extent to which the preserved chemistry of fossil melanosomes is biased by biotic and abiotic factors is, however, unknown. Here we report the discovery of hierarchical controls on the inorganic chemistry of melanosomes from fossil vertebrates from nine biotas. The chemical data are dominated by a strong biota-level signal, indicating that the primary taphonomic control is the diagenetic history of the host sediment. This extrinsic control is superimposed by a biological, tissue-level control; tissue-specific chemical variation is most likely to survive in fossils where the inorganic chemistry of preserved melanosomes is distinct from that of the host sediment. Comparative analysis of our data for fossil and modern amphibians reveals that most fossil specimens show tissue-specific melanosome chemistries that differ from those of extant analogues, strongly suggesting alteration of original melanosome chemistry. Collectively, these findings form a predictive tool for the identification of fossil deposits with well-preserved melanosomes amenable to studies of fossil colour and anatomy.

Thymosin β4 Identified by Transcriptomic Analysis from HF Anagen to Telogen Promotes Proliferation of SHF-DPCs in Albas Cashmere Goat

Increasing cashmere yield is one of the important goals of cashmere goat breeding. To achieve this goal, we screened the key genes that can improve cashmere performance. In this study, we used the RNA raw datasets of the skin and dermal papilla cells of secondary hair follicle (SHF-DPCs) samples of hair follicle (HF) anagen and telogen of Albas cashmere goats and identified a set of significant differentially expressed genes (DEGs). To explore potential associations between gene sets and SHF growth features and to identify candidate genes, we detected functional enrichment and constructed protein-protein interaction (PPI) networks. Through comprehensive analysis, we selected Thymosin β4 (Tβ4), Rho GTPase activating protein 6 (ARHGAP6), ADAM metallopeptidase with thrombospondin type 1 motif 15, (ADAMTS15), Chordin (CHRD), and SPARC (Osteonectin), cwcv and kazal-like domains proteoglycan 1 (SPOCK1) as candidate genes. Gene set enrichment analysis (GSEA) for these genes revealed Tβ4 and ARHGAP6 have a close association with the growth and development of SHF-DPCs. However, the expression of Tβ4 in the anagen was higher than that in the telogen, so we finally chose Tβ4 as the ultimate research object. Overexpressing Tβ4 promoted and silencing Tβ4 inhibited the proliferation of SHF-DPCs. These findings suggest that Tβ4 can promote the growth and development of SHF-DPCs and indicate that this molecule may be a valuable target for increasing cashmere production.

Recent advances in amniote palaeocolour reconstruction and a framework for future research

Preserved melanin pigments have been discovered in fossilised integumentary appendages of several amniote lineages (fishes, frogs, snakes, marine reptiles, non-avialan dinosaurs, birds, and mammals) excavated from lagerstätten across the globe. Melanisation is a leading factor in organic integument preservation in these fossils. Melanin in extant vertebrates is typically stored in rod- to sphere-shaped, lysosome-derived, membrane-bound vesicles called melanosomes. Black, dark brown, and grey colours are produced by eumelanin, and reddish-brown colours are produced by phaeomelanin. Specific morphotypes and nanostructural arrangements of melanosomes and their relation to the keratin matrix in integumentary appendages create the so-called 'structural colours'. Reconstruction of colour patterns in ancient animals has opened an exciting new avenue for studying their life, behaviour and ecology. Modern relationships between the shape, arrangement, and size of avian melanosomes, melanin chemistry, and feather colour have been applied to reconstruct the hues and colour patterns of isolated feathers and plumages of the dinosaurs Anchiornis, Sinosauropteryx, and Microraptor in seminal papers that initiated the field of palaeocolour reconstruction. Since then, further research has identified countershading camouflage patterns, and informed subsequent predictions on the ecology and behaviour of these extinct animals. However, palaeocolour reconstruction remains a nascent field, and current approaches have considerable potential for further refinement, standardisation, and expansion. This includes detailed study of non-melanic pigments that might be preserved in fossilised integuments. A common issue among existing palaeocolour studies is the lack of contextualisation of different lines of evidence and the wide variety of techniques currently employed. To that end, this review focused on fossil amniotes: (i) produces an overarching framework that appropriately reconstructs palaeocolour by accounting for the chemical signatures of various pigments, morphology and local arrangement of pigment-bearing vesicles, pigment concentration, macroscopic colour patterns, and taphonomy; (ii) provides background context for the evolution of colour-producing mechanisms; and (iii) encourages future efforts in palaeocolour reconstructions particularly of less-studied groups such as non-dinosaur archosaurs and non-archosaur amniotes.

The Early Origin of Feathers

Feathers have long been regarded as the innovation that drove the success of birds. However, feathers have been reported from close dinosaurian relatives of birds, and now from ornithischian dinosaurs and pterosaurs, the cousins of dinosaurs. Incomplete preservation makes these reports controversial. If true, these findings shift the origin of feathers back 80 million years before the origin of birds. Gene regulatory networks show the deep homology of scales, feathers, and hairs. Hair and feathers likely evolved in the Early Triassic ancestors of mammals and birds, at a time when synapsids and archosaurs show independent evidence of higher metabolic rates (erect gait and endothermy), as part of a major resetting of terrestrial ecosystems following the devastating end-Permian mass extinction.