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In animals, pigments but also nanostructures determine skin coloration, and many shades are produced by combining both mechanisms. Recently, we discovered a new mechanism for blue coloration in the ribbontail stingray Taeniura lymma, a species with electric blue spots on its yellow-brown skin. Here, we characterize finescale differences in cell composition and architecture distinguishing blue from non-blue regions, the first description of elasmobranch chromatophores and the nanostructures responsible for the stingray’s novel structural blue, contrasting with other known mechanisms for making nature’s rarest color. In blue regions, the upper dermis comprised a layer of chromatophore units —iridophores and melanophores entwined in compact clusters framed by collagen bundles— this structural stability perhaps the root of the skin color’s robustness. Stingray iridophores were notably different from other vertebrate light-reflecting cells in having numerous fingerlike processes, which surrounded nearby melanophores like fists clenching a black stone. Iridophores contained spherical iridosomes enclosing guanine nanocrystals, suspended in a 3D quasi-order, linked by a cytoskeleton of intermediate filaments. We argue that intermediate filaments form a structural scaffold with a distinct optical role, providing the iridosome spacing critical to produce the blue color. In contrast, black-pigmented melanosomes within melanophores showed space-efficient packing, consistent with their hypothesized role as broadband-absorbers for enhancing blue color saturation. The chromatophore layer’s ultrastructure was similar in juvenile and adult animals, indicating that skin color and perhaps its ecological role are likely consistent through ontogeny. In non-blue areas, iridophores were replaced by pale cells, resembling iridophores in some morphological and nanoscale features, but lacking guanine crystals, suggesting that the cell types arise from a common progenitor cell. The particular cellular associations and structural interactions we demonstrate in stingray skin suggest that pigment cells induce differentiation in the progenitor cells of iridophores, and that some features driving color production may be shared with bony fishes, although the lineages diverged hundreds of millions of years ago and the iridophores themselves differ drastically.

The Devonian-Carboniferous (D-C; 359 Ma) boundary is marked by widespread deposition of organic-matter-rich black shales associated with the Hangenberg mass extinction event. The Exshaw Formation spans the D-C boundary in the Western Canada Sedimentary Basin (WCSB) and includes the basal Exshaw Shale deposited under broadly anoxic waters. The sediments at the base of the Exshaw Shale were deposited synchronously during a transgressive event across the WCSB, spanning the geographic variability of the basin. The variable Corg content of the shale was affected by local nutrient upwelling and paleotectonic features impacting water depth and circulation. To characterize the link between paleogeography and nutrient cycling, geographic (N = 20 locations) and stratigraphic (N = 6 locations) trends of δ13Corg and δ15Nbulk were examined throughout the WCSB, representing a range of depositional settings. The δ15Nbulk values range between 0.0 and 6.3‰ and δ13Corg from −29.5 to −26.8‰. Phytoplankton production in focused upwelling zones acquired a relatively 15N-depleted signature through isotopic fractionation during nutrient assimilation, and the residual nutrient pool was 15N-enriched. The advection of surface waters away from the location of upwelling supported additional phytoplankton growth and the deposition of sediments with higher δ15N values. The stratigraphic sections include black laminated and burrowed mudrock sequences that record changes in paleoredox conditions, water depth, and tectonism over time. Up-core from the base of the Exshaw, the Corg content decreases and simultaneously δ15Nbulk increases, suggesting a decrease in eutrophic conditions. Variable δ13Corg and δ15Nbulk trends demonstrate that there is no “type” isotopic profile spanning the D-C boundary in the WCSB.

Graduation rates are a key measure of the long-term efficacy of academic interventions. However, challenges to using traditional estimates of graduation rates for underrepresented students include inherently small sample sizes and high data requirements. Here, we show that a Markov model increases confidence and reduces biases in estimated graduation rates for underrepresented minority and first-generation students. We use a Learning Assistant program to demonstrate the Markov model’s strength for assessing program efficacy. We find that Learning Assistants in gateway science courses are associated with a 9% increase in the six-year graduation rate. These gains are larger for underrepresented minority (21%) and first-generation students (18%). Our results indicate that Learning Assistants can improve overall graduation rates and address inequalities in graduation rates for underrepresented students.

Crushing and eating hard prey (durophagy) is mechanically demanding. The cartilage jaws of durophagous stingrays are known to be reinforced relative to non-durophagous relatives, with a thickened external cortex of mineralized blocks (tesserae), reinforcing struts inside the jaw (trabeculae), and pavement-like dentition. These strategies for skeletal strengthening against durophagy, however, are largely understood only from myliobatiform stingrays, although a hard prey diet has evolved multiple times in batoid fishes (rays, skates, guitarfishes). We perform a quantitative analysis of micro-CT data, describing jaw strengthening mechanisms in Rhina ancylostoma (Bowmouth Guitarfish) and Rhynchobatus australiae (White-spotted Wedgefish), durophagous members of the Rhinopristiformes, the sister taxon to Myliobatiformes. Both species possess trabeculae, more numerous and densely packed in Rhina, albeit simpler structurally than those in stingrays like Aetobatus and Rhinoptera. Rhina and Rhynchobatus exhibit impressively thickened jaw cortices, often involving >10 tesseral layers, most pronounced in regions where dentition is thickest, particularly in Rhynchobatus. Age series of both species illustrate that tesserae increase in size during growth, with enlarged and irregular tesserae associated with the jaws’ oral surface in larger (older) individuals of both species, perhaps a feature of ageing. Unlike the flattened teeth of durophagous myliobatiform stingrays, both rhinopristiform species have oddly undulating dentitions, comprised of pebble-like teeth interlocked to form compound “meta-teeth” (large spheroidal structures involving multiple teeth). This is particularly striking in Rhina, where the upper/lower occlusal surfaces are mirrored undulations, fitting together like rounded woodworking finger-joints. Trabeculae were previously thought to have arisen twice independently in Batoidea; our results show they are more widespread among batoid groups than previously appreciated, albeit apparently absent in the phylogenetically basal Rajiformes. Comparisons with several other durophagous and non-durophagous species illustrate that batoid skeletal reinforcement architectures are modular: trabeculae can be variously oriented and are dominant in some species (e.g. Rhina, Aetobatus), whereas cortical thickening is more significant in others (e.g. Rhynchobatus), or both reinforcing features can be lacking (e.g. Raja, Urobatis). We discuss interactions and implications of character states, framing a classification scheme for exploring cartilage structure evolution in the cartilaginous fishes.

Abstract Tessellated cartilage is a distinctive composite tissue forming the bulk of the skeleton of cartilaginous fishes (e.g. sharks and rays), built from unmineralized cartilage covered at the surface by a thin layer of mineralized tiles called tesserae. The finescale structure and composition of elasmobranch tessellated cartilage has largely been investigated with electron microscopy, micro-computed tomography and histology, but many aspects of tissue structure and composition remain uncharacterized. In our study, we demonstrate that the tessellated cartilage of a stingray exhibits a strong and diverse autofluorescence, a native property of the tissue which can be harnessed as an effective label-free imaging technique. The autofluorescence signal was excited using a broad range of wavelengths in confocal and light sheet microscopy, comparing several sample preparations (fresh; demineralized and paraffin-embedded; non-demineralized and plastic-embedded) and imaging the tissue at different scales. Autofluorescence varied with sample preparation with the signal in both plastic- and paraffin-embedded samples strong enough to allow visualization of finescale (≥ 1 μm) cellular and matrix structures, such as cell nuclei and current and former mineralization fronts, identifiable by globular mineralized tissue. A defined pericellular matrix (PCM) surrounding chondrocytes was also discernible, described here for the first time in elasmobranchs. The presence of a PCM suggests similarities with mammalian cartilage regarding how chondrocytes interact with their environment, the PCM in mammals acting as a transducer for biomechanical and biochemical signals. A posterior analysis of hyperspectral images by an MCR-ALS unmixing algorithm allowed identification of several distinct fluorescence signatures associated to specific regions in the tissue. Some fluorescence signatures identified could be correlated with collagen type II, the most abundant structural molecule of cartilage. Other fluorescence signatures, however, remained unidentified, spotlighting tissue regions that deserve deeper characterization and suggesting the presence of molecules still unidentified in elasmobranch skeletal cartilage. Our results show that autofluorescence can be a powerful exploratory imaging tool for characterizing less-studied skeletal tissues, such as tessellated cartilage. The images obtained are largely comparable with more commonly used techniques, but without the need for complicated sample preparations or external staining reagents standard in histology and electron microscopy (TEM, SEM).

Advancing equity and justice in undergraduate biology education requires research to address the experiences of disabled students. Scholars working in disability studies have developed models of disability that inform Discipline-Based Education Research (DBER). To date, DBER literature has been predominantly informed by the medical and social models of disability. The medical model focuses on challenges that affect people with disabilities on an individual basis, while the social model focuses on how one's surrounding environment contributes to the construction of disability. In this essay, we discuss past DBER research and opportunities for future research using each of these models. We will also discuss a third, less commonly used model that offers exciting opportunities to drive future research: complex embodiment. Complex embodiment positions disability as a social location that reflects a greater societal value structure. Further examining this value structure reveals how ability itself is constructed and conventionally understood to be hierarchical. Additionally, we explain epistemic injustice as it affects disabled people, and how future education research can both address and counteract this injustice. We discuss how expanding the frameworks that serve as lenses for DBER scholarship on disability will offer new research directions.

Shark teeth have short lifespans yet can be subject to significant mechanical damage. Here, the authors report on a site-specific damage mechanism in shark teeth enameloid, which maintains tooth functional shape, providing experimental evidence that tooth architecture may have influenced the diversification of shark ecologies over evolution.

Biology has often served as the inspiration for the design of body armor; one common limitation is the flexibility of the resultant armor. Here, the authors examine the armour of chiton and use the observed design principles to 3D print flexible armor.

Members of the Chondrichthyes (Elasmobranchii and Holocephali) are distinguished by their largely cartilaginous endoskeletons, which comprise an uncalcified core overlain by a mineralized layer; in the Elasmobranchii (sharks, skates, rays) most of this mineralization takes the form of calcified polygonal tiles known as tesserae. In recent years, these skeletal tissues have been described in ever increasing detail in sharks and rays, but those of Holocephali (chimaeroids) have been less well-studied, with conflicting accounts as to whether or not tesserae are present. During embryonic ontogeny in holocephalans, cervical vertebrae fuse to form a structure called the synarcual. The synarcual mineralizes early and progressively, anteroposteriorly and dorsoventrally, and therefore presents a good skeletal structure in which to observe mineralized tissues in this group. Here, we describe the development and mineralization of the synarcual in an adult and stage 36 elephant shark embryo (Callorhinchus milii). Small, discrete, but irregular blocks of cortical mineralization are present in stage 36, similar to what has been described recently in embryos of other chimaeroid taxa such as Hydrolagus, while in Callorhinchus adults, the blocks of mineralization are more irregular, but remain small. This differs from fossil members of the holocephalan crown group (Edaphodon), as well as from stem group holocephalans (e.g., Symmorida, Helodus, Iniopterygiformes), where tesserae are notably larger than in Callorhinchus and show similarities to elasmobranch tesserae, for example with respect to polygonal shape.

A prerequisite for many analysis tasks in modern comparative biology is the segmentation of 3-dimensional (3D) images of the specimens being investigated (e.g. from microCT data). Depending on the specific imaging technique that was used to acquire the images and on the image resolution, different segmentation tools are required. While some standard tools exist that can often be applied for specific subtasks, building whole processing pipelines solely from standard tools is often difficult. Some tasks may even necessitate the implementation of manual interaction tools to achieve a quality that is sufficient for subsequent analysis. In this work, we present a pipeline of segmentation tools that can be used for the semiautomatic segmentation and quantitative analysis of voids in tissue (i.e. internal structural porosity). We use this pipeline to analyze lacuno-canalicular networks in stingray tesserae from 3D images acquired with synchrotron microCT. • The first step of this pipeline, the segmentation of the tesserae, was performed using standard marker-based watershed segmentation. • The efficient processing of the next two steps, that is, the segmentation of all lacunae spaces belonging to a specific tessera and the separation of these spaces into individual lacunae required recently developed, novel tools. • For error correction, we developed an interactive method that allowed us to quickly split lacunae that were accidentally merged, and to merge lacunae that were wrongly split. • Finally, the tesserae and their corresponding lacunae were subdivided into structural wedges (i.e. specific anatomical regions) using a semi-manual approach.With this processing pipeline, analysis of a variety of interconnected structural networks (e.g. vascular or lacuno-canalicular networks) can be achieved in a comparatively high-throughput fashion. In our study system, we were able to efficiently segment more than 12,000 lacunae in high-resolution scans of nine tesserae, providing a robust data set for statistical analysis.

Mussels attach to rocks using a byssus, which possesses unique properties of adhesion, toughness and self-healing. Here, the authors explore the fabrication process of mussel byssus demonstrating the self-assembly of specific proteins into multi-scale organized structures using artificially induced byssus threads.

Osteocytes, cells forming an elaborate network within the bones of most vertebrate taxa, are thought to be the master regulators of bone modeling, a process of coordinated, local bone-tissue deposition and removal that keeps bone strains at safe levels throughout life. Neoteleost fish, however, lack osteocytes and yet are known to be capable of bone modeling, although no osteocyte-independent modeling regulatory mechanism has so far been described. Here, we characterize a novel, to our knowledge, bone-modeling regulatory mechanism in a fish species (medaka), showing that although lacking osteocytes (i.e., internal mechanosensors), when loaded, medaka bones model in mechanically directed ways, successfully reducing high tissue strains. We establish that as in mammals, modeling in medaka is regulated by the SOST gene, demonstrating a mechanistic link between skeletal loading, SOST down-regulation, and intense bone deposition. However, whereas mammalian SOST is expressed almost exclusively by osteocytes, in both medaka and zebrafish (a species with osteocytic bones), SOST is expressed by a variety of nonosteocytic cells, none of which reside within the bone bulk. These findings argue that in fishes (and perhaps other vertebrates), nonosteocytic skeletal cells are both sensors and responders, shouldering duties believed exclusive to osteocytes. This previously unrecognized, SOST-dependent, osteocyte-independent mechanism challenges current paradigms of osteocyte exclusivity in bone-modeling regulation, suggesting the existence of multivariate feedback networks in bone modeling-perhaps also in mammalian bones-and thus arguing for the possibility of untapped potential for cell targets in bone therapeutics.

Many biological structures show recurring tiling patterns on one structural level or the other. Current image acquisition techniques are able to resolve those tiling patterns to allow quantitative analyses. The resulting image data, however, may contain an enormous number of elements. This renders manual image analysis infeasible, in particular when statistical analysis is to be conducted, requiring a larger number of image data to be analyzed. As a consequence, the analysis process needs to be automated to a large degree. In this paper, we describe a multi-step image segmentation pipeline for the automated segmentation of the calcified cartilage into individual tesserae from computed tomography images of skeletal elements of stingrays.Besides applying state-of-the-art algorithms like anisotropic diffusion smoothing, local thresholding for foreground segmentation, distance map calculation, and hierarchical watershed, we exploit a graph-based representation for fast correction of the segmentation. In addition, we propose a new distance map that is computed only in the plane that locally best approximates the calcified cartilage. This distance map drastically improves the separation of individual tesserae. We apply our segmentation pipeline to hyomandibulae from three individuals of the round stingray (Urobatis halleri), varying both in age and size.Each of the hyomandibula datasets contains approximately 3000 tesserae. To evaluate the quality of the automated segmentation, four expert users manually generated ground truth segmentations of small parts of one hyomandibula. These ground truth segmentations allowed us to compare the segmentation quality w.r.t. individual tesserae. Additionally, to investigate the segmentation quality of whole skeletal elements, landmarks were manually placed on all tesserae and their positions were then compared to the segmented tesserae. With the proposed segmentation pipeline, we sped up the processing of a single skeletal element from days or weeks to a few hours.

The shapes of vertebrate teeth are often used as hallmarks of diet. Here, however, we demonstrate evidence of frequent piscivory by cartilaginous fishes with pebble-like teeth that are typically associated with durophagy, the eating of hard-shelled prey. High-resolution micro-computed tomography observation of a jaw specimen from one batoid species and visual investigation of those of two additional species reveal large numbers of embedded stingray spines, arguing that stingray predation of a scale rivalling that of the largest carnivorous sharks may not be uncommon for large, predatory batoids with rounded, non-cutting dentition. Our observations demonstrate that tooth morphology is not always a reliable indicator of diet and that stingray spines are not as potent a deterrent to predation as normally believed. In addition, we show that several spines in close contact with the jaw skeleton of a wedgefish (Rhynchobatus) have become encased in a disorganized mineralized tissue with a distinctive ultrastructure, the first natural and unequivocal evidence of a callus-building response in the tessellated cartilage unique to elasmobranch skeletons. Our findings reveal sampling and analysis biases in vertebrate ecology, especially with regard to the role of large, predatory species, while also illustrating that large body size may provide an escape from anatomical constraints on diet (e.g. gape size, specialist dentition). Our observations inform our concepts of skeletal biology and evolution in showing that tessellated cartilage—an ancient alternative to bone—is incapable of foreign tissue resorption or of restoring damaged skeletal tissue to its original state, and attest to the value of museum and skeletal specimens as records of important aspects of animal life history.

Macroscopic, periodic, dark and bright patterns are observed on sections of elephant tusk, in the dentin part (ivory). The motifs-also called Schreger pattern-vary depending on the orientation in the tusk: on sections perpendicular to the tusk axis, a checkerboard pattern is present whereas on sections longitudinal to it, alternating stripes are observed. This pattern has been used to identify elephant and mammoth ivory in archeological artifacts and informs on the continuous tissue growth mechanisms of tusk. However, its origin, assumed to be related to the 3D structure of empty microtubules surrounded by the ivory matrix has yet to be characterized unequivocally. Based on 2D observations of the ivory microtubules by means of a variety of imaging techniques of three different planes (transverse, longitudinal and tangential to the tusk axis), we show that the dark areas of the macroscopic pattern are due to tubules oblique to the surface whereas bright areas are related to tubules parallel to it. The different microstructures observed in the three planes as well as the 3D data obtained by SR-μCT analysis allow us to propose a 3D model of the microtubule network with helical tubules phase-shifted in the tangential direction. The phase shift is a combination of a continuous phase shift of π every 1 mm with a stepwise phase shift of π/2 every 500 μm. By using 3D modeling, we show how the 3D helical model better represents the experimental microstructure observed in 2D planes compared to previous models in the literature. This brings new information on the origin of the unique Schreger pattern of elephant ivory, crucial for better understanding how archaeological objects were processed and for opening new routes to rethink how biological materials are built.

The detection of various molecular species, including complex organic molecules relevant to biochemical and geochemical processes, in astronomical settings, such as the interstellar medium or the outer solar system, has led to the increased need for a better understanding of the chemistry occurring in these cold regions of space. In this context, the chemistry of ices prepared and processed at cryogenic temperatures has proven to be of particular interest due to the fact that many interstellar molecules are believed to originate within the icy mantles adsorbed on nano- and micro-scale dust particles. The chemistry leading to the formation of such molecules may be initiated by ionizing radiation in the form of galactic cosmic rays or stellar winds, and thus, there has been an increased interest in commissioning experimental setups capable of simulating and better characterizing this solid-phase radiation astrochemistry. In this article, we describe a new facility called AQUILA (Atomki-Queen's University Ice Laboratory for Astrochemistry), which has been purposefully designed to study the chemical evolution of ices analogous to those that may be found in the dense interstellar medium or the outer solar system as a result of their exposure to keV ion beams. The results of some ion irradiation studies of CH3OH ice at 20 K are discussed to exemplify the experimental capabilities of the AQUILA as well as to highlight its complementary nature to another laboratory astrochemistry setup at our institute. [ABSTRACT FROM AUTHOR]