3D Maps of Mineral Composition and Hydroxyapatite Orientation in Fossil Bone Samples Obtained by X-ray Diffraction Computed Tomography

Revisiting the physical and chemical nature of the mineral component of bone

The physico-chemical characteristics of bone mineral remain heavily debated. On the nanoscale, bone mineral resides both inside and outside the collagen fibril as distinct compartments fused together into a cohesive continuum. On the micrometre level, larger aggregates are arranged in a staggered pattern described as crossfibrillar tessellation. Unlike geological and synthetic hydroxy(l)apatite, bone mineral is a unique form of apatite deficient in calcium and hydroxyl ions with distinctive carbonate and acid phosphate substitutions (CHAp), together with a minor contribution of amorphous calcium phosphate as a surface layer around a crystalline core of CHAp. In mammalian bone, an amorphous solid phase has not been observed, though an age-dependent shift in the amorphous-to-crystalline character is observed. Although octacalcium phosphate has been postulated as a bone mineral precursor, there is inconsistent evidence of calcium phosphate phases other than CHAp in the extracellular matrix. In association with micropetrosis, magnesium whitlockite is occasionally detected, indicating pathological calcification rather than a true extracellular matrix component. Therefore, the terms 'biomimetic' or 'bone-like' should be used cautiously in descriptions of synthetic biomaterials. The practice of reporting the calcium-to-phosphorus ratio (Ca/P) as proxy for bone mineral maturity oversimplifies the chemistry since both Ca2+ and PO43- ions are partially substituted. Moreover, non-mineral sources of phosphorus are ignored. Alternative compositional metrics should be considered. In the context of bone tissue and bone mineral, the term 'mature' must be used carefully, with clear criteria that consider both compositional and structural parameters and the potential impact on mechanical properties. STATEMENT OF SIGNIFICANCE: Bone mineral exhibits a unique hierarchical structure and is classified into intrafibrillar and extrafibrillar mineral compartments with distinct physico-chemical characteristics. The dynamic nature of bone mineral, i.e., evolving chemical composition and physical form, is poorly understood. For instance, bone mineral is frequently described as "hydroxy(l)apatite", even though the OH- content of mature bone mineral is negligible. Moreover, the calcium-to-phosphorus ratio is often taken as an indicator of bone mineral maturity without acknowledging substitutions at calcium and phosphate sites. This review takes a comprehensive look at the structure and composition of bone mineral, highlighting how experimental data are misinterpreted and unresolved concerns that warrant further investigation, which have implications for characterisation of bone material properties and development of bone repair biomaterials.

Multimodal 2D and 3D microscopic mapping of growth cartilage by computational imaging techniques - a short review including new research

Being able to image the microstructure of growth cartilage is important for understanding the onset and progression of diseases such as osteochondrosis and osteoarthritis, as well as for developing new treatments and implants. Studies of cartilage using conventional optical brightfield microscopy rely heavily on histological staining, where the added chemicals provide tissue-specific colours. Other microscopy contrast mechanisms include polarization, phase- and scattering contrast, enabling non-stained or 'label-free' imaging that significantly simplifies the sample preparation, thereby also reducing the risk of artefacts. Traditional high-performance microscopes tend to be both bulky and expensive.Computational imagingdenotes a range of techniques where computers with dedicated algorithms are used as an integral part of the image formation process. Computational imaging offers many advantages like 3D measurements, aberration correction and quantitative phase contrast, often combined with comparably cheap and compact hardware. X-ray microscopy is also progressing rapidly, in certain ways trailing the development of optical microscopy. In this study, we first briefly review the structures of growth cartilage and relevant microscopy characterization techniques, with an emphasis on Fourier ptychographic microscopy (FPM) and advanced x-ray microscopies. We next demonstrate with our own results computational imaging through FPM and compare the images with hematoxylin eosin and saffron (HES)-stained histology. Zernike phase contrast, and the nonlinear optical microscopy techniques of second harmonic generation (SHG) and two-photon excitation fluorescence (TPEF) are explored. Furthermore, X-ray attenuation-, phase- and diffraction-contrast computed tomography (CT) images of the very same sample are presented for comparisons. Future perspectives on the links to artificial intelligence, dynamic studies andin vivopossibilities conclude the article.

Recent developments in X-ray diffraction/scattering computed tomography for materials science

X-ray diffraction/scattering computed tomography (XDS-CT) methods are a non-destructive class of chemical imaging techniques that have the capacity to provide reconstructions of sample cross-sections with spatially resolved chemical information. While X-ray diffraction CT (XRD-CT) is the most well-established method, recent advances in instrumentation and data reconstruction have seen greater use of related techniques like small angle X-ray scattering CT and pair distribution function CT. Additionally, the adoption of machine learning techniques for tomographic reconstruction and data analysis are fundamentally disrupting how XDS-CT data is processed. The following narrative review highlights recent developments and applications of XDS-CT with a focus on studies in the last five years. This article is part of the theme issue 'Exploring the length scales, timescales and chemistry of challenging materials (Part 2)'.

Synchrotron X-ray Studies of the Structural and Functional Hierarchies in Mineralised Human Dental Enamel: A State-of-the-Art Review

Hard dental tissues possess a complex hierarchical structure that is particularly evident in enamel, the most mineralised substance in the human body. Its complex and interlinked organisation at the Ångstrom (crystal lattice), nano-, micro-, and macro-scales is the result of evolutionary optimisation for mechanical and functional performance: hardness and stiffness, fracture toughness, thermal, and chemical resistance. Understanding the physical-chemical-structural relationships at each scale requires the application of appropriately sensitive and resolving probes. Synchrotron X-ray techniques offer the possibility to progress significantly beyond the capabilities of conventional laboratory instruments, i.e., X-ray diffractometers, and electron and atomic force microscopes. The last few decades have witnessed the accumulation of results obtained from X-ray scattering (diffraction), spectroscopy (including polarisation analysis), and imaging (including ptychography and tomography). The current article presents a multi-disciplinary review of nearly 40 years of discoveries and advancements, primarily pertaining to the study of enamel and its demineralisation (caries), but also linked to the investigations of other mineralised tissues such as dentine, bone, etc. The modelling approaches informed by these observations are also overviewed. The strategic aim of the present review was to identify and evaluate prospective avenues for analysing dental tissues and developing treatments and prophylaxis for improved dental health.

Orientational mapping of minerals in Pierre shale using X-ray diffraction tensor tomography

Shales have a complex mineralogy with structural features spanning several length scales, making them notoriously difficult to fully understand. Conventional attenuation-based X-ray computed tomography (CT) measures density differences, which, owing to the heterogeneity and sub-resolution features in shales, makes reliable interpretation of shale images a challenging task. CT based on X-ray diffraction (XRD-CT), rather than intensity attenuation, is becoming a well established technique for non-destructive 3D imaging, and is especially suited for heterogeneous and hierarchical materials. XRD patterns contain information about the mineral crystal structure, and crucially also crystallite orientation. Here, we report on the use of orientational imaging using XRD-CT to study crystallite-orientation distributions in a sample of Pierre shale. Diffraction-contrast CT data for a shale sample measured with its bedding-plane normal aligned parallel to a single tomographic axis perpendicular to the incoming X-ray beam are discussed, and the spatial density and orientation distribution of clay minerals in the sample are described. Finally, the scattering properties of highly attenuating inclusions in the shale bulk are studied, which are identified to contain pyrite and clinochlore. A path forward is then outlined for systematically improving the structural description of shales.

Mapping Bone Surface Composition Using Real-Time Surface Tracked Micro-Raman Spectroscopy

The surface of bone tells a story - one that is worth a thousand words - of how it is built and how it is repaired. Chemical (i.e., composition) and physical (i.e., morphology) characteristics of the bone surface are analogous to a historical record of osteogenesis and provide key insights into bone quality. Analysis of bone chemistry is of particular relevance to the advancement of human health, cell biology, anthropology/archaeology, and biomedical engineering. Although scanning electron microscopy remains a popular and versatile technique to image bone across multiple length scales, limited chemical information can be obtained. Micro-Raman spectroscopy is a valuable tool for nondestructive chemical/compositional analysis of bone. However, signal integrity losses occur frequently during wide-field mapping of non-planar surfaces. Samples for conventional Raman imaging are, therefore, rendered planar through polishing or sectioning to ensure uniform signal quality. Here, we demonstrate ν1 PO43- and ν1 CO32- peak intensity losses where the sample surface and the plane of focus are offset by over 1-2 μm when underfocused and 2-3 μm when overfocused at 0.5-1 s integration time (15 mW, 633 nm laser). A technique is described for mapping the composition of the inherently irregular/non-planar surface of bone. The challenge posed by the native topology characteristic of this unique biological system is circumvented via real-time focus-tracking based on laser focus optimization by continuous closed-loop feedback. At the surface of deproteinized and decellularized/defatted sheep tibial cortical bone, regions of interest up to 1 mm2 were scanned at micrometer and submicrometer resolution. Despite surface height deviations exceeding 100 μm, it is possible to seamlessly probe local gradients in organic and inorganic constituents of the extracellular matrix as markers of bone metabolism and bone turnover, blood vessels and osteocyte lacunae, and the rope-like mineralized bundles that comprise the mineral phase at the bone surface.

Lacunar-canalicular bone remodeling: Impacts on bone quality and tools for assessment

Osteocytes can resorb as well as replace bone adjacent to the expansive lacunar-canalicular system (LCS). Suppressed LCS remodeling decreases bone fracture toughness, but it is unclear how altered LCS remodeling impacts bone quality. The first goal of this review is to assess how LCS remodeling impacts LCS morphology as well as the composition and mechanical properties of surrounding bone tissue. The second goal is to compare tools available for the assessment of bone quality at length-scales that are physiologically-relevant to LCS remodeling. We find that changes to LCS morphology occur in response to a variety of physiological conditions and diseases and can be classified in two general phenotypes. In the 'aging phenotype', seen in aging and in some disuse models, the LCS is truncated and osteocytes apoptosis is increased. In the 'osteocytic osteolysis' phenotype, which is adaptive in some physiological settings and possibly maladaptive in others, the LCS enlarges and osteocytes generally maintain viability. Bone composition and mechanical properties vary near the osteocyte and change with at least some conditions that alter LCS morphology. However, few studies have evaluated bone composition and mechanical properties close to the LCS and so the impacts of LCS remodeling phenotypes on bone tissue quality are still undetermined. We summarize the current understanding of how LCS remodeling impacts LCS morphology, tissue-scale bone composition and mechanical properties, and whole-bone material properties. Tools are compared for assessing tissue-scale bone properties, as well as the resolution, advantages, and limitations of these techniques.

Quantifying the hydroxyapatite orientation near the ossification front in a piglet femoral condyle using X-ray diffraction tensor tomography

While a detailed knowledge of the hierarchical structure and morphology of the extracellular matrix is considered crucial for understanding the physiological and mechanical properties of bone and cartilage, the orientation of collagen fibres and carbonated hydroxyapatite (HA) crystallites remains a debated topic. Conventional microscopy techniques for orientational imaging require destructive sample sectioning, which both precludes further studies of the intact sample and potentially changes the microstructure. In this work, we use X-ray diffraction tensor tomography to image non-destructively in 3D the HA orientation in a medial femoral condyle of a piglet. By exploiting the anisotropic HA diffraction signal, 3D maps showing systematic local variations of the HA crystallite orientation in the growing subchondral bone and in the adjacent mineralized growth cartilage are obtained. Orientation maps of HA crystallites over a large field of view (~ 3 × 3 × 3 mm³) close to the ossification (bone-growth) front are compared with high-resolution X-ray propagation phase-contrast computed tomography images. The HA crystallites are found to predominantly orient with their crystallite c-axis directed towards the ossification front. Distinct patterns of HA preferred orientation are found in the vicinity of cartilage canals protruding from the subchondral bone. The demonstrated ability of retrieving 3D orientation maps of bone-cartilage structures is expected to give a better understanding of the physiological properties of bones, including their propensity for bone-cartilage diseases.

Application of mid-infrared free-electron laser for structural analysis of biological materials

A mid-infrared free-electron laser (MIR-FEL) is a synchrotron-radiation-based femto- to pico-second pulse laser. It has unique characteristics such as variable wavelengths in the infrared region and an intense pulse energy. So far, MIR-FELs have been utilized to perform multi-photon absorption reactions against various gas molecules and protein aggregates in physical chemistry and biomedical fields. However, the applicability of MIR-FELs for the structural analysis of solid materials is not well recognized in the analytical field. In the current study, an MIR-FEL is applied for the first time to analyse the internal structure of biological materials by using fossilized inks from cephalopods as the model sample. Two kinds of fossilized inks that were collected from different strata were irradiated at the dry state by tuning the oscillation wavelengths of the MIR-FEL to the phosphoryl stretching mode of hydroxyapatite (9.6 µm) and to the carbonyl stretching mode of melanin (5.8 µm), and the subsequent structural changes in those materials were observed by using infrared microscopy and far-infrared spectroscopy. The structural variation of these biological fossils is discussed based on the infrared-absorption spectral changes that were enhanced by the MIR-FEL irradiation, and the potential use of MIR-FELs for the structural evaluation of biomaterials is suggested.

Nanoscale imaging of shale fragments with coherent X-ray diffraction

Despite the abundance of shales in the Earth's crust and their industrial and environmental importance, their microscale physical properties are poorly understood, owing to the presence of many structurally related mineral phases and a porous network structure spanning several length scales. Here, the use of coherent X-ray diffraction imaging (CXDI) to study the internal structure of microscopic shale fragments is demonstrated. Simultaneous wide-angle X-ray diffraction (WAXD) measurement facilitated the study of the mineralogy of the shale microparticles. It was possible to identify pyrite nanocrystals as inclusions in the quartz-clay matrix and the volume of closed unconnected pores was estimated. The combined CXDI-WAXD analysis enabled the establishment of a correlation between sample morphology and crystallite shape and size. The results highlight the potential of the combined CXDI-WAXD approach as an upcoming imaging modality for 3D nanoscale studies of shales and other geological formations via serial measurements of microscopic fragments.

On the Crystallization of Hydroxyapatite under Hydrothermal Conditions: Role of Sebacic Acid as an Additive

Hydroxyapatite (HAp) is a major inorganic component in bone minerals and is often used for bone tissue engineering. Herein, we synthesized HAp using sebacic acid as an additive at different pH values by a hydrothermal method. Sebacic acid, which has two carboxyl group ends of the carbonate chain, binds with Ca ions during the hydrothermal process to become a crystal nucleation site in (001) and at the same time could act as an inhibitor in a specific direction [i.e., (110)] for the HAp crystal growth. Sebacic acid and the hydroxyl ion (OH^-) are competitively attracted to the a(b)-plane of HAp. Depending on the pH condition, the crystal growth resulted in different morphologies depending on the ratio of sebacic acid and hydroxide ions. It was confirmed through Fourier-transform infrared spectroscopy and Raman spectroscopy that dicalcium phosphate anhydrous with HPO₄ was produced under acidic conditions and HAp was produced under neutral and basic conditions. The plate- and nanorod-HAp crystals' preferential growth along the c-axis, which were obtained under neutral and basic conditions, was analyzed by transmission electron microscopy. Growth control in the c-axis direction of HAp is necessary for the understanding of crystallization of bone minerals because the mineral inside the collagen fibrils in bone tissue also shows a c-axis orientation.

Biomimetic cues from poly(lactic-co-glycolic acid)/hydroxyapatite nano-fibrous scaffolds drive osteogenic commitment in human mesenchymal stem cells in the absence of osteogenic factor supplements

Mimicking the complex hierarchical architecture of the 'osteon', the functional unit of cortical bone, from the bottom-up offers the possibility of generating mature bone tissue in tissue engineered bone substitutes. In this work, a modular 'bottom-up' approach has been developed to assemble bone niche-mimicking nanocomposite scaffolds composed of aligned electrospun nanofibers of poly(lactic-co-glycolic acid) (PLGA) encapsulating aligned rod-shape nano-sized hydroxyapatite (nHA). By encoding axial orientation of the nHA within these aligned nanocomposite fibers, significant improvements in mechanical properties, surface roughness, hydrophilicity and in vitro simulated body fluid (SBF) mineral deposition were achieved. Moreover, these hierarchical scaffolds induced robust formation of bone hydroxyapatite and osteoblastic maturation of human bone marrow-derived mesenchymal stem cells (hBMSCs) in growth media that was absent of any soluble osteogenic differentiation factors. The results of this investigation confirm that these tailored, aligned nanocomposite fibers, in the absence of media-bone inductive factors, offer the requisite biophysical and biochemical cues to hBMSCs to promote and support their differentiation into mature osteoblast cells and form early bone-like tissue in vitro.

Visualizing mineralization processes and fossil anatomy using synchronous synchrotron X-ray fluorescence and X-ray diffraction mapping

Fossils, including those that occasionally preserve decay-prone soft tissues, are mostly made of minerals. Accessing their chemical composition provides unique insight into their past biology and/or the mechanisms by which they preserve, leading to a series of developments in chemical and elemental imaging. However, the mineral composition of fossils, particularly where soft tissues are preserved, is often only inferred indirectly from elemental data, while X-ray diffraction that specifically provides phase identification received little attention. Here, we show the use of synchrotron radiation to generate not only X-ray fluorescence elemental maps of a fossil, but also mineralogical maps in transmission geometry using a two-dimensional area detector placed behind the fossil. This innovative approach was applied to millimetre-thick cross-sections prepared through three-dimensionally preserved fossils, as well as to compressed fossils. It identifies and maps mineral phases and their distribution at the microscale over centimetre-sized areas, benefitting from the elemental information collected synchronously, and further informs on texture (preferential orientation), crystallite size and local strain. Probing such crystallographic information is instrumental in defining mineralization sequences, reconstructing the fossilization environment and constraining preservation biases. Similarly, this approach could potentially provide new knowledge on other (bio)mineralization processes in environmental sciences. We also illustrate that mineralogical contrasts between fossil tissues and/or the encasing sedimentary matrix can be used to visualize hidden anatomies in fossils.

X-ray computed tomography in life sciences

Recent developments within micro-computed tomography (μCT) imaging have combined to extend our capacity to image tissue in three (3D) and four (4D) dimensions at micron and sub-micron spatial resolutions, opening the way for virtual histology, live cell imaging, subcellular imaging and correlative microscopy. Pivotal to this has been the development of methods to extend the contrast achievable for soft tissue. Herein, we review the new capabilities within the field of life sciences imaging, and consider how future developments in this field could further benefit the life sciences community.

X-ray Diffraction Mapping for Cultural Heritage Science: a Review of Experimental Configurations and Applications

X-ray diffraction (XRD) mapping consists in the acquisition of XRD patterns at each pixel (or voxel) of an area (or volume). The spatial resolution ranges from the micrometer (μXRD) to the millimeter (MA-XRD) scale, making the technique relevant for tiny samples up to large objects. Although XRD is primarily used for the identification of different materials in (complex) mixtures, additional information regarding the crystallite size, their orientation, and their in-depth distribution can also be obtained. Through mapping, these different types of information can be located on the studied sample/object. Cultural heritage objects are usually highly heterogeneous, and contain both original and later (degradation, conservation) materials. Their structural characterization is required both to determine ancient manufacturing processes and to evaluate their conservation state. Together with other mapping techniques, XRD mapping is increasingly used for these purposes. Here, the authors review applications as well as the various configurations for XRD mapping (synchrotron/laboratory X-ray source, poly-/monochromatic beam, micro/macro beam, 2D/3D, transmission/reflection mode). On-going hardware and software developments will further establish the technique as a key tool in heritage science.

High-speed tensor tomography: iterative reconstruction tensor tomography (IRTT) algorithm

The recent advent of tensor tomography techniques has enabled tomographic investigations of the 3D nanostructure organization of biological and material science samples. These techniques extended the concept of conventional X-ray tomography by reconstructing not only a scalar value such as the attenuation coefficient per voxel, but also a set of parameters that capture the local anisotropy of nanostructures within every voxel of the sample. Tensor tomography data sets are intrinsically large as each pixel of a conventional X-ray projection is substituted by a scattering pattern, and projections have to be recorded at different sample angular orientations with several tilts of the rotation axis with respect to the X-ray propagation direction. Currently available reconstruction approaches for such large data sets are computationally expensive. Here, a novel, fast reconstruction algorithm, named iterative reconstruction tensor tomography (IRTT), is presented to simplify and accelerate tensor tomography reconstructions. IRTT is based on a second-rank tensor model to describe the anisotropy of the nanostructure in every voxel and on an iterative error backpropagation reconstruction algorithm to achieve high convergence speed. The feasibility and accuracy of IRTT are demonstrated by reconstructing the nanostructure anisotropy of three samples: a carbon fiber knot, a human bone trabecula specimen and a fixed mouse brain. Results and reconstruction speed were compared with those obtained by the small-angle scattering tensor tomography (SASTT) reconstruction method introduced by Liebi et al. [Nature (2015), 527, 349-352]. The principal orientation of the nanostructure within each voxel revealed a high level of agreement between the two methods. Yet, for identical data sets and computer hardware used, IRTT was shown to be more than an order of magnitude faster. IRTT was found to yield robust results, it does not require prior knowledge of the sample for initializing parameters, and can be used in cases where simple anisotropy metrics are sufficient, i.e. the tensor approximation adequately captures the level of anisotropy and the dominant orientation within a voxel. In addition, by greatly accelerating the reconstruction, IRTT is particularly suitable for handling large tomographic data sets of samples with internal structure or as a real-time analysis tool during the experiment for online feedback during data acquisition. Alternatively, the IRTT results might be used as an initial guess for models capturing a higher complexity of structural anisotropy such as spherical harmonics based SASTT in Liebi et al. (2015), improving both overall convergence speed and robustness of the reconstruction.