Atom Probe Tomography for Biomaterials and Biomineralization

Bone hierarchical organization through the lens of materials science: Present opportunities and future challenges

Multiscale characterization is essential to better understand the hierarchical architecture of bone and an array of analytical methods contributes to exploring the various structural and compositional aspects. Incorporating X-ray tomography, X-ray scattering, vibrational spectroscopy, and atom probe tomography alongside electron microscopy provides a comprehensive approach, offering insights into the diverse levels of organization within bone. X-ray scattering techniques reveal information about collagen-mineral spatial relationships, while X-ray tomography captures 3D structural details, especially at the microscale. Electron microscopy, such as scanning and transmission electron microscopy, extends resolution to the nanoscale, showcasing intricate features such as collagen fibril organization. Additionally, atom probe tomography achieves sub-nanoscale resolution and high chemical sensitivity, enabling detailed examination of bone composition. Despite various technical challenges, a correlative approach allows for a comprehensive understanding of bone material properties. Real-time investigations through in situ and in operando approaches shed light on the dynamic processes in bone. Recently developed techniques such as liquid, in situ transmission electron microscopy provide insights into calcium phosphate formation and collagen mineralization. Mechanical models developed in the effort to link structure, composition, and function currently remain oversimplified but can be improved. In conclusion, correlative analytical platforms provide a holistic perspective of bone extracellular matrix and are essential for unraveling the intricate interplay between structure and composition within bone.

Initial solution pH value for the construction of a 3D hydroxyapatite via the trisodium citrate-assisted hydrothermal route

In this study, a trisodium citrate (TSC)-assisted hydrothermal method is utilized to prepare three-dimensional hydroxyapatite (3D HA). Understanding the role of TSC in the preparation of 3D HA crystals may provide valuable methods to design advanced biomaterials. As one of the indexes of solution supersaturation, the initial pH (ipH) value can not only directly affect the nucleation rate, but also affect the growth of HA crystals. In this work, the effect of the ipH on the microstructure, particle size distribution, and specific surface area of the 3D HA is explored. Results showed that the morphology of 3D HA transformed from a bundle to a dumbbell ball and then a dumbbell with an increase in the ipH. A corresponding mechanism of such a structural evolution was proposed, providing inspiration for the fabrication of innovative 3D HA structures with enhanced biological functionality and performance.

Biomineral deposits and coatings on stone monuments as biodeterioration fingerprints

Biominerals deposition processes, also called biomineralisation, are intimately related to biodeterioration on stone surfaces. They include complex processes not always completely well understood. The study of biominerals implies the identification of organisms, their molecular mechanisms, and organism/rock/atmosphere interactions. Sampling restrictions of monument stones difficult the biominerals study and the in situ demonstrating of biodeterioration processes. Multidisciplinary works are required to understand the whole process. Thus, studies in heritage buildings have taken advantage of previous knowledge acquired thanks to laboratory experiments, investigations carried out on rock outcrops and within caves from some years ago. With the extrapolation of such knowledge to heritage buildings and the advances in laboratory techniques, there has been a huge increase of knowledge regarding biomineralisation and biodeterioration processes in stone monuments during the last 20 years. These advances have opened new debates about the implications on conservation interventions, and the organism's role in stone conservation and decay. This is a review of the existing studies of biominerals formation, biodeterioration on laboratory experiments, rocks, caves, and their application to building stones of monuments.

In Situ Metallic Coating of Atom Probe Specimen for Enhanced Yield, Performance, and Increased Field-of-View

Atom probe tomography requires needle-shaped specimens with a diameter typically below 100 nm, making them both very fragile and reactive, and defects (notches at grain boundaries or precipitates) are known to affect the yield and data quality. The use of a conformal coating directly on the sharpened specimen has been proposed to increase yield and reduce background. However, to date, these coatings have been applied ex situ and mostly are not uniform. Here, we report on the controlled focused-ion beam in situ deposition of a thin metal film on specimens immediately after specimen preparation. Different metallic targets e.g. Cr were attached to a micromanipulator via a conventional lift-out method and sputtered using Ga or Xe ions. We showcase the many advantages of coating specimens from metallic to nonmetallic materials. We have identified an increase in data quality and yield, an improvement of the mass resolution, as well as an increase in the effective field-of-view. This wider field-of-view enables visualization of the entire original specimen, allowing to detect the complete surface oxide layer around the specimen. The ease of implementation of the approach makes it very attractive for generalizing its use across a very wide range of atom probe analyses.

Intrafibrillar mineralization of type I collagen with calcium carbonate and strontium carbonate induced by polyelectrolyte-cation complexes

Calcium carbonate (CaCO3), possessing excellent biocompatibility, bioactivity, osteoconductivity and superior biodegradability, may serve as an alternative to hydroxyapatite (HAp), the natural inorganic component of bone and dentin. Intrafibrillar mineralization of collagen with CaCO3 was achieved through the polymer-induced liquid precursor (PILP) process for at least 2 days. This study aims to propose a novel pathway for rapid intrafibrillar mineralization with CaCO3 by sequential application of the carbonate-bicarbonate buffer and polyaspartic acid (pAsp)-Ca suspension. Fourier transform infrared (FTIR) spectroscopy, zeta potential measurements, atomic force microscopy/Kelvin probe force microscopy (AFM/KPFM), and three-dimensional stochastic optical reconstruction microscopy (3D STORM) demonstrated that the carbonate-bicarbonate buffer significantly decreased the surface potential of collagen and CO32-/HCO3- ions could attach to collagen fibrils via hydrogen bonds. The electropositive pAsp-Ca complexes and free Ca2+ ions are attracted to and interact with CO32-/HCO3- ions through electrostatic attractions to form amorphous calcium carbonate that crystallizes gradually. Moreover, like CaCO3, strontium carbonate (SrCO3) can deposit inside the collagen fibrils through this pathway. The CaCO3-mineralized collagen gels exhibited better biocompatibility and cell proliferation ability than SrCO3. This study provides a feasible strategy for rapid collagen mineralization with CaCO3 and SrCO3, as well as elucidating the tissue engineering of CaCO3-based biomineralized materials.

Scalable substrate development for aqueous sample preparation for atom probe tomography

Reliable and consistent preparation of atom probe tomography (APT) specimens from aqueous and hydrated biological specimens remains a significant challenge. One particularly difficult process step is the use of a focused ion beam (FIB) instrument for preparing the required needle-shaped specimen, typically involving a 'lift-out' procedure of a small sample of material. Here, two alternative substrate designs are introduced that enable using FIB only for sharpening, along with example APT datasets. The first design is a laser-cut FIB-style half-grid close to those used for transmission electron microscopy (TEM) that can be used in a grid holder compatible with APT pucks. The second design is a larger, standalone self-supporting substrate called a 'crown', with several specimen positions, which self-aligns in APT pucks, prepared by electrical discharge machining (EDM). Both designs are made nanoporous, to provide strength to the liquid-substrate interface, using chemical and vacuum dealloying. Alpha brass, a simple, widely available, lower-cost alternative to previously proposed substrates, was selected for this work. The resulting designs and APT data are presented and suggestions are provided to help drive wider community adoption.

Novel Focused Ion Beam Liftouts for Spatial Characterization of Spherical Biominerals With Transmission Electron Microscopy

Focused ion beam (FIB) is frequently used to prepare electron- and X-ray-beam-transparent thin sections of samples, called lamellae. Typically, lamellae are prepared from only a subregion of a sample. In this paper, we present a novel approach for FIB lamella preparation of microscopic samples, wherein the entire cross-section of the whole sample can be investigated. The approach was demonstrated using spherical, porous, and often hollow microprecipitates of biologically precipitated calcium carbonate. The microprecipitate morphology made these biogenic samples more fragile and challenging than materials commonly investigated using FIB lamellae. Our method enables the appropriate orientation of the lamellae required for further electron/X-ray analyses after attachment to the transmission electron microscopy (TEM) grid post and facilitates more secure adhesion onto the grid post. We present evidence of autofluorescence in bacterially precipitated vaterite using this lamella preparation method coupled with TEM selected area diffraction. This innovative approach allows studying biomineralization at the micro to nano scales, which can provide novel insights into bacterial responses to microenvironmental conditions.

In Situ Sputtering From the Micromanipulator to Enable Cryogenic Preparation of Specimens for Atom Probe Tomography by Focused-Ion Beam

Workflows have been developed in the past decade to enable atom probe tomography analysis at cryogenic temperatures. The inability to control the local deposition of the metallic precursor from the gas-injection system (GIS) at cryogenic temperatures makes the preparation of site-specific specimens by using lift-out extremely challenging in the focused-ion beam. Schreiber et al. exploited redeposition to weld the lifted-out sample to a support. Here, we build on their approach to attach the region-of-interest and additionally strengthen the interface with locally sputtered metal from the micromanipulator. Following standard focused-ion beam annular milling, we demonstrate atom probe analysis of Si in both laser pulsing and voltage mode, with comparable analytical performance as a presharpened microtip coupon. Our welding approach is versatile, as various metals could be used for sputtering, and allows similar flexibility as the GIS in principle.

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.

Nanoscale analysis of frozen honey by atom probe tomography

Three-dimensional reconstruction of the analysed volume is one of the main goals of atom probe tomography (APT) and can deliver nearly atomic resolution (~ 0.2 nm spatial resolution) and chemical information with a mass sensitivity down to the ppm range. Extending this technique to frozen biological systems would have an enormous impact on the structural analysis of biomolecules. In previous works, we have shown that it is possible to measure frozen liquids with APT. In this paper, we demonstrate the ability of APT to trace nanoscale precipitation in frozen natural honey. While the mass signals of the common sugar fragments CxHy and CxOyHz overlap with (H2O)nH from water, we achieved correct stoichiometric values via different interpretation approaches for the peaks and thus determined the water content reliably. Next, we use honey to investigate the spatial resolution capabilities as a step toward the measurement of biological molecules in solution in 3D with sub-nanometer resolution. This may take analytical techniques to a new level, since methods of chemical characterization for cryogenic samples, especially biological samples, are still limited.