Biology subjects

Gault, B.

Publications and source records attributed to Gault, B..

4 recordsLinked to original sources

bioRxiv2026

Nanoscale identification of organic pigments in biogenic calcite by atom probe tomography

Spatially-resolved mass spectrometry could contribute to the understanding of biological processes. Atom probe tomography (APT) is a technique which could, in principle, fill an analytical gap for nanoscale mass spectrometry. Yet, because of a limited understanding of the process of fragmentation of biomolecules, biological or biochemical interpretation of the obtained data has so far not been successful. Here, we report on analyses of synthetic and biogenic pigmented calcite minerals. The purple coloration of Sphaerechinus granularis sea urchin spines is due to the occlusion of polyhydroxylated naphthoquinone (PHNQ) molecules, mainly spinochrome A, within the calcite phase. Peaks relating to these pigments as well as to other intra-crystalline macromolecules were identified by APT analysis of the purple spine region with comparison to measurements of synthetic calcite single crystals, calcite crystals doped with PHNQ, and the uncoloured (white) region of sea urchin spines. To facilitate the molecular identification of peaks appearing solely in purple-coloured spines, which are possible fragments from PHNQ, we introduce novel APT data filtering techniques based on spatial and temporal correlations in the detection of ions of targeted mass-to-charge state ratios. This allows us to discuss the fragmentation of organic molecules under field conditions and improve the identification of peaks in the mass spectrum, while also determining nanoscale spatial distribution of fragments related to specifically targeted biomolecules in 3D and elucidate the relationship these organic pigment molecules have to the calcite lattice and inorganic elements such as magnesium. The study aims to improve identification of complex molecular structures by APT, including organic molecules, with the potential ability to provide structural information at a near-atomic scale for a range of materials.

biophysics↗

bioRxiv2026

Nanoscale chemical tomography reveals organic and inorganic clusters in fossilised dinosaur tooth

Mineralized dental tissues are formed through biomineralization processes involving the growth and self-organisation of hydroxylapatite (HAP) nanoscale grains. There remain open questions regarding the way elements such as Mg or Na are incorporated in the organic matter between HAP grains or within the grain structure where they influence the nucleation and growth of HAP. Here, mapping the enamel structure and composition of a well-preserved ca. 150-million-year-old Giraffatitan brancai sauropod dinosaur tooth from millimeters down to the near-atomic scale, we reveal the nanoscale accumulation of Mg at HAP grain boundaries, alongside F arising from diagenesis. Within the HAP grains and at HAP grain boundaries organic matter forms clusters that we propose contribute to the fast growth rate of the tooth. Moreover, unexpected Cu3As particles are found across the entire enamel structure. These elements are not in the dentine, that exhibits empty tubules, which suggests that they were integrated during the tooth growth itself. Our multiscale analysis provides new information encouraging to reconsider aspects of the biomineralization and fossilization processes.

paleontology↗

bioRxiv2025

Exploring the potential for scanning electron microscopy/focused ion beam - based diffraction for screening cryo-transmission electron microscopy samples

The study of biological and organic materials at high resolution using cryogenic transmission-electron microscopy (cryo-TEM) necessitates vitrification to preserve the native structure. Assessing sample integrity is essential, particularly as ice crystallization during freezing and handling can cause irrecoverable structural damage. Usually, a secondary cryo-TEM is used for initial screening, only possible after a time-consuming sample preparation workflow. In the present work, we propose simple methods that exploit existing workflows developed for materials science analyses and demonstrate on-grid in situ assessment of ice crystallinity with electron backscatter diffraction (EBSD) on a direct electron detector (DED) in a cryo-scanning-electron microscope (SEM). This evaluation step can be performed prior to sample preparation for cryo-TEM by using cryogenic focused ion beam (cryo-FIB) milling. Custom grid holders and jigs were developed to integrate the clipped cryo-TEM grids and evolve the sample preparation workflow. EBSD detects hexagonal ice in some areas of the samples, whereas other areas show an absence of EBSD signal, consistent with vitreous ice, that enable targeting the further steps of sample preparation for cryo-TEM. Off-axis transmission Kikuchi diffraction (TKD) was attempted, but led to severe damage to polished TEM-lamellae and appears unsuitable. A proof-of-concept lift-out from a clipped cryo-TEM grid mounted on a support is introduced, demonstrating possibilities for expanded cryogenic correlative workflows beyond the acceleration of sample screening for cryo-TEM.

molecular biology↗

bioRxiv2018

An atomic-scale view at the composition ofamyloid-beta fibrils by atom probe tomography

Amyloid-beta (A{beta}) proteins play an important role in a number of neurodegenerative diseases. A{beta} is found in senile plaques in brains of Alzeimers disease patients. The 42 residues of the monomer form dimers which stack to fibrils gaining several micrometers in length. Using A{beta} fibrils with 13C and 15N marker substitution, we developed an innovative approach to obtain insights to structural and chemical information of the protein. We deposited the modified protein fibrils to pre-sharped aluminium needles with >100-nm apex diameters and, using the position-sensitive mass-to-charge spectrometry technique of atom probe tomography, we acquired the chemically-resolved three dimensional information for every detected ion evaporated in small fragments from the protein. We also discuss the influence of experimental parameters such as pulse energy and pulse frequency of the used Laser beam which lead to differences in the size of the gained fragments, developing the capability of localising metal atom within A{beta} plaques.

biochemistry↗