Quantifying the Structure and Composition of Flocculated Suspended Particulate Matter Using Focused Ion Beam Nanotomography.

Suspended particulate matter (SPM) is present in the natural aquatic environment as loosely bound aggregates or "flocs" and is responsible for the transport and fate of sediment, carbon, nutrients, pollutants, pathogens and manufactured nanoparticles from catchment to coast. Accurate prediction of SPM hydrodynamics requires the quantification of 3D floc properties (size, shape, density and porosity) that span several spatial scales. Yet, current techniques (video camera systems, optical microscopy and transmission electron microscopy, TEM) can only provide 2D simplifications of size and shape with a spatial resolution gap between the "gross" (>100s µm) and nanoscale (<1 µm). Here, we translate 3D-microscopy techniques (focused ion beam nanotomography, FIB-nt) typically used in the biomedical sciences to the study of natural flocculated SPM filling both this spatial and dimensional gap. Fragile 3D floc samples were successfully captured and stabilized, identifying five basic organic and inorganic floc components and quantifying porosity and bacteria numbers. This provides new 3D floc geometric data sets at the nanoscale that will be critical in the development of cohesive sediment transport models. Detailed compositional and structural information could provide novel insights into the association of pathogens and pollutants with SPM and their impact on aquatic life.

Three-dimensional aspects of matrix assembly by cells in the developing cornea.

Cell-directed deposition of aligned collagen fibrils during corneal embryogenesis is poorly understood, despite the fact that it is the basis for the formation of a corneal stroma that must be transparent to visible light and biomechanically stable. Previous studies of the structural development of the specialized matrix in the cornea have been restricted to examinations of tissue sections by conventional light or electron microscopy. Here, we use volume scanning electron microscopy, with sequential removal of ultrathin surface tissue sections achieved either by ablation with a focused ion beam or by serial block face diamond knife microtomy, to examine the microanatomy of the cornea in three dimensions and in large tissue volumes. The results show that corneal keratocytes occupy a significantly greater tissue volume than was previously thought, and there is a clear orthogonality in cell and matrix organization, quantifiable by Fourier analysis. Three-dimensional reconstructions reveal actin-associated tubular cell protrusions, reminiscent of filopodia, but extending more than 30 µm into the extracellular space. The highly extended network of these membrane-bound structures mirrors the alignment of collagen bundles and emergent lamellae and, we propose, plays a fundamental role in dictating the orientation of collagen in the developing cornea.

Control of starch granule numbers in Arabidopsis chloroplasts.

The aim of this work was to investigate starch granule numbers in Arabidopsis (Arabidopsis thaliana) leaves. Lack of quantitative information on the extent of genetic, temporal, developmental, and environmental variation in granule numbers is an important limitation in understanding control of starch degradation and the mechanism of granule initiation. Two methods were developed for reliable estimation of numbers of granules per chloroplast. First, direct measurements were made on large series of consecutive sections of mesophyll tissue obtained by focused ion beam-scanning electron microscopy. Second, average numbers were calculated from the starch contents of leaves and chloroplasts and estimates of granule mass based on granule dimensions. Examination of wild-type plants and accumulation and regulation of chloroplast (arc) mutants with few, large chloroplasts provided the following new insights. There is wide variation in chloroplast volumes in cells of wild-type leaves. Granule numbers per chloroplast are correlated with chloroplast volume, i.e. large chloroplasts have more granules than small chloroplasts. Mature leaves of wild-type plants and arc mutants have approximately the same number of granules per unit volume of stroma, regardless of the size and number of chloroplasts per cell. Granule numbers per unit volume of stroma are also relatively constant in immature leaves but are greater than in mature leaves. Granule initiation occurs as chloroplasts divide in immature leaves, but relatively little initiation occurs in mature leaves. Changes in leaf starch content over the diurnal cycle are largely brought about by changes in the volume of a fixed number of granules.

A structure-function based approach to floc hierarchy and evidence for the non-fractal nature of natural sediment flocs.

Natural sediment flocs are fragile, highly irregular, loosely bound aggregates comprising minerogenic and organic material. They contribute a major component of suspended sediment load and are critical for the fate and flux of sediment, carbon and pollutants in aquatic environments. Understanding their behaviour is essential to the sustainable management of waterways, fisheries and marine industries. For several decades, modelling approaches have utilised fractal mathematics and observations of two dimensional (2D) floc size distributions to infer levels of aggregation and predict their behaviour. Whilst this is a computationally simple solution, it is highly unlikely to reflect the complexity of natural sediment flocs and current models predicting fine sediment hydrodynamics are not efficient. Here, we show how new observations of fragile floc structures in three dimensions (3D) demonstrate unequivocally that natural flocs are non-fractal. We propose that floc hierarchy is based on observations of 3D structure and function rather than 2D size distribution. In contrast to fractal theory, our data indicate that flocs possess characteristics of emergent systems including non-linearity and scale-dependent feedbacks. These concepts and new data to quantify floc structures offer the opportunity to explore new emergence-based floc frameworks which better represent natural floc behaviour and could advance our predictive capacity.

Composite bounds on the elastic modulus of bone.

Advances in diagnosis and treatment of some bone disorders can be made by understanding the linkage between mineral content and mechanical function. Bone is approximately half by volume a hydrated protein network, and the remainder is a biomineral analogue of hydroxyapatite. In the current work, paired measurements of mechanical properties, using nanoindentation, and of bone mineral volume fraction, computed from quantitative back-scattered electron imaging, were made on six different types of normal and outlier bone samples. Local elastic modulus was plotted against mineral fraction and compared with predictions of engineering bounds for a two-phase composite material. Experimental data spanning the composite bounds showed no one-to-one relationship between mechanical stiffness and bone composition, excluding the possibility of any single, simple composites model for bone at nanometer length-scales.

Elastin-Like Protein, with Statherin Derived Peptide, Controls Fluorapatite Formation and Morphology.

The process of enamel biomineralization is multi-step, complex and mediated by organic molecules. The lack of cells in mature enamel leaves it unable to regenerate and hence novel ways of growing enamel-like structures are currently being investigated. Recently, elastin-like protein (ELP) with the analog N-terminal sequence of statherin (STNA15-ELP) has been used to regenerate mineralized tissue. Here, the STNA15-ELP has been mineralized in constrained and unconstrained conditions in a fluoridated solution. We demonstrate that the control of STNA15-ELP delivery to the mineralizing solution can form layered ordered fluorapatite mineral, via a brushite precursor. We propose that the use of a constrained STNA15-ELP system can lead to the development of novel, bioinspired enamel therapeutics.

Characterization of a novel intrinsically radiopaque Drug-eluting Bead for image-guided therapy: DC Bead LUMI™.

We have developed a straightforward and efficient method of introducing radiopacity into Polyvinyl alcohol (PVA)-2-Acrylamido-2-methylpropane sulfonic acid (AMPS) hydrogel beads (DC Bead™) that are currently used in the clinic to treat liver malignancies. Coupling of 2,3,5-triiodobenzaldehyde to the PVA backbone of pre-formed beads yields a uniformly distributed level of iodine attached throughout the bead structure (~150mg/mL) which is sufficient to be imaged under standard fluoroscopy and computed tomography (CT) imaging modalities used in treatment procedures (DC Bead LUMI™). Despite the chemical modification increasing the density of the beads to ~1.3g/cm3 and the compressive modulus by two orders of magnitude, they remain easily suspended, handled and administered through standard microcatheters. As the core chemistry of DC Bead LUMI™ is the same as DC Bead™, it interacts with drugs using ion-exchange between sulfonic acid groups on the polymer and the positively charged amine groups of the drugs. Both doxorubicin (Dox) and irinotecan (Iri) elution kinetics for all bead sizes evaluated were within the parameters already investigated within the clinic for DC Bead™. Drug loading did not affect the radiopacity and there was a direct relationship between bead attenuation and Dox concentration. The ability (Dox)-loaded DC Bead LUMI™ to be visualized in vivo was demonstrated by the administration of into hepatic arteries of a VX2 tumor-bearing rabbit under fluoroscopy, followed by subsequent CT imaging.

Interfacial modulus mapping of layered dental ceramics using nanoindentation.

PURPOSE: The aim of this study was to test the modulus of elasticity (E) across the interfaces of yttria stabilized zirconia (YTZP) / veneer multilayers using nanoindentation. MATERIALS AND METHODS: YTZP core material (KaVo-Everest, Germany) specimens were either coated with a liner (IPS e.max ZirLiner, Ivoclar-Vivadent) (Type-1) or left as-sintered (Type-2) and subsequently veneered with a pressable glass-ceramic (IPS e.max ZirPress, Ivoclar-Vivadent). A 5 µm (nominal tip diameter) spherical indenter was used with a UMIS CSIRO 2000 (ASI, Canberra, Australia) nanoindenter system to test E across the exposed and polished interfaces of both specimen types. The multiple point load - partial unload method was used for E determination. All materials used were characterized using Scanning Electron Microscopy (SEM) and X - ray powder diffraction (XRD). E mappings of the areas tested were produced from the nanoindentation data. RESULTS: A significantly (P<.05) lower E value between Type-1 and Type-2 specimens at a distance of 40 µm in the veneer material was associated with the liner. XRD and SEM characterization of the zirconia sample showed a fine grained bulk tetragonal phase. IPS e-max ZirPress and IPS e-max ZirLiner materials were characterized as amorphous. CONCLUSION: The liner between the YTZP core and the heat pressed veneer may act as a weak link in this dental multilayer due to its significantly (P<.05) lower E. The present study has shown nanoindentation using spherical indentation and the multiple point load - partial unload method to be reliable predictors of E and useful evaluation tools for layered dental ceramic interfaces.

Nanoscale-targeted patch-clamp recordings of functional presynaptic ion channels.

Direct electrical access to presynaptic ion channels has hitherto been limited to large specialized terminals such as the calyx of Held or hippocampal mossy fiber bouton. The electrophysiology and ion-channel complement of far more abundant small synaptic terminals (≤ 1 µm) remain poorly understood. Here we report a method based on superresolution scanning ion conductance imaging of small synapses in culture at approximately 100-150 nm 3D resolution, which allows presynaptic patch-clamp recordings in all four configurations (cell-attached, inside-out, outside-out, and whole-cell). Using this technique, we report presynaptic recordings of K(+), Na(+), Cl(-), and Ca(2+) channels. This semiautomated approach allows direct investigation of the distribution and properties of presynaptic ion channels at small central synapses.

Correlative light and volume electron microscopy: using focused ion beam scanning electron microscopy to image transient events in model organisms.

The study of a biological event within a live model organism has become routine through the use of fluorescent labeling of specific proteins in conjunction with laser confocal imaging. These methods allow 3D visualization of temporal events that can elucidate biological function but cannot resolve the tissue organization, extracellular and subcellular details of the tissues. Here, we present a method for correlating electron microscopy image data with the light microscopy data from the same sample volume to reveal the 3D structural information: "correlative light and volume electron microscopy." The methods for live video confocal microscopy, fixation and embedding of the tissue for electron microscopy, the focused ion beam scanning electron microscopy method for sequentially slicing and imaging the volume of interest, and the treatment of the resulting 3D dataset are presented. The method is illustrated with data collected during the angiogenesis of blood vessels in a transgenic zebrafish embryo.

High phosphate content significantly increases apatite formation of fluoride-containing bioactive glasses.

Bioactive glass-containing toothpastes for treating dentine hypersensitivity work by precipitating hydroxycarbonate apatite (HCA) onto the tooth surface, but concerns exist over the long-term durability of HCA in the mouth. Fluoride-containing bioactive glasses form fluorapatite (FAp) in physiological solutions, which is more chemically stable against acid attack. The influence of phosphate content on apatite formation was investigated by producing a low-phosphate (about 1 mol% P(2)O(5)) and a high-phosphate (about 6 mol%) series of melt-derived bioactive glasses in the system SiO(2)P(2)O(5)CaONa(2)O; increasing amounts of CaF(2) were added by keeping the ratio of all other components constant. pH change, ion release and apatite formation during immersion in Tris buffer at 37°C over up to 7 days were investigated. Crystal phases formed in Tris buffer were characterized using infrared spectroscopy, X-ray diffraction and solid-state nuclear magnetic resonance (NMR) spectroscopy. An increase in phosphate or fluoride content allowed for apatite formation at lower pH; fluoride enhanced apatite formation due to lower solubility of FAp compared to hydroxyapatite or HCA. High phosphate content glasses formed apatite significantly faster (within 6h) than low phosphate content glasses (within 3 days). In addition, an increase in phosphate content favoured apatite formation rather than fluorite (CaF(2)). (19)F magic angle spinning NMR showed the apatite formed by fluoride-containing glasses to be FAp, which makes these glasses of particular interest for dental applications. This study shows that by varying the phosphate content, the reactivity and apatite formation of bioactive glasses can be controlled successfully.

Imaging three-dimensional tissue architectures by focused ion beam scanning electron microscopy.

In this protocol, we describe a 3D imaging technique known as 'volume electron microscopy' or 'focused ion beam scanning electron microscopy (FIB/SEM)' applied to biological tissues. A scanning electron microscope equipped with a focused gallium ion beam, used to sequentially mill away the sample surface, and a backscattered electron (BSE) detector, used to image the milled surfaces, generates a large series of images that can be combined into a 3D rendered image of stained and embedded biological tissue. Structural information over volumes of tens of thousands of cubic micrometers is possible, revealing complex microanatomy with subcellular resolution. Methods are presented for tissue processing, for the enhancement of contrast with osmium tetroxide/potassium ferricyanide, for BSE imaging, for the preparation and platinum deposition over a selected site in the embedded tissue block, and for sequential data collection with ion beam milling; all this takes approximately 90 h. The imaging conditions, procedures for alternate milling and data acquisition and techniques for processing and partitioning the 3D data set are also described; these processes take approxiamtely 30 h. The protocol is illustrated by application to developing chick cornea, in which cells organize collagen fibril bundles into complex, multilamellar structures essential for transparency in the mature connective tissue matrix. The techniques described could have wide application in a range of fields, including pathology, developmental biology, microstructural anatomy and regenerative medicine.

Microstructure and mineral composition of dystrophic calcification associated with the idiopathic inflammatory myopathies.

INTRODUCTION: Calcified deposits (CDs) in skin and muscles are common in juvenile dermatomyositis (DM), and less frequent in adult DM. Limited information exists about the microstructure and composition of these deposits, and no information is available on their elemental composition and contents, mineral density (MD) and stiffness. We determined the microstructure, chemical composition, MD and stiffness of CDs obtained from DM patients. METHODS: Surgically-removed calcinosis specimens were analyzed with fourier transform infrared microspectroscopy in reflectance mode (FTIR-RM) to map their spatial distribution and composition, and with scanning electron microscopy/silicon drift detector energy dispersive X-ray spectrometry (SEM/SDD-EDS) to obtain elemental maps. X-ray diffraction (XRD) identified their mineral structure, X-ray micro-computed tomography (microCT) mapped their internal structure and 3D distribution, quantitative backscattered electron (qBSE) imaging assessed their morphology and MD, nanoindentation measured their stiffness, and polarized light microscopy (PLM) evaluated the organic matrix composition. RESULTS: Some specimens were composed of continuous carbonate apatite containing small amounts of proteins with a mineral to protein ratio much higher than in bone, and other specimens contained scattered agglomerates of various sizes with similar composition (FTIR-RM). Continuous or fragmented mineralization was present across the entire specimens (microCT). The apatite was much more crystallized than bone and dentin, and closer to enamel (XRD) and its calcium/phosphorous ratios were close to stoichiometric hydroxyapatite (SEM/SDD-EDS). The deposits also contained magnesium and sodium (SEM/SDD-EDS). The MD (qBSE) was closer to enamel than bone and dentin, as was the stiffness (nanoindentation) in the larger dense patches. Large mineralized areas were typically devoid of collagen; however, collagen was noted in some regions within the mineral or margins (PLM). qBSE, FTIR-RM and SEM/SDD-EDS maps suggest that the mineral is deposited first in a fragmented pattern followed by a wave of mineralization that incorporates these particles. Calcinosis masses with shorter duration appeared to have islands of mineralization, whereas longstanding deposits were solidly mineralized. CONCLUSIONS: The properties of the mineral present in the calcinosis masses are closest to that of enamel, while clearly differing from bone. Calcium and phosphate, normally present in affected tissues, may have precipitated as carbonate apatite due to local loss of mineralization inhibitors.

Imaging transient blood vessel fusion events in zebrafish by correlative volume electron microscopy.

The study of biological processes has become increasingly reliant on obtaining high-resolution spatial and temporal data through imaging techniques. As researchers demand molecular resolution of cellular events in the context of whole organisms, correlation of non-invasive live-organism imaging with electron microscopy in complex three-dimensional samples becomes critical. The developing blood vessels of vertebrates form a highly complex network which cannot be imaged at high resolution using traditional methods. Here we show that the point of fusion between growing blood vessels of transgenic zebrafish, identified in live confocal microscopy, can subsequently be traced through the structure of the organism using Focused Ion Beam/Scanning Electron Microscopy (FIB/SEM) and Serial Block Face/Scanning Electron Microscopy (SBF/SEM). The resulting data give unprecedented microanatomical detail of the zebrafish and, for the first time, allow visualization of the ultrastructure of a time-limited biological event within the context of a whole organism.

Nanomechanical properties and mineral concentration in articular calcified cartilage and subchondral bone.

We studied articular calcified cartilage (ACC) and the immediately subchondral bone (SCB) in normal and osteoarthritic human femoral heads. Thick slices of human normal reference post mortem (PM) and osteoarthritic (OA) femoral heads (age 55-89 years) were embedded in PMMA, micromilled, carbon coated and studied using quantitative backscattered electron (qBSE) imaging to determine variations in degree of mineralization. With exact microanatomical location, nanoindentation was performed on the same block faces in representative superior (more highly loaded) and medial regions of the joint surface. Using a partial unloading method, elastic modulus as a function of indenter penetration depth was determined using a spherical tipped diamond indenter. A pointed indenter was used to determine the tissue hardness in selected locations. The relationship between mineralization and indentation modulus was more distinct in ACC than in SCB, the latter having a higher matrix concentration with variable collagen orientation. In OA, the bulk of the measurements were coincident with those in the PM samples, although there was a greater range in the levels of mineralization and modulus in ACC. In OA, extremely hypermineralized ACC was found in ACC proper, especially in superior regions, and translocated into SCB and hyaline cartilage. The very highly mineralized cartilage fragments may function as a hard grinding abrasive, accelerating wear rates whether attached to or fragmented from the eburnated surfaces of OA ACC. Highly mineralized regions would also alter loading patterns and thereby contribute to further destruction of the joint tissues.