Live small-animal X-ray lung velocimetry and lung micro-tomography at the Australian Synchrotron Imaging and Medical Beamline.

The high flux and coherence produced at long synchrotron beamlines makes them well suited to performing phase-contrast X-ray imaging of the airways and lungs of live small animals. Here, findings of the first live-animal imaging on the Imaging and Medical Beamline (IMBL) at the Australian Synchrotron are reported, demonstrating the feasibility of performing dynamic lung motion measurement and high-resolution micro-tomography. Live anaesthetized mice were imaged using 30 keV monochromatic X-rays at a range of sample-to-detector propagation distances. A frame rate of 100 frames s(-1) allowed lung motion to be determined using X-ray velocimetry. A separate group of humanely killed mice and rats were imaged by computed tomography at high resolution. Images were reconstructed and rendered to demonstrate the capacity for detailed, user-directed display of relevant respiratory anatomy. The ability to perform X-ray velocimetry on live mice at the IMBL was successfully demonstrated. High-quality renderings of the head and lungs visualized both large structures and fine details of the nasal and respiratory anatomy. The effect of sample-to-detector propagation distance on contrast and resolution was also investigated, demonstrating that soft tissue contrast increases, and resolution decreases, with increasing propagation distance. This new capability to perform live-animal imaging and high-resolution micro-tomography at the IMBL enhances the capability for investigation of respiratory diseases and the acceleration of treatment development in Australia.

Feasibility study of propagation-based phase-contrast X-ray lung imaging on the Imaging and Medical beamline at the Australian Synchrotron.

Propagation-based phase-contrast X-ray imaging (PB-PCXI) using synchrotron radiation has achieved high-resolution imaging of the lungs of small animals both in real time and in vivo. Current studies are applying such imaging techniques to lung disease models to aid in diagnosis and treatment development. At the Australian Synchrotron, the Imaging and Medical beamline (IMBL) is well equipped for PB-PCXI, combining high flux and coherence with a beam size sufficient to image large animals, such as sheep, due to a wiggler source and source-to-sample distances of over 137 m. This study aimed to measure the capabilities of PB-PCXI on IMBL for imaging small animal lungs to study lung disease. The feasibility of combining this technique with computed tomography for three-dimensional imaging and X-ray velocimetry for studies of airflow and non-invasive lung function testing was also investigated. Detailed analysis of the role of the effective source size and sample-to-detector distance on lung image contrast was undertaken as well as phase retrieval for sample volume analysis. Results showed that PB-PCXI of lung phantoms and mouse lungs produced high-contrast images, with successful computed tomography and velocimetry also being carried out, suggesting that live animal lung imaging will also be feasible at the IMBL.

Tracking extended mucociliary transport activity of individual deposited particles: longitudinal synchrotron X-ray imaging in live mice.

To assess potential therapies for respiratory diseases in which mucociliary transit (MCT) is impaired, such as cystic fibrosis and primary ciliary dyskinesia, a novel and non-invasive MCT quantification method has been developed in which the transit rate and behaviour of individual micrometre-sized deposited particles are measured in live mice using synchrotron phase-contrast X-ray imaging. Particle clearance by MCT is known to be a two-phase process that occurs over a period of minutes to days. Previous studies have assessed MCT in the fast-clearance phase, ∼20 min after marker particle dosing. The aim of this study was to non-invasively image changes in particle presence and MCT during the slow-clearance phase, and simultaneously determine whether repeat synchrotron X-ray imaging of mice was feasible over periods of 3, 9 and 25 h. All mice tolerated the repeat imaging procedure with no adverse effects. Quantitative image analysis revealed that the particle MCT rate and the number of particles present in the airway both decreased with time. This study successfully demonstrated for the first time that longitudinal synchrotron X-ray imaging studies are possible in live small animals, provided appropriate animal handling techniques are used and care is taken to reduce the delivered radiation dose.

The sharpest tools in the box? Quantitative analysis of conodont element functional morphology.

Conodonts have been considered the earliest skeletonizing vertebrates and their mineralized feeding apparatus interpreted as having performed a tooth function. However, the absence of jaws in conodonts and the small size of their oropharyngeal musculature limits the force available for fracturing food items, presenting a challenge to this interpretation. We address this issue quantitatively using engineering approaches previously applied to mammalian dentitions. We show that the morphology of conodont food-processing elements was adapted to overcome size limitations through developing dental tools of unparalleled sharpness that maximize applied pressure. Combined with observations of wear, we also show how this morphology was employed, demonstrating how Wurmiella excavata used rotational kinematics similar to other conodonts, suggesting that this occlusal style is typical for the clade. Our work places conodont elements within a broader dental framework, providing a phylogenetically independent system for examining convergence and scaling in dental tools.

Dry deposition of pollutant and marker particles onto live mouse airway surfaces enhances monitoring of individual particle mucociliary transit behaviour.

Particles suspended in the air are inhaled during normal respiration and unless cleared by airway defences, such as the mucociliary transit (MCT) system, they can remain and affect lung and airway health. Synchrotron phase-contrast X-ray imaging (PCXI) methods have been developed to non-invasively monitor the behaviour of individual particles in live mouse airways and in previous studies the MCT behaviour of particles and fibres in the airways of live mice after deposition in a saline carrier fluid have been examined. In this study a range of common respirable pollutant particles (lead dust, quarry dust and fibreglass fibres) as well as marker particles (hollow glass micro-spheres) were delivered into the trachea of live mice using a dry powder insufflator to more accurately mimic normal environmental particulate exposure and deposition via inhalation. The behaviour of the particles once delivered onto the airway surface was tracked over a five minute period via PCXI. All particles were visible after deposition. Fibreglass fibres remained stationary throughout while all other particle types transited the tracheal surface throughout the imaging period. In all cases the majority of the particle deposition and any airway surface activity was located close to the dorsal tracheal wall. Both the individual and bulk motions of the glass bead marker particles were visible and their behaviour enabled otherwise hidden MCT patterns to be revealed. This study verified the value of PCXI for examining the post-deposition particulate MCT behaviour in the mouse trachea and highlighted that MCT is not a uniform process as suggested by radiolabel studies. It also directly revealed the advantages of dry particle delivery for establishing adequate particulate presence for visualizing MCT behaviour. The MCT behaviour and rate seen after dry particle delivery was different from that in previous carrier-fluid studies. It is proposed that dry particle delivery is essential for producing environmentally realistic particle deposition and studying how living airway surfaces handle different types of inhaled particles by MCT processes.

Testing microstructural adaptation in the earliest dental tools.

Conodont elements are the earliest vertebrate dental structures. The dental tools on elements responsible for food fracture-cusps and denticles-are usually composed of lamellar crown tissue (a putative enamel homologue) and the enigmatic tissue known as 'white matter'. White matter is unique to conodonts and has been hypothesized to be a functional adaptation for the use of elements as teeth. We test this quantitatively using finite-element analysis. Our results indicate that white matter allowed cusps and denticles to withstand greater tensile stresses than do cusps comprised solely of lamellar crown tissue. Microstructural variation is demonstrably associated with dietary and loading differences in teeth, so secondary loss of white matter through conodont phylogeny may reflect changes in diet and element occlusal kinematics. The presence, development and distribution of white matter could thus provide constraints on function in the first vertebrate dental structures.

Mechanism of substrate specificity in 5'-methylthioadenosine/S-adenosylhomocysteine nucleosidases.

5'-Methylthioadenosine/S-adenosylhomocysteine (MTA/SAH) nucleosidase (MTAN) plays a key role in the methionine-recycling pathway of bacteria and plants. Despite extensive structural and biochemical studies, the molecular mechanism of substrate specificity for MTAN remains an outstanding question. Bacterial MTANs show comparable efficiency in hydrolyzing MTA and SAH, while the plant enzymes select preferentially for MTA, with either no or significantly reduced activity towards SAH. Bacterial and plant MTANs show significant conservation in the overall structure, and the adenine- and ribose-binding sites. The observation of a more constricted 5'-alkylthio binding site in Arabidopsis thalianaAtMTAN1 and AtMTAN2, two plant MTAN homologues, led to the hypothesis that steric hindrance may play a role in substrate selection in plant MTANs. We show using isothermal titration calorimetry that SAH binds to both Escherichia coli MTAN (EcMTAN) and AtMTAN1 with comparable micromolar affinity. To understand why AtMTAN1 can bind but not hydrolyze SAH, we determined the structure of the protein-SAH complex at 2.2Å resolution. The lack of catalytic activity appears to be related to the enzyme's inability to bind the substrate in a catalytically competent manner. The role of dynamics in substrate selection was also examined by probing the amide proton exchange rates of EcMTAN and AtMTAN1 via deuterium-hydrogen exchange coupled mass spectrometry. These results correlate with the B factors of available structures and the thermodynamic parameters associated with substrate binding, and suggest a higher level of conformational flexibility in the active site of EcMTAN. Our results implicate dynamics as an important factor in substrate selection in MTAN.

Quantitative single-exposure x-ray phase contrast imaging using a single attenuation grid.

A single-exposure quantitative method of x-ray phase contrast imaging, suitable for animal in vivo observations, is described and shown experimentally both for a known static sample and an ex vivo biological airway. The ability to acquire the desired information within a single exposure is important for dynamic samples, as is sufficient sensitivity to reveal small variations in the composition or thickness of such a sample. This approach satisfies both these needs by analyzing how a reference grid pattern is deformed by the presence of the sample, similar to a Shack-Hartmann sensor. By resolving the shift of the pattern into horizontal and vertical components, a quantitative phase depth map is recovered, sensitive to both sharp edges as well as low phase gradients.

Quantitative x-ray phase-contrast imaging using a single grating of comparable pitch to sample feature size.

The ability to quantitatively retrieve transverse phase maps during imaging by using coherent x rays often requires a precise grating or analyzer-crystal-based setup. Imaging of live animals presents further challenges when these methods require multiple exposures for image reconstruction. We present a simple method of single-exposure, single-grating quantitative phase contrast for a regime in which the grating period is much greater than the effective pixel size. A grating is used to create a high-visibility reference pattern incident on the sample, which is distorted according to the complex refractive index and thickness of the sample. The resolution, along a line parallel to the grating, is not restricted by the grating spacing, and the detector resolution becomes the primary determinant of the spatial resolution. We present a method of analysis that maps the displacement of interrogation windows in order to retrieve a quantitative phase map. Application of this analysis to the imaging of known phantoms shows excellent correspondence.

Biotin synthase exhibits burst kinetics and multiple turnovers in the absence of inhibition by products and product-related biomolecules.

Biotin synthase (BS) is a member of the "SAM radical" superfamily of enzymes, which catalyze reactions in which the reversible or irreversible oxidation of various substrates is coupled to the reduction of the S-adenosyl-l-methionine (AdoMet) sulfonium to generate methionine and 5'-deoxyadenosine (dAH). Prior studies have demonstrated that these products are modest inhibitors of BS and other members of this enzyme family. In addition, the in vivo catalytic activity of Escherichia coli BS requires expression of 5'-methylthioadenosine/S-adenosyl-l-homocysteine nucleosidase, which hydrolyzes 5'-methylthioadenosine (MTA), S-adenosyl-l-homocysteine (AdoHcy), and dAH. In the present work, we confirm that dAH is a modest inhibitor of BS (K(i) = 20 µM) and show that cooperative binding of dAH with excess methionine results in a 3-fold enhancement of this inhibition. However, with regard to the other substrates of MTA/AdoHcy nucleosidase, we demonstrate that AdoHcy is a potent inhibitor of BS (K(i) ≤ 650 nM) while MTA is not an inhibitor. Inhibition by both dAH and AdoHcy likely accounts for the in vivo requirement for MTA/AdoHcy nucleosidase and may help to explain some of the experimental disparities between various laboratories studying BS. In addition, we examine possible inhibition by other AdoMet-related biomolecules present as common contaminants in commercial AdoMet preparations and/or generated during an assay, as well as by sinefungin, a natural product that is a known inhibitor of several AdoMet-dependent enzymes. Finally, we examine the catalytic activity of BS with highly purified AdoMet in the presence of MTAN to relieve product inhibition and present evidence suggesting that the enzyme is half-site active and capable of undergoing multiple turnovers in vitro.

A new technique to examine individual pollutant particle and fibre deposition and transit behaviour in live mouse trachea.

During respiration, particles suspended in the air are inhaled and unless cleared by airway defences they can remain and affect lung health. Their size precludes the use of standard imaging modalities so we have developed synchrotron phase-contrast X-ray imaging (PCXI) methods to non-invasively monitor the behaviour of individual particles in live mouse airways. In this study we used these techniques to examine post-deposition particle behaviour in the trachea. PCXI was used to monitor the deposition and subsequent behaviour of particles of quarry dust and lead ore; fibres of asbestos and fibreglass; and hollow glass micro-spheres. Visibility was examined in vitro and ex vivo to avoid the complicating effects of surrounding tissue and respiratory or cardiac motion. Particle behaviour was then examined after deposition onto the tracheal airway surfaces of live mice. Each particle and fibre looked and behaved differently on the airway surface. Particles lodged on the airway shortly after deposition, and the rate at which this occurred was dependent on the particle type and size. After the live-imaging experiments, excised airway samples were examined using light and electron microscopy. Evidence of particle capture into the airway surface fluids and the epithelial cell layer was found. PCXI is a valuable tool for examining post-deposition particulate behaviour in the tracheal airway. These first indications that the interaction between airways and individual particles may depend on the particle type and size should provide a novel approach to studying the early effects of respired particles on airway health.

Real-time non-invasive detection of inhalable particulates delivered into live mouse airways.

Fine non-biological particles small enough to be suspended in the air are continually inhaled as we breathe. These particles deposit on airway surfaces where they are either cleared by airway defences or can remain and affect lung health. Pollutant particles from vehicles, building processes and mineral and industrial dusts have the potential to cause both immediate and delayed health problems. Because of their small size, it has not been possible to non-invasively examine how individual particles deposit on live airways, or to consider how they behave on the airway surface after deposition. In this study, synchrotron phase-contrast X-ray imaging (PCXI) has been utilized to detect and monitor individual particle deposition. The in vitro detectability of a range of potentially respirable particulates was first determined. Of the particulates tested, only asbestos, quarry dust, fibreglass and galena (lead sulfate) were visible in vitro. These particulates were then examined after delivery into the nasal airway of live anaesthetized mice; all were detectable in vivo but each exhibited different surface appearances and behaviour along the airway surface. The two fibrous particulates appeared as agglomerations enveloped by fluid, while the non-fibrous particulates were present as individual particles. Synchrotron PCXI provides the unique ability to non-invasively detect and track deposition of individual particulates in live mouse airways. With further refinement of particulate sizing and delivery techniques, PCXI should provide a novel approach for live animal monitoring of airway particulates relevant to lung health.

Inspiration regulates the rate and temporal pattern of lung liquid clearance and lung aeration at birth.

At birth, the initiation of pulmonary gas exchange is dependent on air entry into the lungs, and recent evidence indicates that pressures generated by inspiration may be involved. We have used simultaneous plethysmography and phase-contrast X-ray imaging to investigate the contribution of inspiration and expiratory braking maneuvers (EBMs) to lung aeration and the formation of a functional residual capacity (FRC) after birth. Near-term rabbit pups (n = 26) were delivered by cesarean section, placed in a water plethysmograph, and imaged during the initiation of spontaneous breathing. Breath-by-breath changes in lung gas volumes were measured using plethysmography and visualized using phase-contrast X-ray imaging. Pups rapidly (1-5 breaths) generate a FRC (16.2 +/- 1.2 ml/kg) by inhaling a greater volume than they expire (by 2.9 +/- 0.4 ml.kg(-1).breath(-1) over the first 5 breaths). As a result, 94.8 +/- 1.4% of lung aeration occurred during inspiration over multiple breaths. The incidence of EBMs was rare early during lung aeration, with most (>80%) occurring after >80% of max FRC was achieved. Although EBMs were associated with an overall increase in FRC, 34.8 +/- 5.3% of EBMs were associated with a decrease in FRC. We conclude that lung aeration is predominantly achieved by inspiratory efforts and that EBMs help to maintain FRC following its formation.

Mapping structural changes in breast tissue disease using x-ray scattering.

Spread of invasive carcinoma throughout breast tissue is believed to occur at supramolecular levels, beyond the range of standard histopathology identification. Small angle x-ray scattering (SAXS) is capable of characterizing the structural properties of collagen and tissue found in the breast at the scale of tens to hundreds of nanometers. Fifty-six patients who were treated with wide-local excision or mastectomy had tissue biopsy samples analyzed at 2 cm intervals along two perpendicular axes over their excised mass, up to 6 cm away from the primary site of the tumor. Two SAXS parameters, the integrated amorphous scatter and the third order collagen axial d spacing, showed significant differences between the center (0 cm) and distant tissues (2, 4, or 6 cm from the primary lesion). There was no evidence of directional trends (superior, inferior, or lateral sides of the nipple) of these two parameters over the breast. Mapping of these two variables over a two-dimensional grid showed good matching with independent histopathology diagnosis. These results suggest that SAXS may be capable of identifying areas of invasion or directional spread of disease as well as providing more information at the supramolecular level for aiding tissue diagnosis.

Imaging lung aeration and lung liquid clearance at birth using phase contrast X-ray imaging.

The transition to extra-uterine life at birth is critically dependent on airway liquid clearance to allow the entry of air and the onset of gaseous ventilation. We have used phase contrast X-ray imaging to identify factors that regulate lung aeration at birth in spontaneously breathing term and mechanically ventilated preterm rabbit pups. Phase contrast X-ray imaging exploits the difference in refractive index between air and water to enhance image contrast, enabling the smallest air-filled structures of the lung (alveoli; < 100 microm) to be resolved. Using this technique, the lungs become visible as they aerate, allowing the air-liquid interface to be observed as it moves distally during lung aeration. Spontaneously breathing term rabbit pups rapidly aerate their lungs, with most fully recruiting their functional residual capacity (FRC) within the first few breaths. The increase in FRC occurs mainly during individual breaths, demonstrating that airway liquid clearance and lung aeration is closely associated with inspiration. We suggest that transpulmonary pressures generated by inspiration provide a hydrostatic pressure gradient for the movement of water out of the airways and into the surrounding lung tissue after birth. In mechanically ventilated preterm pups, lung aeration is closely associated with lung inflation and a positive end-expiratory pressure is required to generate and maintain FRC after birth. In summary, phase contrast X-ray imaging can image the air-filled lung with high temporal and spatial resolution and is ideal for identifying factors that regulate lung aeration at birth in both spontaneously breathing term and mechanically ventilated preterm neonates.

Imaging lung aeration and lung liquid clearance at birth.

Aeration of the lung and the transition to air-breathing at birth is fundamental to mammalian life and initiates major changes in cardiopulmonary physiology. However, the dynamics of this process and the factors involved are largely unknown, because it has not been possible to observe or measure lung aeration on a breath-by-breath basis. We have used the high contrast and spatial resolution of phase contrast X-ray imaging to study lung aeration at birth in spontaneously breathing neonatal rabbits. As the liquid-filled fetal lungs provide little absorption or phase contrast, they are not visible and only become visible as they aerate, allowing a detailed examination of this process. Pups were imaged live from birth to determine the timing and spatial pattern of lung aeration, and relative levels of lung aeration were measured from the images using a power spectral analysis. We report the first detailed observations and measurements of lung aeration, demonstrating its dependence on inspiratory activity and body position; dependent regions aerated at much slower rates. The air/liquid interface moved toward the distal airways only during inspiration, with little proximal movement during expiration, indicating that trans-pulmonary pressures play an important role in airway liquid clearance at birth. Using these imaging techniques, the dynamics of lung aeration and the critical role it plays in regulating the physiological changes at birth can be fully explored.

X-ray scattering for classifying tissue types associated with breast disease.

Collagen types I and III can be characterized at the molecular level (at the tens to hundreds of nanometers scale) using small angle x-ray scattering (SAXS). Although collagen fibril structural parameters at this length scale have shown differences between diseased and nondiseased breast tissues, a comprehensive analysis involving a multitude of features with a large (>50) patient cohort has not previously been investigated. Breast tissue samples were excised from 80 patients presenting with either a breast lump or reduction mammoplasty. From these, invasive carcinoma, benign tissue, and normal parenchyma were analyzed. Parameters related to collagen structure, including longitudinal (axial) and lateral (equatorial) features, polar angle features, total scattering intensity, and tissue heterogeneity effects, were extracted from the SAXS patterns and examined. The amplitude of the third-order axial peak and the total scattering intensity (amorphous scatter) showed the most separation between tissue groups and a classification model using these two parameters demonstrated an accuracy of over 95% between invasive carcinoma and mammoplasty patients. Normal tissue taken from disease-free patients (mammoplasty) and normal tissue taken from patients with presence of disease showed significant differences, suggesting that SAXS may provide different diagnostic information from that of conventional histopathology.

Structure of Staphylococcus aureus 5'-methylthioadenosine/S-adenosylhomocysteine nucleosidase.

5'-Methylthioadenosine/S-adenosylhomocysteine nucleosidase (MTAN) catalyzes the irreversible cleavage of the glycosidic bond in 5'-methylthioadenosine (MTA) and S-adenosylhomocysteine (SAH) and plays a key role in four metabolic processes: biological methylation, polyamine biosynthesis, methionine recycling and bacterial quorum sensing. The absence of the nucleosidase in mammalian species has implicated this enzyme as a target for antimicrobial drug design. MTAN from the pathogenic bacterium Staphylococcus aureus (SaMTAN) has been kinetically characterized and its structure has been determined in complex with the transition-state analogue formycin A (FMA) at 1.7 A resolution. A comparison of the SaMTAN-FMA complex with available Escherichia coli MTAN structures shows strong conservation of the overall structure and in particular of the active site. The presence of an extra water molecule, which forms a hydrogen bond to the O4' atom of formycin A in the active site of SaMTAN, produces electron withdrawal from the ribosyl group and may explain the lower catalytic efficiency that SaMTAN exhibits when metabolizing MTA and SAH relative to the E. coli enzyme. The implications of this structure for broad-based antibiotic design are discussed.

Quantification of heterogeneity in lung disease with image-based pulmonary function testing.

Computed tomography (CT) and spirometry are the mainstays of clinical pulmonary assessment. Spirometry is effort dependent and only provides a single global measure that is insensitive for regional disease, and as such, poor for capturing the early onset of lung disease, especially patchy disease such as cystic fibrosis lung disease. CT sensitively measures change in structure associated with advanced lung disease. However, obstructions in the peripheral airways and early onset of lung stiffening are often difficult to detect. Furthermore, CT imaging poses a radiation risk, particularly for young children, and dose reduction tends to result in reduced resolution. Here, we apply a series of lung tissue motion analyses, to achieve regional pulmonary function assessment in ß-ENaC-overexpressing mice, a well-established model of lung disease. The expiratory time constants of regional airflows in the segmented airway tree were quantified as a measure of regional lung function. Our results showed marked heterogeneous lung function in ß-ENaC-Tg mice compared to wild-type littermate controls; identified locations of airway obstruction, and quantified regions of bimodal airway resistance demonstrating lung compensation. These results demonstrate the applicability of regional lung function derived from lung motion as an effective alternative respiratory diagnostic tool.