Gene expression detection in developing mouse tissue using in situ hybridization and µCT imaging.

High resolution and noninvasiveness have made soft-tissue X-ray microtomography (µCT) a widely applicable three-dimensional (3D) imaging method in studies of morphology and development. However, scarcity of molecular probes to visualize gene activity with µCT has remained a challenge. Here, we apply horseradish peroxidase-assisted reduction of silver and catalytic gold enhancement of the silver deposit to in situ hybridization in order to detect gene expression in developing tissues with µCT (here called GECT, gene expression CT). We show that GECT detects expression patterns of collagen type II alpha 1 and sonic hedgehog in developing mouse tissues comparably with an alkaline phosphatase-based detection method. After detection, expression patterns are visualized with laboratory µCT, demonstrating that GECT is compatible with varying levels of gene expression and varying sizes of expression regions. Additionally, we show that the method is compatible with prior phosphotungstic acid staining, a conventional contrast staining approach in µCT imaging of soft tissues. Overall, GECT is a method that can be integrated with existing laboratory routines to obtain spatially accurate 3D detection of gene expression.

Xylem embolism and bubble formation during freezing suggest complex dynamics of pressure in Betula pendula stems.

Freeze-thaw-induced embolism, a key limiting factor for perennial plants results from the formation of gas bubbles during freezing and their expansion during thawing. However, the ice volumetric increase generates local pressures, which can affect the formation of bubbles. To characterize local dynamics of pressure tension and the physical state of the sap during freeze-thaw cycles, we simultaneously used ultrasonic acoustic emission analysis and synchrotron-based high-resolution computed tomography on the diffuse-porous species Betula pendula. Visualization of individual air-filled vessels and the distribution of gas bubbles in frozen xylem were performed.. Ultrasonic emissions occurred after ice formation, together with bubble formation, whereas the development of embolism took place after thawing. The pictures of frozen tissues indicated that the positive pressure induced by the volumetric increase of ice can provoke inward flow from the cell wall toward the lumen of the vessels. We found no evidence that wider vessels within a tissue were more prone to embolism, although the occurrence of gas bubbles in larger conduits would make them prone to earlier embolism. These results highlight the need to monitor local pressure as well as ice and air distribution during xylem freezing to understand the mechanism leading to frost-induced embolism.

Brown Coal and Logwood Combustion in a Modern Heating Appliance: The Impact of Combustion Quality and Fuel on Organic Aerosol Composition.

Residential heating with solid fuels is one of the major drivers for poor air quality in Central and Eastern Europe, and coal is still one of the major fuels in countries, such as Poland, the Czech Republic, and Hungary. In this work, emissions from a single-room heater fueled with brown coal briquettes (BCBs) and spruce logs (SLs) were analyzed for signatures of inorganic as well as semivolatile aromatic and low-volatile organic constituents. High variations in organic carbon (OC) emissions of BCB emissions, ranging from 5 to 22 mg MJ-1, were associated to variations in carbon monoxide (CO) emissions, ranging from 900 to 1900 mg MJ-1. Residential BCB combustion turned out to be an equally important source of levoglucosan, an established biomass burning marker, as spruce logwood combustion, but showed distinct higher ratios to manosan and galactosan. Signatures of polycyclic aromatic hydrocarbons emitted by BCB combustion exhibited defunctionalization and desubstitution with increasing combustion quality. Lastly, the concept of island and archipelago structural motifs adapted from petroleomics is used to describe the fraction low-volatile organic compounds in particulate emissions, where a transition from archipelago to island motifs in relation with decreasing CO emissions was observed in BCB emissions, while emissions from SL combustion exhibited the island motif.

The impact and recovery of asteroid 2018 LA.

The June 2, 2018, impact of asteroid 2018 LA over Botswana is only the second asteroid detected in space prior to impacting over land. Here, we report on the successful recovery of meteorites. Additional astrometric data refine the approach orbit and define the spin period and shape of the asteroid. Video observations of the fireball constrain the asteroid's position in its orbit and were used to triangulate the location of the fireball's main flare over the Central Kalahari Game Reserve. 23 meteorites were recovered. A consortium study of eight of these classifies Motopi Pan as a HED polymict breccia derived from howardite, cumulate and basaltic eucrite, and diogenite lithologies. Before impact, 2018 LA was a solid rock of ~156 cm diameter with high bulk density ~2.85 g/cm3, a relatively low albedo pv ~ 0.25, no significant opposition effect on the asteroid brightness, and an impact kinetic energy of ~0.2 kt. The orbit of 2018 LA is consistent with an origin at Vesta (or its Vestoids) and delivery into an Earth-impacting orbit via the v6 resonance. The impact that ejected 2018 LA in an orbit towards Earth occurred 22.8 ± 3.8 Ma ago. Zircons record a concordant U-Pb age of 4563 ± 11 Ma and a consistent 207Pb/206Pb age of 4563 ± 6 Ma. A much younger Pb-Pb phosphate resetting age of 4234 ± 41 Ma was found. From this impact chronology, we discuss what is the possible source crater of Motopi Pan and the age of Vesta's Veneneia impact basin.

Influence of wood species on toxicity of log-wood stove combustion aerosols: a parallel animal and air-liquid interface cell exposure study on spruce and pine smoke.

BACKGROUND: Wood combustion emissions have been studied previously either by in vitro or in vivo models using collected particles, yet most studies have neglected gaseous compounds. Furthermore, a more accurate and holistic view of the toxicity of aerosols can be gained with parallel in vitro and in vivo studies using direct exposure methods. Moreover, modern exposure techniques such as air-liquid interface (ALI) exposures enable better assessment of the toxicity of the applied aerosols than, for example, the previous state-of-the-art submerged cell exposure techniques. METHODS: We used three different ALI exposure systems in parallel to study the toxicological effects of spruce and pine combustion emissions in human alveolar epithelial (A549) and murine macrophage (RAW264.7) cell lines. A whole-body mouse inhalation system was also used to expose C57BL/6 J mice to aerosol emissions. Moreover, gaseous and particulate fractions were studied separately in one of the cell exposure systems. After exposure, the cells and animals were measured for various parameters of cytotoxicity, inflammation, genotoxicity, transcriptome and proteome. RESULTS: We found that diluted (1:15) exposure pine combustion emissions (PM1 mass 7.7 ± 6.5 mg m- 3, 41 mg MJ- 1) contained, on average, more PM and polycyclic aromatic hydrocarbons (PAHs) than spruce (PM1 mass 4.3 ± 5.1 mg m- 3, 26 mg MJ- 1) emissions, which instead showed a higher concentration of inorganic metals in the emission aerosol. Both A549 cells and mice exposed to these emissions showed low levels of inflammation but significantly increased genotoxicity. Gaseous emission compounds produced similar genotoxicity and a higher inflammatory response than the corresponding complete combustion emission in A549 cells. Systems biology approaches supported the findings, but we detected differing responses between in vivo and in vitro experiments. CONCLUSIONS: Comprehensive in vitro and in vivo exposure studies with emission characterization and systems biology approaches revealed further information on the effects of combustion aerosol toxicity than could be achieved with either method alone. Interestingly, in vitro and in vivo exposures showed the opposite order of the highest DNA damage. In vitro measurements also indicated that the gaseous fraction of emission aerosols may be more important in causing adverse toxicological effects. Combustion aerosols of different wood species result in mild but aerosol specific in vitro and in vivo effects.

Direct three-dimensional imaging of polymer-water interfaces by nanoscale hard X-ray phase tomography.

We report three-dimensional (3D) direct imaging of complex surface-liquid interfaces by hard X-ray phase contrast tomography as a non-destructive approach for the morphological characterization of surfaces at the micro- and nanoscale in contact with water. Specifically, we apply this method to study the solid-air-water interface in hydrophobic macroporous polymethacrylate surfaces, and the solid-oil-water interface in slippery liquid-infused porous surfaces (SLIPS). Varying the isotropic spatial resolution allows the 3D quantitative characterization of individual polymer globules, globular clusters (porosity) as well as the infused lubricant layer on SLIPS. Surface defects were resolved at the globular level. We show the first application of X-ray nanotomography to hydrated surface characterizations and we anticipate that X-ray nanoscale imaging will open new ways for various surface/interface studies.

Optimization of contrast and dose in x-ray phase-contrast tomography with a Talbot-Lau interferometer.

X-ray phase-contrast imaging has become a valuable tool for biomedical research due to its improved contrast abilities over regular attenuation-based imaging. The recently emerged Talbot-Lau interferometer can provide quantitative attenuation, phase-contrast and dark-field image data, even with low-brilliance x-ray tube sources. Thus, it has become a valid option for clinical environments. In this study, we analyze the effects of x-ray tube voltage and total number of images on the contrast-to-noise ratio (CNR) and dose-weighted CNR (CNRD) calculated from tomographic transmission and phase-contrast data of a phantom sample. Constant counting statistics regardless of the voltage was ensured by adjusting the image exposure time for each voltage setting. The results indicate that the x-ray tube voltage has a clear effect on both image contrast and noise. This effect is amplified in the case of phase-contrast images, which is explained by the polychromatic x-ray spectrum and the dependence of interferometer visibility on the spectrum. CNRD is additionally affected by the total imaging time. While submerging the sample into a water container effectively reduces image artefacts and improves the CNR, the additional attenuation of the water must be compensated with a longer exposure time. This reduces dose efficiency. Both the CNR and CNRD are higher in the phase-contrast images compared to transmission images. For transmission images, and phase-contrast images without the water container, CNRD can be increased by using higher tube voltages (in combination with a lower exposure time). For phase-contrast images with the water container, CNRD is increased with lower tube voltages. In general, the CNRD does not strongly depend on the number of tomographic angles or phase steps used.

Multi-scale correlation of impact-induced defects in carbon fiber composites using X-ray scattering and machine learning.

Impact-induced defects in carbon fiber-reinforced polymers (CFRPs)-spanning from nanometer to macroscopic length scales-can be monitored using an aggregate of X-ray-based methods, but this is impractical in typical field conditions. We report on a low-velocity impacted CFRP, which is mapped using small- and wide-angle X-ray scattering and X-ray computed tomography, and employ machine learning for correlating material parameterizations derived from these techniques. The observed 1 µ m to 1 mm-sized defects are parameterized in terms of relative density and fiber orientation indicative of fiber failures (kink bands), and the nanometer sized defects in terms of crystal size and unit cell frustration. The 30 to 300 nm defects are parameterized by a power-law scattering decay, differentiating fractal-like behaviors. We find three spatial domains experimentally and by K-means Clustering: Domains of severe damage (with a visual dent), intact domains (without visual or measurable defects) and a transition domain (defects measurable by X-rays). How the parameters are correlated and how they overlap between the domains are discussed. All parameters are able to point to the detrimental fiber breakage in the severe damage domain, and scattering decay also in the transition domain, for example. How individual parameters determined from one experimental technique can be predicted from that of another is also described.

The origins of mammal growth patterns during the Jurassic mammalian radiation.

We use synchrotron x-ray tomography of annual growth increments in the dental cementum of mammaliaforms (stem and crown fossil mammals) from three faunas across the Jurassic to map the origin of patterns of mammalian growth patterns, which are intrinsically related to mammalian endothermy. Although all fossils studied exhibited slower growth rates, longer life spans, and delayed sexual maturity relative to comparably sized extant mammals, the earliest crown mammals developed significantly faster growth rates in early life that reduced at sexual maturity, compared to stem mammaliaforms. Estimation of basal metabolic rates (BMRs) suggests that some fossil crown mammals had BMRs approaching the lowest rates of extant mammals. We suggest that mammalian growth patterns first evolved during their mid-Jurassic adaptive radiation, although growth remained slower than in extant mammals.

Improved light extraction in the bioluminescent lantern of a Photuris firefly (Lampyridae).

A common problem of light sources emitting from an homogeneous high-refractive index medium into air is the loss of photons by total internal reflection. Bioluminescent organisms, as well as artificial devices, have to face this problem. It is expected that life, with its mechanisms for evolution, would have selected appropriate optical structures to get around this problem, at least partially. The morphology of the lantern of a specific firefly in the genus Photuris has been examined. The optical properties of the different parts of this lantern have been modelled, in order to determine their positive or adverse effect with regard to the global light extraction. We conclude that the most efficient pieces of the lantern structure are the misfit of the external scales (which produce abrupt roughness in air) and the lowering of the refractive index at the level of the cluster of photocytes, where the bioluminescent production takes place.

Phase retrieval in in-line x-ray phase contrast imaging based on total variation minimization.

State-of-the-art techniques for phase retrieval in propagation based X-ray phase-contrast imaging are aiming to solve an underdetermined linear system of equations. They commonly employ Tikhonov regularization - an L2-norm regularized deconvolution scheme - despite some of its limitations. We present a novel approach to phase retrieval based on Total Variation (TV) minimization. We incorporated TV minimization for deconvolution in phase retrieval using a variety of the most common linear phase-contrast models. The results of our TV minimization was compared with Tikhonov regularized deconvolution on simulated as well as experimental data. The presented method was shown to deliver improved accuracy in reconstructions based on a single distance as well as multiple distance phase-contrast images corrupted by noise and hampered by errors due to nonlinear imaging effects.

Effect of positive end-expiratory pressure on regional ventilation distribution during mechanical ventilation after surfactant depletion.

BACKGROUND: Ventilator-induced lung injury occurs due to exaggerated local stresses, repeated collapse, and opening of terminal air spaces in poorly aerated dependent lung, and increased stretch in nondependent lung. The aim of this study was to quantify the functional behavior of peripheral lung units in whole-lung lavage-induced surfactant depletion, and to assess the effect of positive end-expiratory pressure. METHODS: The authors used synchrotron imaging to measure lung aeration and regional specific ventilation at positive end-expiratory pressure of 3 and 9 cm H2O, before and after whole-lung lavage in rabbits. Respiratory mechanical parameters were measured, and helium-washout was used to assess end-expiratory lung volume. RESULTS: Atelectatic, poorly, normally aerated, hyperinflated, and trapped regions could be identified using the imaging technique used in this study. Surfactant depletion significantly increased atelectasis (6.3±3.3 [mean±SEM]% total lung area; P=0.04 vs. control) and poor aeration in dependent lung. Regional ventilation was distributed to poorly aerated regions with high (16.4±4.4%; P<0.001), normal (20.7±5.9%; P<0.001 vs. control), and low (5.7±1.2%; P<0.05 vs. control) specific ventilation. Significant redistribution of ventilation to normally aerated nondependent lung regions occurred (41.0±9.6%; P=0.03 vs. control). Increasing positive end-expiratory pressure level to 9 cm H2O significantly reduced poor aeration and recruited atelectasis, but ventilation redistribution persisted (39.2±9.5%; P<0.001 vs. control). CONCLUSIONS: Ventilation of poorly aerated dependent lung regions, which can promote the local concentration of mechanical stresses, was the predominant functional behavior in surfactant-depleted lung. Potential tidal recruitment of atelectatic lung regions involved a smaller fraction of the imaged lung. Significant ventilation redistribution to aerated lung regions places these at risk of increased stretch injury.

Hierarchically guided in situ nanolaminography for the visualisation of damage nucleation in alloy sheets.

Hierarchical guidance is developed for three-dimensional (3D) nanoscale X-ray imaging, enabling identification, refinement, and tracking of regions of interest (ROIs) within specimens considerably exceeding the field of view. This opens up new possibilities for in situ investigations. Experimentally, the approach takes advantage of rapid multiscale measurements based on magnified projection microscopy featuring continuous zoom capabilities. Immediate and continuous feedback on the subsequent experimental progress is enabled by suitable on-the-fly data processing. For this, by theoretical justification and experimental validation, so-called quasi-particle phase-retrieval is generalised to conical-beam conditions, being key for sufficiently fast computation without significant loss of imaging quality and resolution compared to common approaches for holographic microscopy. Exploiting 3D laminography, particularly suited for imaging of ROIs in laterally extended plate-like samples, the potential of hierarchical guidance is demonstrated by the in situ investigation of damage nucleation inside alloy sheets under engineering-relevant boundary conditions, providing novel insight into the nanoscale morphological development of void and particle clusters under mechanical load. Combined with digital volume correlation, we study deformation kinematics with unprecedented spatial resolution. Correlation of mesoscale (i.e. strain fields) and nanoscale (i.e. particle cracking) evolution opens new routes for the understanding of damage nucleation within sheet materials with application-relevant dimensions.

Combined use of hard X-ray phase contrast imaging and X-ray fluorescence microscopy for sub-cellular metal quantification.

Hard X-ray fluorescence microscopy and magnified phase contrast imaging are combined to obtain quantitative maps of the projected metal concentration in whole cells. The experiments were performed on freeze dried cells at the nano-imaging station ID22NI of the European Synchrotron Radiation Facility (ESRF). X-ray fluorescence analysis gives the areal mass of most major, minor and trace elements; it is validated using a biological standard of known composition. Quantitative phase contrast imaging provides maps of the projected mass and is validated using calibration samples and through comparison with Atomic Force Microscopy and Scanning Transmission Ion Microscopy. Up to now, absolute quantification at the sub-cellular level was impossible using X-ray fluorescence microscopy but can be reached with the use of the proposed approach.

Status of the hard X-ray microprobe beamline ID22 of the European Synchrotron Radiation Facility.

The ESRF synchrotron beamline ID22, dedicated to hard X-ray microanalysis and consisting of the combination of X-ray fluorescence, X-ray absorption spectroscopy, diffraction and 2D/3D X-ray imaging techniques, is one of the most versatile instruments in hard X-ray microscopy science. This paper describes the present beamline characteristics, recent technical developments, as well as a few scientific examples from recent years of the beamline operation. The upgrade plans to adapt the beamline to the growing needs of the user community are briefly discussed.

Comparison of image quality in computed laminography and tomography.

In computed tomography (CT), projection images of the sample are acquired over an angular range between 180 to 360 degrees around a rotation axis. A special case of CT is that of limited-angle CT, where some of the rotation angles are inaccessible, leading to artefacts in the reconstrucion because of missing information. The case of flat samples is considered, where the projection angles that are close to the sample surface are either i) completely unavailable or ii) very noisy due to the limited transmission at these angles. Computed laminography (CL) is an imaging technique especially suited for flat samples. CL is a generalization of CT that uses a rotation axis tilted by less than 90 degrees with respect to the incident beam. Thus CL avoids using projections from angles closest to the sample surface. We make a quantitative comparison of the imaging artefacts between CL and limited-angle CT for the case of a parallel-beam geometry. Both experimental and simulated images are used to characterize the effect of the artefacts on the resolution and visible image features. The results indicate that CL has an advantage over CT in cases when the missing angular range is a significant portion of the total angular range. In the case when the quality of the projections is limited by noise, CT allows a better tradeoff between the noise level and the missing angular range.

Physical Properties of Extrudates with Fibrous Structures Made of Faba Bean Protein Ingredients Using High Moisture Extrusion.

Faba bean is a potential ingredient due to its high protein yield and its possible cultivation in colder climate regions. In this study, meat analogues made from faba bean protein isolate (FPI) and concentrate (FPC) blends were produced using high moisture extrusion. The aim of this study was to investigate the effect of the FPI content (FPIc), feed water content (FWC), and temperature of the long cooling die (LT) during extrusion on the mechanical and physicochemical properties as well as on the structure of the meat analogues. Increased FPIc resulted in higher values in hardness, gumminess, chewiness, and cutting strengths as well as in darker colour and decreased water absorption capacity. The effect of increased FWC on these properties was weaker and the opposite. Images from microtomography revealed that higher FPIc led to a less organised fibrous structure. In conclusion, fibrous structures can be achieved by utilising a mixture of faba bean protein ingredients, and a higher FPC content seemed to promote fibre formation in the meat analogue.

Genotoxic and inflammatory effects of spruce and brown coal briquettes combustion aerosols on lung cells at the air-liquid interface.

Solid fuel usage in residential heating and cooking is one of the largest sources of ambient and indoor air particulate matter, which causes adverse effects on the health of millions of peoples worldwide. Emissions from solid fuel combustion, such as biomass or coal, are detrimental to health, but toxicological responses are largely unknown. In the present study, we compared the toxicological responses regarding cytotoxicity, inflammation and genotoxicity of spruce (SPR) and brown coal briquette (BCB) combustion aerosols on human alveolar epithelial cells (A549) as well as a coculture of A549 and differentiated human monocytic cells (THP-1) into macrophages exposed at the air-liquid interface (ALI). We included both the high emissions from the first hour and moderate emissions from the third hour of the batch combustion experiment in one ALI system, whereas, in the second ALI system, we exposed the cells during the whole 4-hour combustion experiment, including all combustion phases. Physico-chemical properties of the combustion aerosol were analysed both online and offline. Both SPR and BCB combustion aerosols caused mild cytotoxic but notable genotoxic effects in co-cultured A549 cells after one-hour exposure. Inflammatory response analysis revealed BCB combustion aerosols to cause a mild increase in CXCL1 and CXCL8 levels, but in the case of SPR combustion aerosol, a decrease compared to control was observed.

Effect of positive end-expiratory pressure on regional ventilation distribution during bronchoconstriction in rabbit studied by synchrotron radiation imaging.

OBJECTIVE: To assess the effects of positive end-expiratory pressure on regional ventilation distribution in normal lung and after histamine-induced bronchoconstriction. DESIGN: Experimental study. SETTING: International research laboratory. SUBJECTS: Six healthy New Zealand rabbits weighing 2.5 ± 0.1 kg. INTERVENTIONS: Rabbits were anesthetized, tracheostomized, paralyzed, and mechanically ventilated. Synchrotron radiation computed tomography images of tissue density and specific ventilation were acquired using K-edge subtraction imaging with inhaled stable xenon gas in middle and caudal thoracic levels on 0 and 5 cm H(2)O positive end-expiratory pressure at baseline and twice after histamine inhalation. MEASUREMENTS AND MAIN RESULTS: At baseline, a positive end-expiratory pressure of 5 cm H(2)O significantly increased lung volume. Histamine inhalation caused patchy areas of decreased specific ventilation, including some areas with no ventilation. After histamine, positive end-expiratory pressure significantly increased the area of well-ventilated lung regions and decreased the heterogeneity of specific ventilation. This improvement went together with a significant but limited increase in the area of hyperinflated lung zones. CONCLUSIONS: The findings of this study suggest that in mechanically ventilated rabbit with severely heterogeneous bronchoconstriction, a positive end-expiratory pressure of 5 cm H(2)O significantly improves regional ventilation homogeneity through dilation of flow-limited airways and recruitment of closed airways.

Acute cigarette smoke inhalation blunts lung responsiveness to methacholine and allergen in rabbit: differentiation of central and peripheral effects.

Despite the prevalence of active smoking in asthmatics, data on the short-term effect of acute mainstream tobacco smoke exposure on airway responsiveness are very scarce. The aim of this study was to assess the immediate effect of acute exposure to mainstream cigarette smoke on airway reactivity to subsequent nonspecific and allergenic challenges in healthy control (n = 5) and ovalbumin-sensitized rabbits (n = 6). We combined low-frequency forced oscillations and synchrotron radiation CT imaging to differentiate central airway and peripheral airway and lung parenchymal components of the response to airway provocation. Acute exposure to smoke generated by four successive cigarettes (CS) strongly inhibited the central airway response to subsequent IV methacholine (MCh) challenge. In the sensitized animals, although the response to ovalbumin was also inhibited in the central airways, mainstream CS did not blunt the peripheral airway response in this group. In additional groups of experiments, exposure to HEPA-filtered CS (n = 6) similarly inhibited the MCh response, whereas CO (10,000 ppm for 4 min, n = 6) or nitric oxide inhalation instead of CS (240 ppm, 4 x 7 min, n = 5) failed to blunt nonspecific airway responsiveness. Pretreatment with alpha-chymotrypsin to inhibit endogenous VIP before CS exposure had no effect (n = 4). Based on these observations, the gas phase of mainstream cigarette smoke may contain one or more short-term inhibitory components acting primarily on central airways and inhibiting the response to both specific and nonspecific airway provocation, but not on the lung periphery where both lung mechanical parameters, and synchrotron-imaging derived parameters, showed large changes in response to allergen challenge in sensitized animals.