Characterization of the Morphological Nature of Hollow Spray Dried Dispersion Particles Using X-ray Submicron-Computed Tomography.

Graphical Abstract.

Resolving complex cartilage structures in developmental biology via deep learning-based automatic segmentation of X-ray computed microtomography images.

The complex shape of embryonic cartilage represents a true challenge for phenotyping and basic understanding of skeletal development. X-ray computed microtomography (µCT) enables inspecting relevant tissues in all three dimensions; however, most 3D models are still created by manual segmentation, which is a time-consuming and tedious task. In this work, we utilised a convolutional neural network (CNN) to automatically segment the most complex cartilaginous system represented by the developing nasal capsule. The main challenges of this task stem from the large size of the image data (over a thousand pixels in each dimension) and a relatively small training database, including genetically modified mouse embryos, where the phenotype of the analysed structures differs from the norm. We propose a CNN-based segmentation model optimised for the large image size that we trained using a unique manually annotated database. The segmentation model was able to segment the cartilaginous nasal capsule with a median accuracy of 84.44% (Dice coefficient). The time necessary for segmentation of new samples shortened from approximately 8 h needed for manual segmentation to mere 130 s per sample. This will greatly accelerate the throughput of µCT analysis of cartilaginous skeletal elements in animal models of developmental diseases.

High-resolution micro-CT for 3D infarct characterization and segmentation in mice stroke models.

Characterization of brain infarct lesions in rodent models of stroke is crucial to assess stroke pathophysiology and therapy outcome. Until recently, the analysis of brain lesions was performed using two techniques: (1) histological methods, such as TTC (Triphenyltetrazolium chloride), a time-consuming and inaccurate process; or (2) MRI imaging, a faster, 3D imaging method, that comes at a high cost. In the last decade, high-resolution micro-CT for 3D sample analysis turned into a simple, fast, and cheaper solution. Here, we successfully describe the application of brain contrasting agents (Osmium tetroxide and inorganic iodine) for high-resolution micro-CT imaging for fine location and quantification of ischemic lesion and edema in mouse preclinical stroke models. We used the intraluminal transient MCAO (Middle Cerebral Artery Occlusion) mouse stroke model to identify and quantify ischemic lesion and edema, and segment core and penumbra regions at different time points after ischemia, by manual and automatic methods. In the transient-ischemic-attack (TIA) mouse model, we can quantify striatal myelinated fibers degeneration. Of note, whole brain 3D reconstructions allow brain atlas co-registration, to identify the affected brain areas, and correlate them with functional impairment. This methodology proves to be a breakthrough in the field, by providing a precise and detailed assessment of stroke outcomes in preclinical animal studies.

X-ray microtomography-based atlas of mouse cranial development.

BACKGROUND: X-ray microtomography (µCT) has become an invaluable tool for non-destructive analysis of biological samples in the field of developmental biology. Mouse embryos are a typical model for investigation of human developmental diseases. By obtaining 3D high-resolution scans of the mouse embryo heads, we gain valuable morphological information about the structures prominent in the development of future face, brain, and sensory organs. The development of facial skeleton tracked in these µCT data provides a valuable background for further studies of congenital craniofacial diseases and normal development. FINDINGS: In this work, reusable tomographic data from 7 full 3D scans of mouse embryo heads are presented and made publicly available. The ages of these embryos range from E12.5 to E18.5. The samples were stained by phosphotungstic acid prior to scanning, which greatly enhanced the contrast of various tissues in the reconstructed images and enabled precise segmentation. The images were obtained on a laboratory-based µCT system. Furthermore, we provide manually segmented masks of mesenchymal condensations (for E12.5 and E13.5) and cartilage present in the nasal capsule of the scanned embryos. CONCLUSION: We present a comprehensive dataset of X-ray 3D computed tomography images of the developing mouse head with high-quality manual segmentation masks of cartilaginous nasal capsules. The provided µCT images can be used for studying any other major structure within the developing mouse heads. The high quality of the manually segmented models of nasal capsules may be instrumental to understanding the complex process of the development of the face in a mouse model.

Differential Responses of Arctic Vegetation to Nutrient Enrichment by Plankton- and Fish-Eating Colonial Seabirds in Spitsbergen.

The role of seabirds as sea-land biovectors of nutrients is well documented. However, no studies have examined whether and how colonial seabirds that differ in diet may influence terrestrial vegetation. Therefore, the purpose of the study was to describe and compare plant communities located in the vicinity of the two most common types of seabird colonies in Arctic, occupied by piscivorous or planktivorous species. Within 46 plots arranged in four transects in the vicinity of planktivorous (little auk, Alle alle) and piscivorous colonies (mixed colony of Brunnich's guillemot, Uria lomvia, and black-legged kittiwake, Rissa tridactyla) we measured the following: guano deposition, physical and chemical characteristics of soil, total nitrogen and its stable isotope signatures in soil and plants, ground vegetation cover of vascular plants and mosses, and the occurrence of lichens, algae and cyanobacteria. Using LINKTREE analysis, we distinguished five plant communities, which reflected declining influence along a birds fertilization gradient measured as guano deposition. SIMPROOF test revealed that these communities differed significantly in species composition, with the differences related to total soil nitrogen content and δ15N, distinctive levels of phosphates, potassium and nitrates, and physical soil properties, i.e., pH, conductivity and moisture. The communities were also clearly distinguished by distance from the bird colony. The two colony types promoted development of specific plant communities: the immediate vicinity of the planktivorous colony characterized by a Deschampsia alpina-Cerastium arcticum community while under the piscivorous colony a Cochlearia groenlandica-Poa alpina community was present. Despite the similar size of the colonies and similar magnitude of guano input, differences between ornithogenic communities were connected mostly to phosphate content in the soil. Our results show that the guano input from seabirds which have different diets can affect High Arctic vegetation in specific and more complex ways than previously realized.

Chalcone Synthase (CHS) Gene Suppression in Flax Leads to Changes in Wall Synthesis and Sensing Genes, Cell Wall Chemistry and Stem Morphology Parameters.

The chalcone synthase (CHS) gene controls the first step in the flavonoid biosynthesis. In flax, CHS down-regulation resulted in tannin accumulation and reduction in lignin synthesis, but plant growth was not affected. This suggests that lignin content and thus cell wall characteristics might be modulated through CHS activity. This study investigated the possibility that CHS affects cell wall sensing as well as polymer content and arrangement. CHS-suppressed and thus lignin-reduced plants showed significant changes in expression of genes involved in both synthesis of components and cell wall sensing. This was accompanied by increased levels of cellulose and hemicellulose. CHS-reduced flax also showed significant changes in morphology and arrangement of the cell wall. The stem tissue layers were enlarged averagely twofold compared to the control, and the number of fiber cells more than doubled. The stem morphology changes were accompanied by reduction of the crystallinity index of the cell wall. CHS silencing induces a signal transduction cascade that leads to modification of plant metabolism in a wide range and thus cell wall structure.