Biology subjects

Hlushchuk, R.

Publications and source records attributed to Hlushchuk, R..

4 recordsLinked to original sources

bioRxiv2023

Microtomographic investigation of a large corpus of cichlids

A large collection of cichlids (N=133) from Lake Victoria in Africa spanning a length range of 6 to 18 cm was nondestructively imaged using micro-computed tomography. We describe our method to efficiently obtain three-dimensional tomographic datasets of the oral and pharyngeal jaws and the whole skull of these fishes for accurately describing their morphology. The tomographic data we acquired (9.8 TB of projection images) yielded 1.5 TB of three-dimensional image stacks used for extracting the relevant features of interest. Herein we present our method and an outlook on analyzing the acquired data; a morphological description of the oral and pharyngeal jaws of the fishes, a three-dimensional geometric morphometrics analysis of landmark features on the fish skulls, and a robust method to automatically extract the otoliths of the fishes from the tomographic data.

ecology↗

bioRxiv2023

MicroCT-based imaging of microvasculature within the bone tissue

Angiogenesis is essential for skeletal development, bone healing, and regeneration. Improved non-destructive, three-dimensional (3D) imaging of the vasculature within bone tissue benefits many research areas, especially implantology and tissue engineering. X-ray microcomputed tomography (microCT) is a well-suited non-destructive 3D imaging technique for bone morphology. For microCT-based detection of vessels, it is paramount to use contrast enhancement. Limited differences in radiopacity between perfusion agents and mineralized bone make their distinct segmentation problematic and have been a major drawback of this approach. A decalcification step resolves this issue but inhibits the simultaneous assessment of bone microstructure and vascular morphology. The problem of contrasting becomes further complicated in samples with metal implants. This study describes contrast-enhanced microCT-based visualization of vasculature within bone tissue in small and large animal models, also in the vicinity of the metal implants. We present simultaneous microvascular and bone imaging in murine tibia, a murine bone metastatic model, the pulp chamber, gingiva, and periodontal ligaments. In a large animal model (minipig), we perform visualization and segmentation of different tissue types and vessels in the hemimandible containing metal implants. We further demonstrate the potential of dual-energy imaging in distinguishing bone tissue from the applied contrast agents. This work introduces a non-destructive approach for 3D imaging of vasculature within soft and hard tissues near metal implants in a large animal model.

physiology↗

bioRxiv2021

Downregulation of WT1 transcription factor gene expression is required to promote myocardial fate

During cardiac development, cells from the precardiac mesoderm fuse to form the primordial heart tube, which then grows by addition of further progenitors to the venous and arterial poles. In the zebrafish, wilms tumor 1 transcription factor a (wt1a) and b (wt1b) are expressed in the pericardial mesoderm at the venous pole of the forming heart tube. The pericardial mesoderm forms a single layered mesothelial sheet that contributes to further the growth of the myocardium, and forms the proepicardium. Proepicardial cells are subsequently transferred to the myocardial surface and give rise to the epicardium, the outer layer covering the myocardium in the adult heart. wt1a/b expression is downregulated during the transition from pericardium to myocardium, but remains high in proepicardial cells. Here we show that sustained wt1 expression impaired cardiomyocyte maturation including sarcomere assembly, ultimately affecting heart morphology and cardiac function. ATAC-seq data analysis of cardiomyocytes overexpressing wt1 revealed that chromatin regions associated with myocardial differentiation genes remain closed upon wt1b overexpression in cardiomyocytes, suggesting that wt1 represses a myocardial differentiation program. Indeed, a subset of wt1a/b-expressing cardiomyocytes changed their cell adhesion properties, delaminated from the myocardial epithelium, and upregulated the expression of epicardial genes, as confirmed by in vivo imaging. Thus, we conclude that wt1 acts as a break for cardiomyocyte differentiation by repressing chromatin opening at specific genomic loci and that sustained ectopic expression of wt1 in cardiomyocytes can lead to their transformation into epicardial cells.

developmental biology↗

bioRxiv2020

Automated segmentation and description of the internal morphology of human permanent teeth by means of micro-CT

Micro-CT is a powerful tool to analyze and visualize the internal morphology of human permanent teeth. It is increasingly used for investigation of epidemiological questions to provide the dentist with the necessary information required for successful endodontic treatment. The aim of the present paper was to propose an image processing method to automate parts of the work needed to fully describe the internal morphology of human permanent teeth. One hundred and four human teeth were scanned on a high-resolution micro-CT using an automatic specimen changer. Python code in a Jupyter notebook was used to verify and process the scans, prepare the datasets for description of the internal morphology and to measure the apical region of he tooth. The presented method offers an easy, non-destructive, rapid and efficient approach to scan, check and preview micro-computer tomographic datasets of a large number of teeth. It is a helpful tool for the detailed description and characterization of the internal morphology of human permanent teeth using automated segmentation by means of micro-CT with full reproducibility and high standardization.

physiology↗