scholarly journals K-means clustering of zebrafish embryos images acquired with AOTF-based hyperspectral microscope

2021 ◽  
Vol 2127 (1) ◽  
pp. 012062
Author(s):  
A B Burlakov ◽  
S V Shirokov ◽  
C C Huang ◽  
D D Khokhlov
Keyword(s):  
Clustering Algorithm ◽  
Hyperspectral Image ◽  
Model Organism ◽  
Tunable Filter ◽  
Zebrafish Embryos ◽  
Non Invasive ◽  
Research Fields ◽  
Automated Observation ◽  
Convenient Model

Abstract Model organism studies are widely implemented in biomedical research fields. Zebrafish is a common and convenient model organism. To provide in vivo investigation of living zebrafish the non-invasive imaging methods are implemented. Hyperspectral imaging utilizing acousto-optic tunable filters is a perspective modality for zebrafish embryos and larvae automated observation. In this paper, the hyperspectral microscope based on the acousto-optical tunable filter is described. Using the hyperspectral image arrays obtained with the described setup, the K-means clustering algorithm is tested. The results obtained for different number of clusters are presented and discussed.

scholarly journals Hyperspectral imaging of retinal microvascular anatomy

2015 ◽  
Vol 2 (1) ◽  
pp. 139 ◽  
Author(s):  
Amir H. Kashani ◽  
Mark Wong ◽  
Nicole Koulisis ◽  
Chein-I Chang ◽  
Gabriel Martin ◽  
...  
Keyword(s):  
Hyperspectral Image ◽  
Model Organism ◽  
Science Research ◽  
Tomographic Imaging ◽  
Diagnostic Methods ◽  
Camera System ◽  
Computed Tomographic ◽  
Non Invasive ◽  
Computed Tomographic Imaging

Background: Hyperspectral image processing has been applied to many aspects of astronomical and earth science research. Furthermore, advances in computed tomographic imaging spectroscopy and diffraction grating design have allowed biological applications for non-invasive tissue analysis. Herein, we describe a hyperspectral computed tomographic imaging spectroscope (HCTIS) that provides high spatial, spectral and temporal resolution ideal for imaging biological tissue in vivo. Methods: We demonstrate proof-of-principle application of the HCTIS by imaging and mapping the microvascular anatomy of the retina of a model organism (rabbit) in vivo. The imaging procedure allows rapid and dense spectral sampling, is non-toxic, non-invasive, and easily adaptable to a commercially available fundus camera system. Results: HCTIS provides highly co-registered temporal, spatial and spectral data with resolution capable of reconstructing the fine vascular tree of the rabbit retina in vivo. Conclusions: We show that HCTIS allows for reliable and reproducible tissue classification and detection using signature discriminant analysis. Future applications of this system may provide promising diagnostic methods for diseases of many tissues. 

scholarly journals High-resolution cardiovascular function confirms functional orthology of myocardial contractility pathways in zebrafish

2010 ◽  
Vol 42 (2) ◽  
pp. 300-309 ◽  
Author(s):  
Jordan T. Shin ◽  
Eugene V. Pomerantsev ◽  
John D. Mably ◽  
Calum A. MacRae
Keyword(s):  
High Speed ◽  
Dynamic Range ◽  
Model Organism ◽  
Cardiovascular Physiology ◽  
Zebrafish Embryos ◽  
Cardiovascular Development ◽  
Zebrafish Model ◽  
Ventricular Performance ◽  
Pharmacological Agents

Phenotype-driven screens in larval zebrafish have transformed our understanding of the molecular basis of cardiovascular development. Screens to define the genetic determinants of physiological phenotypes have been slow to materialize as a result of the limited number of validated in vivo assays with relevant dynamic range. To enable rigorous assessment of cardiovascular physiology in living zebrafish embryos, we developed a suite of software tools for the analysis of high-speed video microscopic images and validated these, using established cardiomyopathy models in zebrafish as well as modulation of the nitric oxide (NO) pathway. Quantitative analysis in wild-type fish exposed to NO or in a zebrafish model of dilated cardiomyopathy demonstrated that these tools detect significant differences in ventricular chamber size, ventricular performance, and aortic flow velocity in zebrafish embryos across a large dynamic range. These methods also were able to establish the effects of the classic pharmacological agents isoproterenol, ouabain, and verapamil on cardiovascular physiology in zebrafish embryos. Sequence conservation between zebrafish and mammals of key amino acids in the pharmacological targets of these agents correlated with the functional orthology of the physiological response. These data provide evidence that the quantitative evaluation of subtle physiological differences in zebrafish can be accomplished at a resolution and with a dynamic range comparable to those achieved in mammals and provides a mechanism for genetic and small-molecule dissection of functional pathways in this model organism.

scholarly journals Transgenic fluorescent zebrafish lines that have revolutionized biomedical research

2021 ◽  
Vol 37 (1) ◽  
Author(s):  
Chong Pyo Choe ◽  
Seok-Yong Choi ◽  
Yun Kee ◽  
Min Jung Kim ◽  
Seok-Hyung Kim ◽  
...  
Keyword(s):  
Biomedical Research ◽  
Digestive System ◽  
Fluorescent Proteins ◽  
Model Organism ◽  
Urogenital System ◽  
Research Fields ◽  
Intracellular Organelle ◽  
Vertebrate Model ◽  
Intracellular Organelles

AbstractSince its debut in the biomedical research fields in 1981, zebrafish have been used as a vertebrate model organism in more than 40,000 biomedical research studies. Especially useful are zebrafish lines expressing fluorescent proteins in a molecule, intracellular organelle, cell or tissue specific manner because they allow the visualization and tracking of molecules, intracellular organelles, cells or tissues of interest in real time and in vivo. In this review, we summarize representative transgenic fluorescent zebrafish lines that have revolutionized biomedical research on signal transduction, the craniofacial skeletal system, the hematopoietic system, the nervous system, the urogenital system, the digestive system and intracellular organelles.

scholarly journals A toolbox for efficient proximity-dependent biotinylation in zebrafish embryos

2021 ◽  
Author(s):  
Shimon M Rosenthal ◽  
Tvisha Misra ◽  
Hala Abdouni ◽  
Tess C Branon ◽  
Alice Y Ting ◽  
...  
Keyword(s):  
Cell Culture ◽  
Fluorescent Protein ◽  
Protein Complexes ◽  
Mammalian Cell Culture ◽  
Model Organism ◽  
Negative Control ◽  
Lamin A ◽  
Zebrafish Embryos ◽  
Time Resolved

Understanding how proteins are organized in compartments is essential to elucidating their function. While proximity-dependent approaches such as BioID have enabled a massive increase in information about organelles, protein complexes and other structures in cell culture, to date there have been only a few studies in living vertebrates. Here, we adapted proximity labeling for protein discovery in vivo in the vertebrate model organism, zebrafish. Using lamin A (LMNA) as bait and green fluorescent protein (GFP) as a negative control, we developed, optimized, and benchmarked in vivo TurboID and miniTurbo labeling in early zebrafish embryos. We developed both an mRNA injection protocol and a transgenic system in which transgene expression is controlled by a heat shock promoter. In both cases, biotin is provided directly in the egg water, and we demonstrate that 12 hours of labeling are sufficient for biotinylation of prey proteins, which should permit time-resolved analysis of development. After statistical scoring, we found that the proximal partners of LMNA detected in each system were enriched for nuclear envelope and nuclear membrane proteins, and included many orthologs of human proteins identified as proximity partners of lamin A in mammalian cell culture. The tools and protocols developed here will allow zebrafish researchers to complement genetic tools with powerful proteomics approaches.

The Mechanisms Behind the Biological Activity of Flavonoids

2019 ◽  
Vol 26 (39) ◽  
pp. 6976-6990 ◽  
Author(s):  
Ana María González-Paramás ◽  
Begoña Ayuda-Durán ◽  
Sofía Martínez ◽  
Susana González-Manzano ◽  
Celestino Santos-Buelga
Keyword(s):  
Gene Expression ◽  
Biological Activity ◽  
Phenolic Compounds ◽  
Intracellular Signaling ◽  
Molecular Mechanisms ◽  
Radical Scavenging ◽  
Model Organism ◽  
Stress Theory ◽  
Radical Scavenging Properties

: Flavonoids are phenolic compounds widely distributed in the human diet. Their intake has been associated with a decreased risk of different diseases such as cancer, immune dysfunction or coronary heart disease. However, the knowledge about the mechanisms behind their in vivo activity is limited and still under discussion. For years, their bioactivity was associated with the direct antioxidant and radical scavenging properties of phenolic compounds, but nowadays this assumption is unlikely to explain their putative health effects, or at least to be the only explanation for them. New hypotheses about possible mechanisms have been postulated, including the influence of the interaction of polyphenols and gut microbiota and also the possibility that flavonoids or their metabolites could modify gene expression or act as potential modulators of intracellular signaling cascades. This paper reviews all these topics, from the classical view as antioxidants in the context of the Oxidative Stress theory to the most recent tendencies related with the modulation of redox signaling pathways, modification of gene expression or interactions with the intestinal microbiota. The use of C. elegans as a model organism for the study of the molecular mechanisms involved in biological activity of flavonoids is also discussed.

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