Dynamic visualization of melanosome endo/phagocytosis during melanin transfer using melanosomes pre-stained with carbocyanine dyes

2021 ◽  
Author(s):  
Seiji Takeuchi ◽  
Takeshi Fukumoto ◽  
Chikako Nishigori ◽  
Lieve Declercq ◽  
Daniel B. Yarosh ◽  
...  
Keyword(s):  
Dynamic Visualization ◽  
Carbocyanine Dyes

scholarly journals Lantern: an integrative repository of functional annotations for lncRNAs in the human genome

2021 ◽  
Vol 22 (1) ◽  
Author(s):  
Swapna Vidhur Daulatabad ◽  
Rajneesh Srivastava ◽  
Sarath Chandra Janga
Keyword(s):  
Human Genome ◽  
Cellular Localization ◽  
Expression Profiles ◽  
Free Text ◽  
Dynamic Visualization ◽  
Specific Expression ◽  
Web Resource ◽  
Functional Dynamics ◽  
Non Coding Rnas ◽  
Retrieval Engine

Abstract Background With advancements in omics technologies, the range of biological processes where long non-coding RNAs (lncRNAs) are involved, is expanding extensively, thereby generating the need to develop lncRNA annotation resources. Although, there are a plethora of resources for annotating genes, despite the extensive corpus of lncRNA literature, the available resources with lncRNA ontology annotations are rare. Results We present a lncRNA annotation extractor and repository (Lantern), developed using PubMed’s abstract retrieval engine and NCBO’s recommender annotation system. Lantern’s annotations were benchmarked against lncRNAdb’s manually curated free text. Benchmarking analysis suggested that Lantern has a recall of 0.62 against lncRNAdb for 182 lncRNAs and precision of 0.8. Additionally, we also annotated lncRNAs with multiple omics annotations, including predicted cis-regulatory TFs, interactions with RBPs, tissue-specific expression profiles, protein co-expression networks, coding potential, sub-cellular localization, and SNPs for ~ 11,000 lncRNAs in the human genome, providing a one-stop dynamic visualization platform. Conclusions Lantern integrates a novel, accurate semi-automatic ontology annotation engine derived annotations combined with a variety of multi-omics annotations for lncRNAs, to provide a central web resource for dissecting the functional dynamics of long non-coding RNAs and to facilitate future hypothesis-driven experiments. The annotation pipeline and a web resource with current annotations for human lncRNAs are freely available on sysbio.lab.iupui.edu/lantern.

ExpanDrogram: Dynamic Visualization of Big Data Segmentation over Time

2021 ◽  
Vol 13 (2) ◽  
pp. 1-27
Author(s):  
A. Khalemsky ◽  
R. Gelbard
Keyword(s):  
Big Data ◽  
Visual Presentation ◽  
Trend Detection ◽  
Dynamic Visualization ◽  
Segmentation Process ◽  
Key Points ◽  
Wide Range ◽  
History Of ◽  
The Individual ◽  
Over Time

In dynamic and big data environments the visualization of a segmentation process over time often does not enable the user to simultaneously track entire pieces. The key points are sometimes incomparable, and the user is limited to a static visual presentation of a certain point. The proposed visualization concept, called ExpanDrogram, is designed to support dynamic classifiers that run in a big data environment subject to changes in data characteristics. It offers a wide range of features that seek to maximize the customization of a segmentation problem. The main goal of the ExpanDrogram visualization is to improve comprehensiveness by combining both the individual and segment levels, illustrating the dynamics of the segmentation process over time, providing “version control” that enables the user to observe the history of changes, and more. The method is illustrated using different datasets, with which we demonstrate multiple segmentation parameters, as well as multiple display layers, to highlight points such as new trend detection, outlier detection, tracking changes in original segments, and zoom in/out for more/less detail. The datasets vary in size from a small one to one of more than 12 million records.

scholarly journals Odontoblast processes in dentin revealed by fluorescent Di-I.

1995 ◽  
Vol 43 (2) ◽  
pp. 159-168 ◽  
Author(s):  
M R Byers ◽  
A Sugaya
Keyword(s):  
Electron Microscopy ◽  
Confocal Microscopy ◽  
Cell Structure ◽  
Carbocyanine Dyes ◽  
Carbocyanine Dye ◽  
Reparative Dentin ◽  
Hard Tissues ◽  
Odontoblast Process ◽  
Odontoblast Processes ◽  
Rat Molars

There has been controversy about the length and structure of the odontoblast process within dentin since the earliest histologic studies of teeth. Our objective was to use the fluorescent carbocyanine dye Di-I combined with a new gelatin embedment procedure and confocal microscopy to determine the structure and extent of odontoblast processes in developing and mature rat teeth, injured rat molars, reparative dentin, and adult monkey teeth. We found that odontoblast processes do not extend into outer dentin or to the dentin-enamel junction except during early stages of development. Those in innervated regions of crown are long and straight, whereas those in roots are extensively branched and shorter. Cavity injury to crown dentin caused odontoblast fragments to be aspirated into outer dentin. In reparative dentin the odontoblast processes were branched and similar to those in roots. We used photoconversion and electron microscopy to show that Di-I fills the entire odontoblast after gelatin embedment, including the cytoplasm. This is a different type of carbocyanine staining from any previously reported, and it also stains other cells in adjacent hard tissues such as bone and cementum. The Di-I-gelatin method is a new way to use carbocyanine dyes. It has enabled us to solve a long-standing controversy about the histology of teeth, and it should be useful for many other studies of cell structure.

scholarly journals ProtozoaDB: dynamic visualization and exploration of protozoan genomes

2007 ◽  
Vol 36 (Database) ◽  
pp. D547-D552 ◽  
Author(s):  
A. M. R. Davila ◽  
P. N. Mendes ◽  
G. Wagner ◽  
D. A. Tschoeke ◽  
R. R. C. Cuadrat ◽  
...  
Keyword(s):  
Dynamic Visualization

scholarly journals Human erythrocytes adhering to schistosomula of Schistosoma mansoni lyse and fail to transfer membrane components to the parasite.

1985 ◽  
Vol 101 (1) ◽  
pp. 158-166 ◽  
Author(s):  
J P Caulfield ◽  
C M Cianci
Keyword(s):  
Schistosoma Mansoni ◽  
Erythrocyte Membrane ◽  
Plasma Membranes ◽  
Freeze Fracture ◽  
Human Erythrocytes ◽  
Transmission Microscopy ◽  
Carbocyanine Dyes ◽  
Host Membrane ◽  
Membrane Components ◽  
20 Nm

We studied the adherence of human erythrocytes to larvae of the intravascular parasite Schistosoma mansoni by transmission microscopy, freeze fracture, and fluorescence techniques. In addition, we used the adherent cells to investigate the problem of host antigen acquisition. Schistosomula were cultured for from 24 to 48 h after transformation in order to clear the remnants of the cercarial glycocalyx. In some cases, the worms were preincubated with wheat germ agglutinin to promote adherence of the erythrocytes. The results were similar with and without the lectin except that more cells attached to the lectin-coated parasites. Erythrocytes adhered within a few hours and, unlike neutrophils, did not fuse with the parasite. A layer of 10-20-nm electron dense material separated the outer leaflets of the tegumental and plasma membranes. In addition, many deformed and lysed cells were seen on the parasite surface. The ability of the worm to acquire erythrocyte membrane constituents was tested with carbocyanine dyes, fluorescein covalently conjugated to glycophorin, monoclonal antibodies against B and H blood group glycolipids, and rabbit alpha-human erythrocyte IgG. In summary, glycophorin, erythrocyte proteins, and glycolipids were not transferred to the parasite membrane within 48 h. Carbocyanine dyes were rapidly transferred to the parasite with or without lectin preincubation. Thus, the dye in the worm membrane came from both adherent and nonadherent cells. These studies suggest that, in the absence of membrane fusion, the parasite may acquire some lipid molecules similar in structure to host membrane glycolipids by simple transfer through the medium but that B and H glycolipids and erythrocyte membrane proteins are not transferred from adhering cells to the worm.

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