Fusion Visualization System as an Open Science Foundation

A Single Defined Sister Chromatid Fusion Destabilizes Cell Cycle through Micronuclei Formation

10.1101/607341 ◽

2019 ◽

Author(s):

Katsushi Kagaya ◽

Naoto Noma ◽

Io Yamamoto ◽

Sanki Tashiro ◽

Fuyuki Ishikawa ◽

...

Keyword(s):

Cell Cycle ◽

Sister Chromatid ◽

Chromosome Fusion ◽

Visualization System ◽

Multiple Tumor ◽

Chromosome Fragmentation ◽

Hierarchical Bayesian Modeling ◽

Structural Abnormalities ◽

Fusion Visualization ◽

Exact Timing

AbstractChromosome fusion is deleterious among oncogenic chromosome rearrangements, and has been proposed to cause multiple tumor-driving abnormalities. Conventional methodologies, however, lack the strictness of the experimental controls on the fusion such as the exact timing, the number and the types of fusion in a given cell. Here, we developed a human cell-based sister chromatid fusion visualization system (FuVis), in which a single defined sister chromatid fusion is induced by CRISPR/Cas9 concomitantly with mCitrine expression. Fused chromosome developed numerical and structural abnormalities, including chromosome fragmentation, an indicative of eventual chromothripsis. Live cell imaging and hierarchical Bayesian modeling indicated that micronucleus (MN) is generated in the first few cell cycle, and that cells with MN tend to possess cell cycle abnormalities. These results demonstrate that, although most cells can tolerate a single fusion, even a single sister chromatid fusion destabilizes cell cycle through MN formation.

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Scalable Scalable Vector Graphics: Automatic Translation of Interactive SVGs to a Multithread VDOM for Fast Rendering

10.31219/osf.io/ypxz2 ◽

2020 ◽

Author(s):

Michail Schwab

Keyword(s):

Open Science ◽

Markup Language ◽

Vector Graphics ◽

Visualization System ◽

Scalable Vector Graphics ◽

Automatic Translation ◽

Function Calls ◽

Data Points ◽

Fast Rendering ◽

Main Thread

The dominant markup language for Web visualizations - Scalable Vector Graphics (SVG) - is comparatively easy to learn, and is open, accessible, customizable via CSS, and searchable via the DOM, with easy interaction handling and debugging. Because these attributes allow visualization creators to focus on design on implementation details, tools built on top of SVG, such as D3.js, are essential to the visualization community. However, slow SVG rendering can limit designs by effectively capping the number of on-screen data points, and this can force visualization creators to switch to Canvas or WebGL. These are less flexible (e.g., no search or styling via CSS), and harder to learn.We introduce Scalable Scalable Vector Graphics (SSVG) to reduce these limitations and allow complex and smooth visualizations to be created with SVG.SSVG automatically translates interactive SVG visualizations into a dynamic virtual DOM (VDOM) to bypass the browser's slow `to specification' rendering by intercepting JavaScript function calls. De-coupling the SVG visualization specification from SVG rendering, and obtaining a dynamic VDOM, creates flexibility and opportunity for visualization system research. SSVG uses this flexibility to free up the main thread for more interactivity and renders the visualization with Canvas or WebGL on a web worker. Together, these concepts create a drop-in JavaScript library which can improve rendering performance by 3-9X with only one line of code added.To demonstrate applicability, we describe the use of SSVG on multiple example visualizations including published visualization research. A free copy of this paper, collected data, and source code are available as open science at osf.io/ge8wp.

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Chromosome instability induced by a single defined sister chromatid fusion

Life Science Alliance ◽

10.26508/lsa.202000911 ◽

2020 ◽

Vol 3 (12) ◽

pp. e202000911

Author(s):

Katsushi Kagaya ◽

Naoto Noma-Takayasu ◽

Io Yamamoto ◽

Sanki Tashiro ◽

Fuyuki Ishikawa ◽

...

Keyword(s):

Cell Cycle ◽

Sister Chromatid ◽

Chromosome Instability ◽

Chromosome Fusion ◽

Visualization System ◽

Cell Cycles ◽

Multiple Tumor ◽

Experimental Systems ◽

Chromosome Fusions ◽

Fusion Visualization

Chromosome fusion is a frequent intermediate in oncogenic chromosome rearrangements and has been proposed to cause multiple tumor-driving abnormalities. In conventional experimental systems, however, these abnormalities were often induced by randomly induced chromosome fusions involving multiple different chromosomes. It was therefore not well understood whether a single defined type of chromosome fusion, which is reminiscent of a sporadic fusion in tumor cells, has the potential to cause chromosome instabilities. Here, we developed a human cell-based sister chromatid fusion visualization system (FuVis), in which a single defined sister chromatid fusion is induced by CRISPR/Cas9 concomitantly with mCitrine expression. The fused chromosome subsequently developed extra-acentric chromosomes, including chromosome scattering, indicative of chromothripsis. Live-cell imaging and statistical modeling indicated that sister chromatid fusion generated micronuclei (MN) in the first few cell cycles and that cells with MN tend to display cell cycle abnormalities. The powerful FuVis system thus demonstrates that even a single sporadic sister chromatid fusion can induce chromosome instability and destabilize the cell cycle through MN formation.

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