Novel visual analytics approach for chromosome territory analysis

This document presents a new and improved, more intuitive version of a novel method for visually representing the location of objects relative to each other in 3D. The motivation and inspiration for developing this new method came from the necessity for objective chromosome territory (CT) adjacency analysis. The earlier version, Distance Profile Chart (DPC), used octants for 3D orientation. This approach did not provide the best 3D space coverage since space was divided into just eight cones and was not intuitive with regard to orientation in 3D. However, the version presented in this article, called DPC12, allows users to achieve better space coverage during conification since space is now divided into twelve cones. DPC12 is faster than DPC and allows for a more precise determination of the location of objects in 3D. In this article a short introduction about the conification idea is presented. Then we explain how DPC12 is designed and created. After that, we show DPC12 on an instructional dataset to make it easier to understand and demonstrate how they appear and how to read them. Finally, using DPC12 we present an example of an adjacency analysis (AA) using the model of Chromosome Territories (CTs) distribution in the rice nucleus

Effect of vernalizing temperature on the level of plant hormones in embryos of germinating grains of winter and spring wheat

In embryos of grains of winter and spring wheat germinating at temperature of 1.8—2.0°C the levels of auxins, gibberellins, cytokinins and abscisic acid-like inhibitor were determined. The analyses were performed after 5, 10, 20, 40 and 60 days of chilling. The levels of these hormones were also determined in embryos of grains germinated at 22°C being in the same growth stage as embryos taken from chilled grains. It was stated, that during the germination at vernalizing temperature the level of auxins, GAs and cytokinins increased in embryos of both varietes. The level of these hormones in winter wheat was however higher. The amount of growth inhibitor increased at the beginning of germination in embryos of both wheats and afterwards decreased. It was concluded that the above mentioned changes in the level of auxins, cytokinins and ABA had no direct relation to the process of vernalization. However, the changes in the levels of gibberellins found in embryos of winter wheat during the thermoinduction may be directly connected with the vernalization process

Metastable β-Phase Ti–Nb Alloys Fabricated by Powder Metallurgy: Effect of Nb on Superelasticity and Deformation Behavior

<p>The data is arranged into 3 folders:</p> <p>1. SEM folder, which contains the raw SEM images of the microstructure of the materials, fracture surfaces, EDS elemental maps and EBSD analysis</p> <p>2. TEM folder, which contains the raw TEM images of the sintered materials with the corresponding selected area diffraction (SAED) patterns and dark field (DF) images</p> <p>3. Mechanical tests folder contains the results of tensile tests and nanoindentation.</p> <p>Details of all of the above experiments are presented in the reference article.</p&gt

The distances between the beads and other nucleus components.

<p>The distance between the beads belonging to the same chromosome is shown as <i>d</i>_<i>1</i> and is calculated using parameter <i>ε</i>_<i>1</i>. Two subsequently drawn beads are tangent. The distance between the beads belonging to different chromosomes or between the beads and nucleus or nucleolus boundary is shown as <i>d</i>_<i>2</i> and is calculated using parameter <i>ε</i>_<i>2</i>. <i>Cen[<a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0160303#pone.0160303.ref001" target="_blank">1</a>]</i> and Cen <i>[<a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0160303#pone.0160303.ref002" target="_blank">2</a>]</i> represent centromeric beads (grey circles).</p

Steps of modelling.

<p>The modelling process is divided into six blocks (numbers I–VI). The middle column gives more detailed description of each step, including the conditions (C1-C5 and C1’-C3’) that have to be met for the program to proceed.</p

Chromosome Territory Modeller and Viewer

<div><p>This paper presents ChroTeMo, a tool for chromosome territory modelling, accompanied by ChroTeVi–a chromosome territory visualisation software that uses the data obtained by ChroTeMo. These tools have been developed in order to complement the molecular cytogenetic research of interphase nucleus structure in a model grass <i>Brachypodium distachyon</i>. Although the modelling tool has been initially created for one particular species, it has universal application. The proposed version of ChroTeMo allows for generating a model of chromosome territory distribution in any given plant or animal species after setting the initial, species-specific parameters. ChroTeMo has been developed as a fully probabilistic modeller. Due to this feature, the comparison between the experimental data on the structure of a nucleus and the results obtained from ChroTeMo can indicate whether the distribution of chromosomes inside a nucleus is also fully probabilistic or is subjected to certain non-random patterns. The presented tools have been written in Python, so they are multiplatform, portable and easy to read. Moreover, if necessary they can be further developed by users writing their portions of code. The source code, documentation, and wiki, as well as the issue tracker and the list of related articles that use ChroTeMo and ChroTeVi, are accessible in a public repository at Github under GPL 3.0 license.</p></div

State of the model after I-IV steps of the modelling process.

<p>The spheres representing nucleus, nucleolus and the centromeres of <i>N</i> chromosomes are drawn. <i>R</i> and <i>r</i> stand for the radius of the nucleus and nucleolus, respectively while (<i>nu</i>) and (<i>no</i>) stand for the coordinates of their centres, also respectively. Checking the conditions <b>C1–C3</b> (see text) ensures that the nucleolus and the centromeres are located inside the nucleus and that the drawn structures do not collide with each other.</p

Step VI of the modelling process: simulating chromatin decondensation.

<p>The condensed state of a chromosome is represented by a chain of beads identified with three numbers (white circles). The chromosome decondensation is simulated by adding new beads (grey circles) along the length of the entire chromosome, not only at the last created bead. The coordinates of the new beads are generated randomly. The candidate beads <i>B4</i>, <i>B5</i>, <i>B6</i> (dotted line circles) will be discarded because they do not pass collision detection procedures: <i>B4</i> and <i>B5</i> are too far from the”own” chromosome (condition <b>C4</b> is not met), <i>B6</i> is too close to the”foreign” beads (condition <b>C5</b> is not met).</p