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

Defining the Traditional Mediterranean Lifestyle: Joint International Consensus Statement

Introduction: The term “Mediterranean lifestyle” has gained increasing prominence in recent years, yet a specific definition remains elusive. In response, the Mediterranean Lifestyle Medicine Institute Board of Directors convened a multidisciplinary panel comprising international experts and leaders in lifestyle medicine. Their goal was to review existing literature and formulate a consensus definition of the “traditional Mediterranean lifestyle (tMedL),” referring to the historical way of living of the people in the Mediterranean region. This paper presents the agreed consensus statement and a comprehensive holistic definition of the term “traditional Mediterranean lifestyle.”. Methods: Major medical and social sciences electronic databases from inception to February 2023 were searched, employing keywords relevant to the Mediterranean lifestyle and its constituent elements (diet, physical activity, sleep, stress, socialization). Subsequently, definitions for each pillar were created and synthesized to derive a comprehensive definition of the “traditional Mediterranean lifestyle.”. Results: This proposed definition received ratification from the Mediterranean Lifestyle Medicine Institute's expert working group during the First International Mediterranean Lifestyle Medicine Conference held in June 2023 on the island of Leros, Greece. “The traditional Mediterranean lifestyle is characterized by its diverse and adaptable nature. Key facets encompass conviviality, lifelong social connectedness, purposeful living, strong community and familial bonds, harmony with nature and the environment, profound spirituality, adherence to religious practices, preservation of local customs, resilience cultivated through adversity, and a commitment to moderation across all spheres of life.”. Conclusions: This definition comprehensively outlines the primary lifestyle factors ingrained in Mediterranean inhabitants across generations. Its holistic nature furnishes a crucial conceptual framework for directing lifestyle medicine practitioners in assisting patients to mitigate diseases, promote overall well-being, devise research initiatives to investigate the health ramifications of this lifestyle, and inform curriculum development

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

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

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

Association of homologous and heterologous chromosome territories in <i>B</i>. <i>distachyon</i> interphase nuclei of roots.

<p>A–an idiogram showing the labelling of Bd5 chromosome (top arm–green, bottom arm–red; each nucleus contains two sets of chromosomes). B–the nucleus with complete separation of Bd5 chromosome arm territories revealed by FISH. Nucleolus is visible as dark blue spherical gap inside the nucleus. C–an idiogram showing the labelling of two heterologous chromosomes (Bd2 –green, Bd5 –red), without discrimination between chromosome arms. D–the nucleus with association of Bd2 and Bd5 chromosome territories revealed by FISH. Photomicrographs in B and D are supplied with diagrams representing the distribution of CTs. Scale bars: 2 μm.</p

Types of homologous CT distribution patterns modelled by ChroTeMo and visualised by ChroTeVi.

<p>A–an idiogram showing the colouring of Bd2 chromosome (top arm–green, bottom arm–red). B–the nucleus with complete association of Bd2 chromosome arm territories. Chromosomes other than Bd2 are coloured white. C–the same nucleus as B. Chromosomes other than Bd2 are transparent. D–the nucleus with the association of Bd2 top arm territories. Chromosomes other than Bd2 are coloured white. E–the same nucleus as D. Chromosomes other than Bd2 are transparent. F–the nucleus with the association of Bd2 bottom arm territories. Chromosomes other than Bd2 are coloured white. G–the same nucleus as F. Chromosomes other than Bd2 are transparent. H–the nucleus with complete separation of Bd2 chromosome arm territories. Chromosomes other than Bd2 are coloured white. I–the same nucleus as G. Chromosomes other than Bd2 are transparent. J–the nucleus with association between the top arm of one Bd2 homologue and the bottom arm of another homologue. Chromosomes other than Bd2 are coloured white. K–the same nucleus as J. Chromosomes other than Bd2 are transparent. Nucleolus is visible as a yellow sphere inside the nucleus.</p

The arrangement of Brachypodium distachyon

The spatial organization of chromatin within the interphase nucleus and the interactions between chromosome territories (CTs) are essential for various biological processes, such as DNA replication, transcription, and repair. However, detailed data about the CT arrangement in monocotyledonous plants are scarce. In this study, chromosome painting was used to analyse the distribution and associations of individual chromosomes in the 3-D preserved nuclei of Brachypodium distachyon root cells in order to determine the factors that may have an impact on the homologous CT arrangement. It was shown that the frequency of CT association is linked to the steric constraints imposed by the limited space within the nucleus and may depend on chromosome size and morphology as well as on the nuclear shape. Furthermore, in order to assess whether the distribution of interphase chromosomes is random or is subject to certain patterns, a comparison between the experimental data and the results of a computer simulation (ChroTeMo), which was based on a fully probabilistic distribution of the CTs, was performed. This comparison revealed that homologous chromosome arm CTs associate more often than if they were randomly arranged inside the interphase nucleus