Isochores

Abstract

Chromosomes of warm‐blooded vertebrates are mosaics of isochores, megabase deoxyribonucleic acid (DNA) stretches that are fairly homogeneous in base composition. In the human genome, isochores can be assigned to five families that cover a very broad range of guanine+cytosine (30–60% GC; this range is narrower in cold‐blooded vertebrates). The isochore structure of the genome led to new insights into a number of important genome features such as (1) the distribution of genes, (2) the structure of chromatin, and (3) the localisation of insertions/deletions and of the integration of proviral sequences. Moreover it also led to (1) the discovery of a set of correlations (collectively called the genomic code) linking coding sequences and extended flanking noncoding sequences, as well as other genome features, (2) the visualisation of the isochore patterns of the genomes as genome phenotypes, that may be conserved or change in evolution, like the classical phenotypes, and (3) the development of the neoselectionist theory of evolution, which explains the two modes, conservative and shifting, of genome evolution. Key Concepts: Isochores are the structural, functional and evolutionary units of the genomes of vertebrates and other eukaryotes. Structurally, isochores correspond to the highest resolution bands of chromosomes. Functionally, isochores from different families are characterised by different frequencies of short oligonucleotides, not only in the extended inter‐ and intragenic noncoding sequences, but also in short regulatory sequences upstream and downstream of coding sequences. Moreover, different categories of genes have a different distribution in isochore families. Evolutionarily, the isochore patterns change in different classes of vertebrates, from the relatively simple (low‐heterogeneity) patterns of cold‐blooded vertebrates to the complex (high‐heterogeneity) of warm‐blooded vertebrates.

The “3 Genomic Numbers” Discovery: How Our Genome Single-Stranded DNA Sequence Is “Self-Designed” as a Numerical Whole

“…Here we have eight (8) numbers that can be reduced to three (3) major numbers, the remaining five (5) This value is very close with Phi the Golden ratio, the error is: Phi-1.610297435 = 0.007736554.…”

“…-Among other approaches, we can mention for example the original research of Professor Giorgio Bernardi on "isochores" [7,8].…”

“…In a forthcoming paper [18], we explore the extraordinary properties of chromosome 4, which seems to be completely built around the Golden ratio, Phi... Figure 6 below illustrates the variability between populations of codons of the 24 chromosomes. Particularly, chromosome 4 and chromosome 19 constitute the end terminals of the hierarchy whose amplitude is 1/Pi (see details in [8]). …”

“…In [8], we have generalized a population analysis of codons across all 24 human chromosomes. It appears extremely DIVERSIFIED between these 24 chromosomes.…”

Radio Continuum Surveys with Square Kilometre Array Pathfinders

“…MWA is focused on four key science projects (Bowman et al 2012): (a) the detection and characterisation of three-dimensional brightness temperature fluctuations in the 21-cm line of neutral hydrogen during the EoR at redshifts from 6 to 10, (b) solar imaging and remote sensing of the inner heliosphere via propagation effects on signals from distant background sources, (c) high-sensitivity exploration of the variable radio sky, and (d) wide-field galactic and extragalactic astrophysics including a deep all-sky survey over the MWA frequency range with full polarimetry and spectral resolution. An initial survey of 2 400 deg 2 on the prototype ‘32T’ system has recently been completed (Bernardi et al 2012) and a full sky survey south of +30° is being planned for the full array.…”