Chirality in a quaternionic representation of the genetic code

A quaternionic representation of the genetic code, previously reported by the authors, is updated in order to incorporate chirality of nucleotide bases and amino acids. The original representation assigns to each nucleotide base a prime integer quaternion of norm 7 and involves a function that associates with each codon, represented by three of these quaternions, another integer quaternion (amino acid type quaternion) in such a way that the essentials of the standard genetic code (particulaty its degeneration) are preserved. To show the advantages of such a quaternionic representation we have, in turn, associated with each amino acid of a given protein, besides of the type quaternion, another real one according to its order along the protein (order quaternion) and have designed an algorithm to go from the primary to the tertiary structure of the protein by using type and order quaternions. In this context, we incorporate chirality in our representation by observing that the set of eight integer quaternions of norm 7 can be partitioned into a pair of subsets of cardinality four each with their elements mutually conjugates and by putting they in correspondence one to one with the two sets of enantiomers (D and L) of the four nucleotide bases adenine, cytosine, guanine and uracil, respectively. Thus, guided by two diagrams proposed for the codes evolution, we define functions that in each case assign a L- (D-) amino acid type integer quaternion to the triplets of D- (L-) bases. The assignation is such that for a given D-amino acid, the associated integer quaternion is the conjugate of that one corresponding to the enantiomer L. The chiral type quaternions obtained for the amino acids are used, together with a common set of order quaternions, to describe the folding of the two classes, L and D, of homochiral proteins.Comment: 17 pages, 9 figures. arXiv admin note: substantial text overlap with arXiv:1505.0465

Quaternionic representation of the genetic code

A heuristic diagram of the evolution of the standard genetic code is presented. It incorporates, in a way that resembles the energy levels of an atom, the physical notion of broken symmetry and it is consistent with original ideas by Crick on the origin and evolution of the code as well as with the chronological order of appearence of the amino acids along the evolution as inferred from work that mixtures known experimental results with theoretical speculations. Suggested by the diagram we propose a Hamilton quaternions based mathematical representation of the code as it stands now-a-days. The central object in the description is a codon function that assigns to each amino acid an integer quaternion in such a way that the observed code degeneration is preserved. We emphasize the advantages of a quaternionic representation of amino acids taking as an example the folding of proteins. With this aim we propose an algorithm to go from the quaternions sequence to the protein three dimensional structure which can be compared with the corresponding experimental one stored at the Protein Data Bank. In our criterion the mathematical representation of the genetic code in terms of quaternions merits to be taken into account because it describes not only most of the known properties of the genetic code but also opens new perspectives that are mainly derived from the close relationship between quaternions and rotations.Comment: 19 pages, 11 figure

A critical analysis of COA research.

Five experts respected for their significant contributions to the scientific literature on children of alcoholics (COA's) offer their perspectives in a panel discussion format. The panel members reflect on the historical roots of COA research and comment on its current status and future direction. Enriched by the panelists' variety of backgrounds, research interests, and approaches, the discussion emphasizes the need to consider multiple variables that influence the risk for alcoholism among COA's

Against the Virtual: Kleinherenbrink’s Externality Thesis and Deleuze’s Machine Ontology

Drawing from Arjen Kleinherenbrink's recent book, Against Continuity: Gilles Deleuze's Speculative Realism (2019), this paper undertakes a detailed review of Kleinherenbrink's fourfold "externality thesis" vis-à-vis Deleuze's machine ontology. Reading Deleuze as a philosopher of the actual, this paper renders Deleuzean syntheses as passive contemplations, pulling other (passive) entities into an (active) experience and designating relations as expressed through contraction. In addition to reviewing Kleinherenbrink's book (which argues that the machine ontology is a guiding current that emerges in Deleuze's work after Difference and Repetition) alongside much of Deleuze's oeuvre, we relate and juxtapose Deleuze's machine ontology to positions concerning externality held by a host of speculative realists. Arguing that the machine ontology has its own account of interaction, change, and novelty, we ultimately set to prove that positing an ontological "cut" on behalf of the virtual realm is unwarranted because, unlike the realm of actualities, it is extraneous to the structure of becoming-that is, because it cannot be homogenous, any theory of change vis-à-vis the virtual makes it impossible to explain how and why qualitatively different actualities are produced

Patterns of base composition within and between animal mitochondrial genomes

Nucleotide composition of a DNA molecule is a product of base substitution. Variation in nucleotide composition indicates a change in the pattern of substitution at either the level of the underlying mutational spectrum or the constraints imposed by natural selection. This work explores patterns of nucleotide usage within and between animal mitochondrial genomes and the evolutionary mechanisms that have shaped these patterns. Fourfold degenerate sites are expected to reflect the underlying mutational spectrum. Three simple measures of compositional bias, taking into account the strand-specific nature of nucleotide distribution in mtDNA, reveal considerable variation among fourfold degenerate sites of metazoan mitochondrial genomes. Log-linear analysis of intramolecular compositional patterns of mammalian mtDNA demonstrates that fourfold degenerate sites from even a single strand of the genome are not homogeneous. Rather, base composition varies among codon families and around the circular genome. A companion analysis of two additional taxonomic groups, molluscs and insects, also reveals compositional variation among codon families and between strands. The observed intramolecular variation cannot be explained solely by a simple strand-specific mutational pressure, but requires either a contextual bias to the mutational process or translational level natural selection as well. First and second codon position base composition and amino acid frequencies regressed on fourfold degenerate site composition show how mutational biases at the DNA level translate to amino acid biases in mitochondrial proteins

Genetic interactions contribute less than additive effects to quantitative trait variation in yeast.

Genetic mapping studies of quantitative traits typically focus on detecting loci that contribute additively to trait variation. Genetic interactions are often proposed as a contributing factor to trait variation, but the relative contribution of interactions to trait variation is a subject of debate. Here we use a very large cross between two yeast strains to accurately estimate the fraction of phenotypic variance due to pairwise QTL-QTL interactions for 20 quantitative traits. We find that this fraction is 9% on average, substantially less than the contribution of additive QTL (43%). Statistically significant QTL-QTL pairs typically have small individual effect sizes, but collectively explain 40% of the pairwise interaction variance. We show that pairwise interaction variance is largely explained by pairs of loci at least one of which has a significant additive effect. These results refine our understanding of the genetic architecture of quantitative traits and help guide future mapping studies

Standard genetic code: p-adic modelling, nucleon balances and selfsimilarity

This paper represents the preliminary results and conclusions on the one of fundamental questions of the genetic code related to the underlying selective mechanisms involved in its origin and evolution, in particular their hypothetical different nature, originally considered in [1,2,3]. A novel approach is introduced, based on known arithmetic regularities inside the genetic code, determined by the nucleon balances of amino acids and their divisibility by the decimal number 37 [4]. As a parameter of the genetic code systematization is introduced an aggregate nucleon number of amino acid and cognate codon, while divisibility test is carried out not only by the number 37, but also by 13.7, the selfsimilarity constant of decimal scaling [5]. Relevant nucleon sums were obtained for the most prominent divisions of the standard genetic code (SGC) according to p-adic model of the vertebrate mitochondrial code (VMC) in [6]. The nucleon number divisibility pattern of 37 and 13.7 for the RNA and DNA codon space, as well as for the amino acid space is also analyzed. The obtained results, particularly a general higher divisibility of the nucleon sums by the numbers 37 and 13.7 in SGC than in VMC, as well as a correspondence between the nucleon number divisibility pattern of both the RNA codon space and the amino acid space of SGC, how separately so conjointly, with the code degeneracy pattern, suggest some conclusions: support the hypothesis [1,2,3,7] that the selective driving forces acting during an emergence (an ancient phase) and an evolution (a modern phase) of the genetic code are different, imply the existence of an environmental-dependent stereochemical mechanism throughout the entire period of the genetic code emergence and support a mineral-mediated origin of the genetic code [7,8]

Evolutionary Analysis of Mitogenomes from Parasitic and Free-Living Flatworms

Copyright: © 2015 Solà et al. This is an open access article distributed under the terms of the Creative Commons Attribution License, which permits unrestricted use, distribution, and reproduction in any medium, provided the original author and source are credited. The attached file is the published version of the article

Minnesota Agricultural Economist 698

Research and Development/Tech Change/Emerging Technologies,