Zea mays iRS1563: A Comprehensive Genome-Scale Metabolic Reconstruction of Maize Metabolism

The scope and breadth of genome-scale metabolic reconstructions have continued to expand over the last decade. Herein, we introduce a genome-scale model for a plant with direct applications to food and bioenergy production (i.e., maize). Maize annotation is still underway, which introduces significant challenges in the association of metabolic functions to genes. The developed model is designed to meet rigorous standards on gene-protein-reaction (GPR) associations, elementally and charged balanced reactions and a biomass reaction abstracting the relative contribution of all biomass constituents. The metabolic network contains 1,563 genes and 1,825 metabolites involved in 1,985 reactions from primary and secondary maize metabolism. For approximately 42% of the reactions direct literature evidence for the participation of the reaction in maize was found. As many as 445 reactions and 369 metabolites are unique to the maize model compared to the AraGEM model for A. thaliana. 674 metabolites and 893 reactions are present in Zea mays iRS1563 that are not accounted for in maize C4GEM. All reactions are elementally and charged balanced and localized into six different compartments (i.e., cytoplasm, mitochondrion, plastid, peroxisome, vacuole and extracellular). GPR associations are also established based on the functional annotation information and homology prediction accounting for monofunctional, multifunctional and multimeric proteins, isozymes and protein complexes. We describe results from performing flux balance analysis under different physiological conditions, (i.e., photosynthesis, photorespiration and respiration) of a C4 plant and also explore model predictions against experimental observations for two naturally occurring mutants (i.e., bm1 and bm3). The developed model corresponds to the largest and more complete to-date effort at cataloguing metabolism for a plant species

Iron Behaving Badly: Inappropriate Iron Chelation as a Major Contributor to the Aetiology of Vascular and Other Progressive Inflammatory and Degenerative Diseases

The production of peroxide and superoxide is an inevitable consequence of aerobic metabolism, and while these particular "reactive oxygen species" (ROSs) can exhibit a number of biological effects, they are not of themselves excessively reactive and thus they are not especially damaging at physiological concentrations. However, their reactions with poorly liganded iron species can lead to the catalytic production of the very reactive and dangerous hydroxyl radical, which is exceptionally damaging, and a major cause of chronic inflammation. We review the considerable and wide-ranging evidence for the involvement of this combination of (su)peroxide and poorly liganded iron in a large number of physiological and indeed pathological processes and inflammatory disorders, especially those involving the progressive degradation of cellular and organismal performance. These diseases share a great many similarities and thus might be considered to have a common cause (i.e. iron-catalysed free radical and especially hydroxyl radical generation). The studies reviewed include those focused on a series of cardiovascular, metabolic and neurological diseases, where iron can be found at the sites of plaques and lesions, as well as studies showing the significance of iron to aging and longevity. The effective chelation of iron by natural or synthetic ligands is thus of major physiological (and potentially therapeutic) importance. As systems properties, we need to recognise that physiological observables have multiple molecular causes, and studying them in isolation leads to inconsistent patterns of apparent causality when it is the simultaneous combination of multiple factors that is responsible. This explains, for instance, the decidedly mixed effects of antioxidants that have been observed, etc...Comment: 159 pages, including 9 Figs and 2184 reference

Conjuntos excepcionais e alguns problemas de Mahler

Dissertação (mestrado)—Universidade de Brasília, Instituto de Ciências Exatas, Departamento de Matemática, 2017.Seja f uma função inteira e transcendente. Denotamos por Sf o conjunto de todos os α ∈ ´Q tais que f(α) ∈ ´Q (o conjunto excepcional de f). Nessa dissertação, mostraremos quais subconjuntos de ´Q podem ser o conjunto excepcional de alguma função inteira e transcendente. Além disso, trataremos de dois problemas de Mahler relacionados a propriedades de funções inteiras e transcendentes. Mostraremos que existem funções inteiras e transcendentes que levam um subconjunto dos números de Liouville nele mesmo e daremos uma resposta positiva ao Problema B de Mahler: Problema B: Existe uma função inteira e transcendente f(z) = Σn =0 ∞ a nz n com coeficientes racionais tal que f( ´Q ) ⊆ ´Q e f−1( ´Q ) ⊆ ´Q ? .Let f be an entire transcendental function. We denote by Sf the set of all α ∈ ´Q such that f(α) ∈ ´Q (exceptional set of f). Throughout this dissertation, we will show which subsets of ´Q can be the exceptional set of some entire transcendental function. Moreover, we will deal with two of Mahler’s problems related to properties of entire transcendental functions. We will show that there are entire transcendental functions that map a subset of Liouville numbers in itself and we will give a positive answer for Mahler’s Problem B: Problem B: Is there an entire transcendental function f(z) = Σn =0 ∞ a nz n with rational coefficients such that que f( ´Q ) ⊆ ´Q e f−1( ´Q ) ⊆ ´Q ?