Information and symmetry: Adumbrating the abstract core of complex systems

Information and symmetry are essential theoretical concepts that underlie the scientific explanation of a variety of complex systems. In spite of clear-cut developments around both concepts, their intersection is really problematic, either in fields related to mathematics, physics, and chemistry, or even more in those pertaining to biology, neurosciences, and social sciences. The present Special Issue explores recent developments, both theoretical and applied, in most of these disciplines

Dihydrolipoamide dehydrogenase from porcine heart catalyzes NADH-dependent scavenging of nitric oxide

Abstract Dihydrolipoamide dehydrogenase (DLDH; EC 1.8.1.4) from porcine heart is capable of using nitric oxide (NO) as an electron acceptor, with NADH as the electron donor, forming nitrate in the reaction. NADPH was not effective as an electron donor. The reaction had a pH optimum near 6 and was not inhibited by cyanide or diphenyleneiodonium ions. The K m for NADH was 10 lM, while that for NO was 0.5 lM. The rate of NO conversion was comparable to the rate of lipoamide conversion (200 lmol min À1 mg À1 protein at pH 6). Cytochrome c or myoglobin were poor electron acceptors by themselves but, in the presence of methylene blue, DLDH had an activity of 5-7 lmol min À1 mg À1 protein with these substrates, indicating that DLDH can act also as a methemoglobin reductase. While the K m of DLDH for NO is relatively low, it is in the physiological range of NO levels encountered in the tissue. The enzyme may, therefore, have a significant role in modifying NO levels under specific cell conditions

Current approaches to measure nitric oxide in plants

Nitric oxide (NO) is now established as an important signalling molecule in plants where it influences growth, development, and responses to stress. Despite extensive research, the most appropriate methods to measure and localize these signalling radicals are debated and still need investigation. Many confounding factors such as the presence of other reactive intermediates, scavenging enzymes, and compartmentation influence how accurately each can be measured. Further, these signalling radicals have short half-lives ranging from seconds to minutes based on the cellular redox condition. Hence, it is necessary to use sensitive and specific methods in order to understand the contribution of each signalling molecule to various biological processes. In this review, we summarize the current knowledge on NO measurement in plant samples, via various methods. We also discuss advantages, limitations, and wider applications of each method

Roles for Plant Mitochondrial Alternative Oxidase Under Normoxia, Hypoxia, and Reoxygenation Conditions

Alternative oxidase (AOX) is a non-energy conserving terminal oxidase in the plant mitochondrial electron transport chain (ETC) that has a lower affinity for oxygen than does cytochrome (cyt) oxidase. To investigate the role(s) of AOX under different oxygen conditions, wild-type (WT) Nicotiana tabacum plants were compared with AOX knockdown and overexpression plants under normoxia, hypoxia (near-anoxia), and during a reoxygenation period following hypoxia. Paradoxically, under all the conditions tested, the AOX amount across plant lines correlated positively with leaf energy status (ATP/ADP ratio). Under normoxia, AOX was important to maintain respiratory carbon flow, to prevent the mitochondrial generation of superoxide and nitric oxide (NO), to control lipid peroxidation and protein S-nitrosylation, and possibly to reduce the inhibition of cyt oxidase by NO. Under hypoxia, AOX was again important in preventing superoxide generation and lipid peroxidation, but now contributed positively to NO amount. This may indicate an ability of AOX to generate NO under hypoxia, similar to the nitrite reductase activity of cyt oxidase under hypoxia. Alternatively, it may indicate that AOX activity simply reduces the amount of superoxide scavenging of NO, by reducing the availability of superoxide. The amount of inactivation of mitochondrial aconitase during hypoxia was also dependent upon AOX amount, perhaps through its effects on NO amount, and this influenced carbon flow under hypoxia. Finally, AOX was particularly important in preventing nitro-oxidative stress during the reoxygenation period, thereby contributing positively to the recovery of energy status following hypoxia. Overall, the results suggest that AOX plays a beneficial role in low oxygen metabolism, despite its lower affinity for oxygen than cytochrome oxidase

Control of Rubisco function via homeostatic equilibration of CO2 supply

Rubisco is the most abundant protein on Earth that serves as the primary engine of carbon assimilation. It is characterized by a slow rate and low specificity for CO2 leading to photorespiration. We analyze here the challenges of operation of this enzyme as the main carbon fixation engine. The high concentration of Rubisco exceeds that of its substrate CO2 by 2–3 orders of magnitude; however, the total pool of available carbon in chloroplast, i.e., mainly bicarbonate, is comparable to the concentration of Rubisco active sites. This makes the reactant stationary assumption (RSA), which is essential as a condition of satisfying the Michaelis–Menten (MM) kinetics, valid if we assume that the delivery of CO2 from this pool is not limiting. The RSA is supported by active carbonic anhydrases (CA) that quickly equilibrate bicarbonate and CO2 pools and supply CO2 to Rubisco. While the operation of stromal CA is independent of light reactions, the thylakoidal CA associated with PSII and pumping CO2 from the thylakoid lumen is coordinated with the rate of electron transport, water splitting and proton gradient across the thylakoid membrane. At high CO2 concentrations, CA becomes less efficient (the equilibrium becomes unfavorable), so a deviation from the MM kinetics is observed, consistent with Rubisco reaching its Vmax at approximately 50% lower level than expected from the classical MM curve. Previously, this deviation was controversially explained by the limitation of RuBP regeneration. At low ambient CO2 and correspondingly limited capacity of the bicarbonate pool, its depletion at Rubisco sites is relieved in that the enzyme utilizes O2 instead of CO2, i.e., by photorespiration. In this process, CO2 is supplied back to Rubisco, and the chloroplastic redox state and energy level are maintained. It is concluded that the optimal performance of photosynthesis is achieved via the provision of continuous CO2 supply to Rubisco by carbonic anhydrases and photorespiration

Time and Life in the Relational Universe: Prolegomena to an Integral Paradigm of Natural Philosophy

Relational ideas for our description of the natural world can be traced to the concept of Anaxagoras on the multiplicity of basic particles, later called “homoiomeroi” by Aristotle, that constitute the Universe and have the same nature as the whole world. Leibniz viewed the Universe as an infinite set of embodied logical essences called monads, which possess inner view, compute their own programs and perform mathematical transformations of their qualities, independently of all other monads. In this paradigm, space appears as a relational order of co-existences and time as a relational order of sequences. The relational paradigm was recognized in physics as a dependence of the spatiotemporal structure and its actualization on the observer. In the foundations of mathematics, the basic logical principles are united with the basic geometrical principles that are generic to the unfolding of internal logic. These principles appear as universal topological structures (“geometric atoms”) shaping the world. The decision-making system performs internal quantum reduction which is described by external observers via the probability function. In biology, individual systems operate as separate relational domains. The wave function superposition is restricted within a single domain and does not expand outside it, which corresponds to the statement of Leibniz that “monads have no windows”