Control of the Generation and Reactions of Free Radicals in Biological Systems by Kinetic and Thermodynamic Factors

Quantifiable redox properties are useful predictors of substrate reactivity in enzyme-catalysed redox reactions of e.g. nitroreductases or peroxidases. Redox properties may also control the rates of electron-transfer reactions between radical products of reduction and oxidation, and endogenous oxidants and reductants respectively. However, in numerous instances prototropic properties of substrate or radical may have profound kinetic consequences, protonation of radicals frequently slowing down electron-transfer reactions. Further, reactions which are thermodynamically extremely unfavourable may still proceed if radical products are removed from the pre-equilibrium efficiently. Thus kinetic considerations often outweigh the purely thermodynamico viewpoint.     

Control of the Generation and Reactions of Free Radicals in Biological Systems by Kinetic and Thermodynamic Factors

Quantifiable redox properties are useful predictors of substrate reactivity in enzyme-catalysed redox reactions of e.g. nitroreductases or peroxidases. Redox properties may also control the rates of electron-transfer reactions between radical products of reduction and oxidation, and endogenous oxidants and reductants respectively. However, in numerous instances prototropic properties of substrate or radical may have profound kinetic consequences, protonation of radicals frequently slowing down electron-transfer reactions. Further, reactions which are thermodynamically extremely unfavourable may still proceed if radical products are removed from the pre-equilibrium efficiently. Thus kinetic considerations often outweigh the purely thermodynamico viewpoint.     

Phototoxic and photoallergic skin reactions

Indirect action of sun together with different exogenous agents (systemic medications and topically applied compounds) sometimes may result in phototoxicic and photoallergic reactions. Drug-induced photosensitivity reactions refer to the development of cutaneous disease as a result of the combined effects of a drug and light (mostly spectrum within the UVA and visible light range or UVB range). The aim of the review was to show the prominent features of phototoxic and photoallergic reactions, which occur in sun-exposed areas, including face, neck, hands and forearms. Phototoxic reactions are significantly more common than photoallergic reactions and mostly resemble to exaggerated sunburn. Photoallergic reactions appear only in a minority of individuals and resemble allergic contact dermatitis on sun-exposed areas, although sometimes may extend into covered areas. Generally, the physical examination and a positive patient's history of photosensitivity reactions on substances are of great importance for the diagnostics. The treatment of these reactions includes identification and avoidance of offending agent and application of anti-inflammatory dressings, ointments and corticosteroids.     

PHENOTHIAZINE ATARAXICS—Extrapyramidal Reactions

Thirty-nine cases of extrapyramidal reactions caused by seven chemically different phenothiazine medications are presented. Historical, pharmacological, diagnostic, and therapeutic factors are considered. It is important that the physician prescribing phenothiazines be well aware of the reactions which may occur so that therapy may be discontinued at the first untoward signs.     

Distinguishing reversible from irreversible virus capsid assembly

Capsids of spherical viruses may be constructed from hundreds or thousands of copies of the major capsid protein(s). These assembly reactions are poorly understood. Here we consider the predicted behavior for assembly where the component reactions have weak association energy and are reversible and compare them to essentially irreversible reactions. The comparisons are based on mass action calculations and the behavior predicted from kinetic simulations where assembly is described as a cascade of low order reactions. Reversible reactions are characterized by a pseudo-critical concentration, whereas irreversible reactions consume all free subunits. Irreversible reactions are more susceptible to kinetic traps comprised of numerous small intermediates. In the case where only the ultimate step is irreversible, very low concentrations of intermediates slow the completion of the reaction so that overall it closely matches the predictions for the reversible reactions that make up the majority of the cascade. Data in the literature strongly support the hypothesis that most viruses are held together by many weak interactions.     

Cellular responses to unsaturated fatty acids mediated by their sensor Ubxd8

Fatty acids (FAs) are crucial nutrient for cell survival because they are required for synthesis of phospholipids in cellular membranes and for generation of energy. However, overaccumulation of FAs is toxic. In response to excessive FAs, cells are able to activate multiple reactions to prevent their overaccumulation. These reactions are mediated by Ubxd8, a cellular protein that specifically interacts with unsaturated but not saturated FAs. The selective interaction of Ubxd8 with unsaturated FAs may explain previous observations that only unsaturated but not saturated FAs are able to stimulate the regulatory reactions that prevent overaccumulation of FAs. Thus, understanding the mechanism through which Ubxd8 maintains cellular FA homeostasis may provide new insights into saturated FAinduced lipotoxicity.     

Modeling speciation effects on biodegradation in mixed metal/chelate systems

A new model, CCBATCH, comprehensively couples microbially catalyzed reactions to aqueous geochemistry. The effect of aqueous speciation on biodegradation reactions and the effect of biological reactions on the concentration of chemical species (e.g. H₂CO₃, NH ₄ ⁺ , O₂) are explicitly included in CCBATCH, allowing systematic investigation of kinetically controlled biological reactions. Bulk-phase chemical speciation reactions including acid/base and complexation are modeled as thermodynamically controlled, while biological reactions are modeled as kinetically controlled. A dual-Monod kinetic formulation for biological degradation reactions is coupled with stoichiometry for the degradation reaction to predict the rate of change of all biological and chemical species affected by the biological reactions. The capability of CCBATCH to capture pH and speciation effects on biological reactions is demonstrated by a series of modeling examples for the citrate/Fe(III) system. pH controls the concentration of potentially biologically available forms of citrate. When the percentage of the degradable substrate is low due to complexation or acid/base speciation, degradation rates may be slow despite high concentrations of substrate Complexation reactions that sequester substratein non-degradable forms may prevent degradation or stopdegradation reactions prior to complete substrate utilization. The capability of CCBATCH to couple aqueous speciation changes to biodegradation reaction kinetics and stoichiometry allows prediction of these key behaviors in mixed metal/chelate systems.     

Specificity of Cellular Immune Reactivity to Virus-induced Tumours

SPECIFICITY is one of the chief hallmarks of immune reactions. In many cases, specificity has been defined by reactivity against some antigens and not against others, but the results of direct tests may be misleading. In many cases, in transplantation and tumour immunology, direct reactivity may be absent in spite of the presence of the antigen. With HL-A antigens, the CYNAP phenomenon (cytotoxicity negative, absorption positive) has been described¹. Virus-induced tumours may have relatively small amounts of tumour specific cell surface antigens which are detectable only by absorption tests^2,3. In addition, immune reactions may occur against a particular antigen on one material and against different antigens on another material. With antibody reactions, specificity can be confirmed by the appropriate absorption experiments^4,5. With cellular immune reactions, comparable demonstration of specificity has been very difficult.     

The temperature dependences of some types of gaseous ionic reactions of astrochemical interest.

The rate constants of ion-molecule reactions which are of potential significance in astrochemical systems are found to exhibit significant, and in many cases, negative temperature dependences. The rate constants of fast ion-polar molecule reactions (e.g., XH+ + B leads to BH+ + X) may increase by a factor of 5-10 between 1000 and 10D. Slow reactions that proceed via reaction complexes (e.g., H- transfer and association reactions) often exhibit temperature dependences of the form k = AT-n, n = 1-5. Both transition state theory considerations and the coupled-oscillator RRK-type model are seen to be able to account qualitatively for the behavior of slow ion-molecule reactions.     

Determination of binding parameters in the presence of coupled reactions

Components of a binding reaction may undergo nonbinding reactions: receptors may be degraded, internalized, or exchanged with cryptic sites; ligand may be degraded or compartmented. In such cases the parameters that characterize the system are not obtained from the usual equilibrium analyses. We have simulated the reactions of such systems and generated association curves, "Scatchard" plots, and "Scatchard-like" plots that permit the calculation of binding affinity and receptor number not normally calculable under nonequilibrium binding conditions. In particular, we show that certain coupled reactions produce local maxima and sigmoid shapes in association curves and that the maxima can be used to obtain affinities and receptor numbers.     

Animal models of idiosyncratic drug reactions

Idiosyncratic drug reactions represent a major problem. In most cases the mechanisms of these reactions are unknown, but circumstantial evidence points to the involvement of reactive metabolites and the characteristics of the reactions suggest involvement of the immune system. If progress is to be made in dealing with these adverse reactions it is essential that we have a better understanding of their mechanisms, and it is hard to imagine testing mechanistic hypotheses without good animal models. Unfortunately, idiosyncratic reactions are also idiosyncratic in animals so few good models exist. The best models, in which a rodent develops a clinical syndrome similar to that which occurs in humans, appear to be penicillamine-induced autoimmunity in Brown Norway rats and nevirapine-induced skin rash in rats. Sulfamethoxazole-induced hypersensitivity in dogs and propylthiouracil-induced autoimmunity in cats are also similar to adverse reactions that occur in people, but they have practical limitations. Halothane-induced liver toxicity in guinea pigs and amodiaquine-induced bone marrow and liver toxicity in rats represent models in which there is an immune response and mild, reversible toxicity. It is possible that the development of immune tolerance is what limits the toxicity in these models, and if this is true, interventions that prevent tolerance might lead to good models. Although the history of developing animal models of idiosyncratic drug reactions is mostly one of failure, such models are essential. A better understanding of immune tolerance may greatly facilitate the development of better models; transgenic technology may also provide an important tool.     

Enzymatic Reactions inside Biological Condensates

Biological enzymes significantly speed up chemical reactions in living organisms. The complex environment within cells has long been appreciated as a major regulator of enzymatic activities. Recent advances in the rapidly evolving field of biological condensates, which are spontaneously formed by macromolecules through phase separation, suggest new possibilities for how enzymatic reactions may be modulated within cells. Here, we review the latest studies of enzymatic reactions in biological condensates focusing on basic concepts in enzymology and discussing some context-dependent roles of phase separation in regulating biochemical reactions.     

Equipment-Free Incubation of Recombinase Polymerase Amplification Reactions Using Body Heat

The development of isothermal amplification platforms for nucleic acid detection has the potential to increase access to molecular diagnostics in low resource settings; however, simple, low-cost methods for heating samples are required to perform reactions. In this study, we demonstrated that human body heat may be harnessed to incubate recombinase polymerase amplification (RPA) reactions for isothermal amplification of HIV-1 DNA. After measuring the temperature of mock reactions at 4 body locations, the axilla was chosen as the ideal site for comfortable, convenient incubation. Using commonly available materials, 3 methods for securing RPA reactions to the body were characterized. Finally, RPA reactions were incubated using body heat while control RPA reactions were incubated in a heat block. At room temperature, all reactions with 10 copies of HIV-1 DNA and 90% of reactions with 100 copies of HIV-1 DNA tested positive when incubated with body heat. In a cold room with an ambient temperature of 10 degrees Celsius, all reactions containing 10 copies or 100 copies of HIV-1 DNA tested positive when incubated with body heat. These results suggest that human body heat may provide an extremely low-cost solution for incubating RPA reactions in low resource settings.     

Allergenic tropomyosins and their cross-reactivities

The ingestion or inhalation of some proteins may lead to adverse immune reactions. Allergens may trigger allergic reactions in genetically predisposed individuals when they are absorbed through the skin or make contact with mucous membranes. An allergic disease often deteriorates the quality of life and may sometimes be life-threatening due to anaphylactic shock. A number of allergens have been characterized from various multicellular organisms to date. It is thought to be reasonable to pay a special attention to the substance which is highly cross-reactive and which causes adverse responses in the molecules that are not sensitized but similar to the sensitized allergen. Tropomyosin has been described as an important food allergen in shrimp, lobster, crab, oysters, squid, and other invertebrates. Allergic reactions to shellfish and mollusks are often cross-reactive, which may be explained by the highly conserved amino acid sequences of tropomyosins among invertebrates, but vertebrate tropomyosins are not known to be allergenic. Several tropomyosins from domestic arthropods have been reported to be allergenic. Recently, it was suggested that an infection of helminthic parasites might lead to sensitization to tropomyosin and elicit allergic reactions to other invertebrates. Much effort has been made to characterize these allergenic tropomyosins from various sources. We will discuss the physicochemical characteristics and the potential application of tropomyosin for the diagnosis and therapeutics of allergic disorders.     

Energy metabolism reactions in ruminant muscle: responses to age, nutrition and hormonal status

Energy expenditure in muscle comprises reactions related to intermediary metabolism and those of posture and activity. The metabolic reactions respond to a wide range of nutritional and hormonal stimuli and are often apparently co-ordinated; in magnitude, however, their contribution to energy requirements can be minor compared with locomotion and posture. Metabolic reactions include protein turnover, ion transport and substrate cycles. In young ruminants muscle protein synthesis responds to intake but effects on energy expenditure are less pronounced; the situation with the adult is unclear. The involvement of insulin in ruminants may differ from that in monogastrics but effects are observed with thyroid hormones. Ruminant muscle may have a higher energy requirement for Na+, K+ transport which responds in proportion to total oxygen uptake to alterations in intake. Thyroid hormone treatment and, probably, the catecholamines enhance both Na+, K+ and Ca2+ transport. Muscle has fewer substrate cycles than liver and each may contribute only 1-3% toward oxygen consumption. Several are sensitive to insulin, but larger responses are observed with thyroxine and epinephrine and under stress conditions, therefore, may account for significant proportions of heat increment. Energy costs of standing may be considerable and posture movements may change with diet quality and quantity. Locomotory activity may mask changes in the contribution of metabolic reactions in response to different stimuli. Approximately 80% of energy costs for muscle in vivo are accounted for by protein turnover (20-25%), ion transport (25-30%), substrate cycling (5-8%) and standing (30%). Better integration of experiments in vivo and in vitro is required to improve the quantification and resolve data anomalies.     

Induced resistance in mountain birch: defence against leaf-chewing insect guild and herbivore competition

Summary The effect of leaf damage simulating the feeding of early season insect herbivore species, e.g. Epirrita autumnata, to mountain birch, Betula pubescens ssp. tortuosa, on the performance of insect larvae was studied with eleven leaf-chewing sawfly species. I found variation in the results that was due to short- and long-term inducible responses and to the phenology of herbivore species. In general, early and mid-season species were more strongly affected by induced reactions than late-season species. This finding is in accordance with earlier results but I could show that the persistance of induced reactions rather than the influence of timing of damage is responsible for the result. The growth of the larvae of mid-season sawfly species was affected by both short- and long-term induced reactions. This result shows that early season species may escape short-term induced reactions of mountain birch in current year but may not avoid long-term effects. It is supposed that seasonal deterioration of leaf quality either masks the effects of induced defences or late-season species are better adapted to low-quality leaves. Some species show variation in their response to induced defence in different years. This may be due to yearly differences in induced reactions as well as to species-specific responses. Induced defence reactions may play a role in competitive interactions between herbivore species in leaf-chewing guild of mountain birch.     

Is glucose the sole source of tissue browning in diabetes mellitus?

Reactions between glucose and protein are held to be responsible for the protein 'browning' reactions which occur in diabetes mellitus. In vitro, however, the formation of such novel protein fluorophores is dependent upon the metal-catalysed oxidation of the monosaccharide (glucose 'autoxidation'). Since other small oxidisable molecules are capable of 'browning' proteins via similar metal-catalysed oxidative mechanisms we suggest that protein modification in diabetes may not be restricted to reactions with monosaccharides but may also include other small autoxidisable molecules.     

Kinetic and thermodynamic principles determining the structural design of ATP-producing systems

It is theoretically analysed whether the structural design of ATP-producing pathways, in particular the design of glycolysis, may be explained by optimization principles. On the basis of kinetic and thermodynamic principles conclusions are derived concerning the stoichiometry of these pathways in states of high ATP production rates. One of the extensions to previous investigations is that the concentrations of the adenine nucleotides are taken into account as variable quantities. This necessitates the consideration of an interaction of the ATP-producing system I with an external ATP-consuming system II. A great variety of pathways is studied which differ in the number and location of ATP-consuming reactions, ATP-producing reactions and reactions involving inorganic phosphate. The corresponding number of possible pathways may be calculated in an explicit manner as a function of the number of those reactions which do not couple to ATP or inorganic phosphate. The kinetics of the individual reactions are described by linear or bilinear functions of reactant concentrations and all rate equations are expressed in terms of equilibrium constants and characteristic times. A thermodynamical analysis of the two coupled systems yields upper and lower limits for the concentration of ATP and an explicit expression for the maximal difference between the number of ATP-producing and ATP-consuming reactions of system I. The following results of the optimization are obtained. (i) The ATP production rate always increases if the ATP-producing reactions as well as those reactions characterized by an uptake of inorganic phosphate are shifted as far as possible towards the end of system I. (ii) Explicit conditions for the optimal location of the ATP-consuming reactions are presented. The results are discussed in the context of characteristic times as well as in terms of enzyme kinetic parameters. (iii) For two sets of characteristic times the resulting stoichiometries and their corresponding steady-state fluxes are investigated in detail. One of these stoichiometries shows a close correspondence to contemporary standard glycolysis. (iv) It is shown that most possible pathways result in a very low steady-state flux, that is, the optimal stoichiometry is characterized by a significant selective advantage. (v) The standard free energy profile of a pathway with an optimal stoichiometry is discussed. It differs significantly from the free energy profiles of nonoptimized pathways.     

Drug surveillance data in a Canadian hospital.

Comparison of results of a Canadian hospital-based drug surveillance program with data from centres in the United States and Israel showed no important difference in the rate of drug exposures or adverse reactions. Drugs for symptomatic relief were frequently used in the Canadian centre. Women received more drugs and had more adverse reactions than men. Life-threatening and potentially fatal reactions were caused by commonly used drugs; autopsy findings may detect previously unsuspected relations between drug events and mechanisms of death. Voluntary reporting and intensive monitoring are both important in the field of adverse drug reactions.     

Some aspects of laboratory cometary models

In this paper, we discuss some aspects of laboratory experiments proposed in the literature, associated with the chemical reactions that may occur in the comets. These comments are made in the light of the use of energetic particles or radiation as energy sources, relevant chemical reactions and compounds detected in those experiments.