Dynamical properties of Discrete Reaction Networks

Reaction networks are commonly used to model the dynamics of populations subject to transformations that follow an imposed stoichiometry. This paper focuses on the efficient characterisation of dynamical properties of Discrete Reaction Networks (DRNs). DRNs can be seen as modeling the underlying discrete nondeterministic transitions of stochastic models of reaction networks. In that sense, a proof of non-reachability in a given DRN has immediate implications for any concrete stochastic model based on that DRN, independent of the choice of kinetic laws and constants. Moreover, if we assume that stochastic kinetic rates are given by the mass-action law (or any other kinetic law that gives non-vanishing probability to each reaction if the required number of interacting substrates is present), then reachability properties are equivalent in the two settings. The analysis of two types of global dynamical properties of DRNs is addressed: irreducibility, i.e., the ability to reach any discrete state from any other state; and recurrence, i.e., the ability to return to any initial state. Our results consider both the verification of such properties when species are present in a large copy number, and in the general case. The necessary and sufficient conditions obtained involve algebraic conditions on the network reactions which in most cases can be verified using linear programming. Finally, the relationship of DRN irreducibility and recurrence with dynamical properties of stochastic and continuous models of reaction networks is discussed.     

Product-Form Stationary Distributions for Deficiency Zero Chemical Reaction Networks

We consider stochastically modeled chemical reaction systems with mass-action kinetics and prove that a product-form stationary distribution exists for each closed, irreducible subset of the state space if an analogous deterministically modeled system with mass-action kinetics admits a complex balanced equilibrium. Feinberg’s deficiency zero theorem then implies that such a distribution exists so long as the corresponding chemical network is weakly reversible and has a deficiency of zero. The main parameter of the stationary distribution for the stochastically modeled system is a complex balanced equilibrium value for the corresponding deterministically modeled system. We also generalize our main result to some non-mass-action kinetics.     

Effects of temperature and pH on the water exchange through erythrocyte membranes: Nuclear magnetic resonance studies

Summary The temperature and pH dependence of water exchange has been studied on isolated erythrocytes suspended in isotonic buffered solutions. At pH 7.4 a break in the Arrhenius plot of water exchange time at around 26°C was found. The mean value of the apparent activation energy of the water exchange time at temperatures higher than that of the discontinuity was 5.7 kcal/mole (±0.4); at lower temperatures the values of the apparent activation energy were below 1.4 kcal/mole. The pH dependence of water exchange time of isolated erythrocytes revealed a marked increase of the water exchange time values in the acid range of pH; a much smaller variation of the same parameter occurs between pH 7.0 and 8.0. These finding could be correlated with other processes involving erythrocyte membranes that showed similar pH and temperature dependence and were considered to indicate state transitions in the membranes. It is suggested that the temperature and pH effects on water diffusion indicate that conformational changes and cooperative effects are implicated in the mechanism of this transport process.Institute for Isotopic and Molecular Technology.     

The basal permeability to water of human red blood cells evaluated by a nuclear magnetic resonance technique

The characteristics of water diffusional permeability (P) of human red blood cells were studied on isolated erythrocytes by a doping nuclear magnetic resonance technique. In order to estimate the basal permeability the maximal inhibition of water diffusion was induced by exposure of red blood cells to p-chloromercuribenzene sulfonate (PCMBS) under various conditions (concentration, duration, temperature). The lowest values of P were around 0.7×10^–3 cm s^–1 at 10°C, 1.2×10^–3 cm s^–1 at 15°C, 1.4×10^–3 cm s^–1 at 20°C, 1.8×10^–3 cm s^–1 at 25°C, 2.1×10^–3 cm s^–1 at 30°C and 3.5×10^–3 cm s^–1 at 37°C. The mean value of the activation energy of water diffusion (E_a,d) was 25 kJ/mol for control and 43.7 kJ/mol for PCMBS-inhibited erythrocytes. The values of P and E_a,d obtained after induction of maximal inhibition of water diffusion by PCMBS can be taken as references for the basal permeability to water of the human red blood cell membrane.     

The Impact of Chemical Compounds on Benthic Invertebrates from the Danube and Danube Delta Systems

The aim of this study is to assess freshwater sediment in terms of biological and preliminary toxicological control linked to a series of variables along the Danube River and Danube Delta systems. The research is focused on eight points of the Romanian sector in the summer to autumn of 2012. Results show a high concentration of metals, pesticides, and petroleum products in sediment samples in the monitored period. The survey is designed to gauge the total chemical pollution effects on the composition, living, and growth of benthic organisms. To assess the toxic hazard of contaminated sediment samples, a microbiotest with meiobenthic ostracods Heterocypris incongruens was performed with evaluation of mortality and growth-inhibition percentages. The preliminary results showed an increase of sediment toxicity, in terms of growth inhibition (>80%), especially at Murighiol and Ivancea. The chemical pressures alongside the temporal conditions were important variables which affected benthic communities. Low benthic diversity was found in the Isaccea–St. Gheorghe Branch sector of the Danube River. In terms of ecological status, the study reveals that the Danube and Danube Delta ecosystem are eutrophic systems equilibrated for good ecological status.     

Expression of 5-lipoxygenase and 15-lipoxygenase in rheumatoid arthritis synovium and effects of intraarticular glucocorticoids

Introduction  

It was previously shown that lipoxygenase (LO) pathways are important in the rheumatoid arthritis (RA) inflammatory process and that synovial fluid from RA patients contains high amounts of leukotrienes. We therefore aimed to investigate the 5-LO and 15-LO-1 expression pattern in RA and ostheoarthritis (OA) synovial tissue and to study the effect of intraarticular glucocorticoid (GC) therapy on enzyme expression.     

Development and validation of an HPLC-MS/MS method to determine clopidogrel in human plasma. Use of incurred samples to test back-conversion

Quantitative methods using LC-MS/MS allow achievement of adequate sensitivity for pharmacokinetic studies with clopidogrel; three such methods, with LLOQs as low as 5 pg/mL, were developed and fully validated according to the well established FDA 2001 guidelines. The chromatographic separations were performed on reversed phase columns Ascentis RP-Amide (15 cm x 2.1 mm, 5 μm), Ascentis Express C8 (10 cm x 2.1 mm, 2.7 μm) and Ascentis Express RP Amide (10 cm x 2.1 mm, 2.7 μm), respectively. Positive electrospray ionization in MRM mode was employed for the detection and a deuterated analogue (d3-clopidogrel) was used as internal standard. Linearity, precision, extraction recovery, matrix effects and stability tests on blank plasma spiked with clopidogrel and stored in different conditions met the acceptance criteria. During the analysis of the real samples from the first pharmacokinetic study, a significant increase (>100%) of the measured clopidogrel concentrations in the extracts kept in the autosampler at 10 °C was observed. Investigations led to the conclusion that most probably a back-conversion of one or more of the clopidogrel metabolites is occurring. The next methods were optimized in order to minimize this back-conversion. After a series of experiments, the adjustment of the sample preparation (e.g. processing at low temperature and introducing a clean-up step on Supelco HybridSPE-Precipitation cartridges) has proven to be the most effective in order to improve the stability of the extracts. Incurred samples of real subjects were successfully used in the validation of the last two analytical methods to evaluate the back-conversion, while tests using only the known metabolites could not detect this important problem.