Optimization of Time-Course Experiments for Kinetic Model Discrimination

Systems biology relies heavily on the construction of quantitative models of biochemical networks. These models must have predictive power to help unveiling the underlying molecular mechanisms of cellular physiology, but it is also paramount that they are consistent with the data resulting from key experiments. Often, it is possible to find several models that describe the data equally well, but provide significantly different quantitative predictions regarding particular variables of the network. In those cases, one is faced with a problem of model discrimination, the procedure of rejecting inappropriate models from a set of candidates in order to elect one as the best model to use for prediction

Discrimination of kinetic models by maximization of the extended Kullback-Leibler distance (<i>I </i>).

<p>Conditions are sought that maximize <i>I</i> in both directions between any two models. In a two candidate model scenario (A) two functions must be simultaneously optimized. In a three candidate model scenario (B) six functions must be simultaneously optimized. After optimization, the set of solutions approximate a Pareto front and represent a compromise between the various objectives in the sense that, for any solution, the value of any objective could only be increased if the value of another objective was simultaneously decreased.</p

Landscapes of different measures of model divergences in the allowed optimization range of concentrations of pathway substrates.

<p>Measures of model distances are <i>I</i>_1,2 : extended Kullback-Leibler distance of model 2 from model 1 (equation 6). <i>I</i>_2,1 : extended Kullback-Leibler distance of model 1 from model 2 (equation 6). <i>L</i>₂ : simple <i>L</i>₂ norm (equation 4). <i>L</i>_2<i>w</i> : weighted <i>L</i>₂ norm (equation 5).</p

Kinetic models of the glyoxalase pathway.

<p>In model 1 (A), glutathione (GSH) and methylglyoxal (MGO) form a hemithioacetal (HTA) which is the substrate of glyoxalase I. In model 2 (B), glutathione and methylglyoxal are sequential substrates of glyoxalase I and the hemithioacetal is formed at the active centre of the enzyme. Glyoxalase II is a one-substrate-one-product irreversible Michaelis Menten enzyme, catalyzing the hydrolysis of <i>S</i>-D-lactoylglutatione (SDLGS) into D-lactate (D-Lac) and glutathione. The rate laws assumed in the models are expressed in equations 15 to 18.</p

Optimization of experimental design for model discrimination.

<p>A - Optimal initial concentrations of methylglyoxal and glutathione (solutions approximating the Pareto front) for the discrimination of the two models presented in <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0032749#pone-0032749-g002" target="_blank">figure 2</a>. B – Corresponding values of the extended Kullback-Leibler distances (optimization objectives); Concentration of glyoxalase I is 2.0×10⁻³ mM and concentration of glyoxalase II is 4.0×10⁻⁴ mM. The red dot indicates the initial concentrations used in the discriminatory experiment.</p

Discriminatory experiment for the kinetics of yeast glyoxalase I.

<p>A - Time courses of SDLGS concentration in the discriminatory setup experiment. Black: experimental result, average of 4 replicates (the grey shaded area is within one standard error of the mean). Blue: prediction by model 1. Red: prediction by model 2. Initial concentrations are 0.221 mM for glutathione, 2.0×10⁻³ mM for glyoxalase I, 0.441 mM for methylglyoxal and 4.0×10⁻³ mM for glyoxalase II. The initial concentrations correspond to the solution chosen from of the Pareto front highlighted in <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0032749#pone-0032749-g004" target="_blank">figure 4A</a>. B and C - rates predicted by model 1 (B) and model 2 (C). Red: net rate of hemithioacetal formation, blue: rate of glyoxalase I reaction. green: rate of glyoxalase II reaction.</p

Glucose intolerance after chronic stress is related with downregulated PPAR-gamma in adipose tissue

Background: Chronic stress is associated with increased risk of glucose intolerance and cardiovascular diseases, albeit through undefined mechanisms. With the aim of gaining insights into the latter, this study examined the metabolic profile of young adult male rats that were exposed to chronic unpredictable stress. Methods: Young adult male rats were submitted to 4 weeks of chronic unpredictable stress and allowed to recover for 5 weeks. An extensive analysis including of morphologic, biochemical and molecular parameters was carried out both after chronic unpredictable stress and after recovery from stress. Results: After 28 days of chronic unpredictable stress (CUS) the animals submitted to this protocol displayed less weight gain than control animals. After 5 weeks of recovery the weight gain rebounded to similar values of controls. In addition, following CUS, fasting insulin levels were increased and were accompanied by signs of impaired glucose tolerance and elevated serum corticosteroid levels. This biochemical profile persisted into the post-stress recovery period, despite the restoration of baseline corticosteroid levels. The mRNA expression levels of peroxisome proliferator-activated receptor (PPAR)-gamma and lipocalin-2 in white adipose tissue were, respectively, down-and up-regulated. Conclusions: Reduction of PPAR-gamma expression and generation of a pro-inflammatory environment by increased lipocalin-2 expression in white adipose tissue may contribute to stress-induced glucose intolerance.info:eu-repo/semantics/publishedVersio

Metabolic impact of redox cofactor perturbations in Saccharomyces cerevisiae

Redox cofactors play a pivotal role in coupling catabolism with anabolism and energy generation during metabolism. There exists a delicate balance in the intracellular level of these cofactors to ascertain an optimal metabolic output. Therefore, cofactors are emerging to be attractive targets to induce widespread changes in metabolism. We present a detailed analysis of the impact of perturbations in redox cofactors in the cytosol or mitochondria on glucose and energy metabolism in Saccharomyces cerevisiae to aid metabolic engineering decisions that involve cofactor engineering. We enhanced NADH oxidation by introducing NADH oxidase or alternative oxidase, its ATP-mediated conversion to NADPH using NADH kinase as well as the interconversion of NADH and NADPH independent of ATP by the soluble, non-proton-translocating bacterial transhydrogenase. Decreasing cytosolic NADH level lowered glycerol production, while decreasing mitochondrial NADH lowered ethanol production. However, when these reactions were coupled with NADPH production, the metabolic changes were more moderated. The direct consequence of these perturbations could be seen in the shift of the intracellular concentrations of the cofactors. The changes in product profile and intracellular metabolite levels were closely linked to the ATP requirement for biomass synthesis and the efficiency of oxidative phosphorylation, as estimated from a simple stoichiometric model. The results presented here will provide valuable insights for a quantitative understanding and prediction of cellular response to redox-based perturbations for metabolic engineering applications

Um olhar sobre a prática desportiva, bem-estar subjetivo e integração social de imigrantes... em Portugal e no mundo

O presente artigo de revisão centrou-se na prática desportiva e na sua relação com o bem-estar subjetivo e a integração social de imigrantes procurando fazer o levantamento da informação disponível na literatura acerca dessa temática a um nível mais global e, particularmente em Portugal, que a partir dos anos 80 se tornou num país de imigração. O levantamento bibliográfico incluiu livros, artigos científicos pesquisados em bases de dados internacionais, sites especializados e institucionais. A revisão da literatura permitiu verificar que: os imigrantes tendem a praticar menos desporto assim como a ter menores níveis de bem-estar subjetivo comparativamente à população autóctone; a prática desportiva relaciona-se positivamente com o bem-estar subjetivo também nos imigrantes; o desporto pode desempenhar um importante papel para a integração social dos imigrantes, apesar de nalguns contextos reforçar as diferenças inter-étnicas; em Portugal, não foram encontrados estudos específicos sobre a prática desportiva de imigrantes

Global economic burden of unmet surgical need for appendicitis

Background There is a substantial gap in provision of adequate surgical care in many low- and middle-income countries. This study aimed to identify the economic burden of unmet surgical need for the common condition of appendicitis. Methods Data on the incidence of appendicitis from 170 countries and two different approaches were used to estimate numbers of patients who do not receive surgery: as a fixed proportion of the total unmet surgical need per country (approach 1); and based on country income status (approach 2). Indirect costs with current levels of access and local quality, and those if quality were at the standards of high-income countries, were estimated. A human capital approach was applied, focusing on the economic burden resulting from premature death and absenteeism. Results Excess mortality was 4185 per 100 000 cases of appendicitis using approach 1 and 3448 per 100 000 using approach 2. The economic burden of continuing current levels of access and local quality was US $92 492 million using approach 1 and$73 141 million using approach 2. The economic burden of not providing surgical care to the standards of high-income countries was $95 004 million using approach 1 and$75 666 million using approach 2. The largest share of these costs resulted from premature death (97.7 per cent) and lack of access (97.0 per cent) in contrast to lack of quality. Conclusion For a comparatively non-complex emergency condition such as appendicitis, increasing access to care should be prioritized. Although improving quality of care should not be neglected, increasing provision of care at current standards could reduce societal costs substantially