Hybrid semi-parametric mathematical systems: bridging the gap between systems biology and process engineering

Systems biology is an integrative science that aims at the global characterization of biological systems. Huge amounts of data regarding gene expression, proteins activity and metabolite concentrations are collected by designing systematic genetic or environmental perturbations. Then the challenge is to integrate such data in a global model in order to provide a global picture of the cell. The analysis of these data is largely dominated by nonparametric modelling tools. In contrast, classical bioprocess engineering has been primarily founded on first principles models, but it has systematically overlooked the details of the embedded biological system. The full complexity of biological systems is currently assumed by systems biology and this knowledge can now be taken by engineers to decide how to optimally design and operate their processes. This paper discusses possible methodologies for the integration of systems biology and bioprocess engineering with emphasis on applications involving animal cell cultures. At the mathematical systems level, the discussion is focused on hybrid semi-parametric systems as a way to bridge systems biology and bioprocess engineering.     

Nuclear estrogen and progesterone receptors in the oviduct of heifers under natural and superovulated estrous cycles

Oviducts from 22 crossbred heifers were examined for the presence of nuclear estrogen (ERalpha) and progesterone (PR) receptors at different phases (estrus, metaestrus and diestrus) of naturally occurring estrous cycles and estrous cycles during which superovulation was induced. Receptors were detected by immunohistochemistry in the epithelial cells, connective tissue and muscular layer of oviductal infundibulum, ampulla, ampullary/isthmic transition and isthmus. Epithelial ERalpha was found along the entire oviduct regardless of the cycle phase and of the circulating concentrations of 17beta-estradiol (E(2)) and progesterone (P(4)). Epithelial PR was found mainly at the ampullary-isthmic transition and isthmus and more intensely at the estrus phase but their amount was not correlated with P(4) concentrations. ERalpha in the connective tissue was more abundant at the infundibulum and ampulla, regardless of the phase of the estrous cycle and of E(2) and P(4) circulating concentrations. PR in the connective tissue was found mostly at the ampulla, regardless of the estrous cycle phase but no correlations were found between amount and P(4) concentrations. ERalpha staining intensity in the muscular layer was similar at all phases of the estrous cycle and at all anatomical segments of the oviducts. However, PR staining was more intense at the isthmus during the metaestrus phase and it was negatively correlated with P(4) concentrations. In general, data from the present research suggest that P(4) exerts an inhibitory role upon ERalpha and PR. Also, no differences were found between animals subjected or not to superovulation.     

High prevalence of multiple paternity within fruits in natural populations of Silene latifolia, as revealed by microsatellite DNA analysis

Data on multiple paternity within broods has been gathered in several animal species, and comparable data in plants would be of great importance to understand the evolution of reproductive traits in a common framework. In this study, we first isolated and characterized six microsatellite loci from the dioecious plant Silene latifolia (Caryophyllaceae). The polymorphism of the loci was assessed in 60 individual females from four different populations. Two of the investigated loci showed a pattern of inheritance consistent with X-linkage. These microsatellite loci were highly polymorphic and therefore useful tools for parentage analysis. We then used four of the markers to determine paternity within naturally pollinated fruits in four European populations. This study revealed widespread multiple paternity in all populations investigated. The minimum number of fathers per fruit varied from one to nine, with population means ranging from 3.4 to 4.9. The number of fathers per fruit was not significantly correlated with offspring sex ratios. High prevalence of multiple paternity within fruits strongly suggest that pollen competition is likely to occur in this species. This may substantially impact male reproductive success and possibly contribute to increase female and offspring fitness, either through postpollination selection or increased genetic diversity. Wide variation in outcrossing rates may be an overlooked aspect of plant mating systems.     

Unified QSAR approach to antimicrobials. Part 2: predicting activity against more than 90 different species in order to halt antibacterial resistance

There are many different kinds of pathogenic bacteria species with very different susceptibility profiles to different antibacterial drugs. One limitation of QSAR models is that they consider the biological activity of drugs against only one species of bacteria. In a previous paper, we developed a unified Markov model to describe the biological activity of different drugs tested in the literature against some antimicrobial species. Consequently, predicting the probability with which a drug is active against different species of bacteria with a single unified model is a goal of major importance. The work described here develops the unified Markov model to describe the biological activity of more than 70 drugs from the literature tested against 96 species of bacteria. We applied linear discriminant analysis (LDA) to classify drugs as active or inactive against the different tested bacterial species. The model correctly classified 199 out of 237 active compounds (83.9%) and 168 out of 200 inactive compounds (84%). Overall training predictability was 84% (367 out of 437 cases). Validation of the model was carried out using an external predicting series, with the model classifying 202 out of 243 (i.e., 83.13%) of the compounds. In order to show how the model functions in practice, a virtual screening was carried out and the model recognized as active 84.5% (480 out of 568) antibacterial compounds not used in the training or predicting series. The current study is an attempt to calculate within a unified framework the probabilities of antibacterial action of drugs against many different species.     

Oxalate modulates thiobarbituric acid reactive species (TBARS) production in supernatants of homogenates from rat brain, liver and kidney: effect of diphenyl diselenide and diphenyl ditelluride

The aim of this paper was to investigate the mechanism(s) involved in the sodium oxalate pro-oxidative activity in vitro and the potential protection by diphenyl diselenide ((PhSe)(2)) and diphenyl ditelluride ((PhTe)(2)) using supernatants of homogenates from brain, liver and kidney. Oxalate causes a significant increase in the TBARS (thiobarbituric acid reactive species) production up to 4mmol/l and it had antioxidant activity from 8 to 16mmol/l in the brain and liver. Oxalate had no effect in kidney homogenates. The difference among tissues may be related to the formation of insoluble crystal of oxalate in kidney, but not in liver and brain homogenates. (PhSe)(2) and (PhTe)(2) reduced both basal and oxalate-induced TBARS in rat brain homogenates, whereas in liver homogenates they were antioxidant only on oxalate-induced TBARS production. (PhSe)(2) showed a modest effect on renal TBARS production, whereas (PhTe)(2) did not modulate TBARS in kidney preparations. Oxalate at 2mmol/l did not change deoxyribose degradation induced by Fe(2+) plus H(2)O(2), whereas at 20mmol/l it significantly prevents its degradation. Oxalate (up to 4mmol/l) did not alter iron (10micromol/l)-induced TBARS production in the brain preparations, whereas at 8mmol/l onwards it prevents iron effect. In liver preparations, oxalate amplifies iron pro-oxidant activity up to 4mmol/l, preventing iron-induced TBARS production at 16mmol/l onwards. These results support the antioxidant effect of organochalcogens against oxalate-induced TBARS production. In addition, our results suggest that oxalate pro- and antioxidant activity in vitro could be related to its interactions with iron ions.     

Preoperative plasma levels of soluble tumor necrosis factor receptor type I (sTNF-RI) predicts adverse events in cardiac surgery

OBJECTIVE: The objective was to estimate the sTNF-RI preoperative measure in the identification of patients with bad outcome and death. METHODS: We assessed prospectively sixty-two patients submitted electively to myocardial revascularization with ECC or heart valve surgery. The sTNF-RI levels were determined by the Sandwich-Type ELISA method before anesthetic induction. Clinical, surgical characteristics and sTNF-RI levels were compared among patients with good (group I, n=46) or bad outcome (group II, n=16--length of stay in the ICU for over 72 h or death). RESULTS: No difference was found between the verified mortality (6.4%) and the predicted by EuroSCORE (3.0%), p=0.48. The sTNF-RI levels were higher in group II (1322) than group I (748) p=0.009 (levels >954, 69% sensitivity and 70% specificity for good outcome, 44% positive predicted value and 85% negative). The sTNF-RI levels were higher in patients who died (1556) versus (759) p=0.029, (levels >1230, 79% sensitivity, 75% specificity, 20% positive predicted value and 98% negative). In the multivariate logistic regression model sTNF-RI (OR=1.002, IC95% 1.000-1.005, p=0.014) and age (OR=1.083, IC95% 1.010-1.161, p=0.025) were independently related to the risk of bad outcome. CONCLUSIONS: Basal levels of sTNF-RI yield prognostic information in patients who undergo heart surgery.     

Analysis of P-body assembly in Saccharomyces cerevisiae

Recent experiments have defined cytoplasmic foci, referred to as processing bodies (P-bodies), that contain untranslating mRNAs in conjunction with proteins involved in translation repression and mRNA decapping and degradation. However, the order of protein assembly into P-bodies and the interactions that promote P-body assembly are unknown. To gain insight into how yeast P-bodies assemble, we examined the P-body accumulation of Dcp1p, Dcp2p, Edc3p, Dhh1p, Pat1p, Lsm1p, Xrn1p, Ccr4p, and Pop2p in deletion mutants lacking one or more P-body component. These experiments revealed that Dcp2p and Pat1p are required for recruitment of Dcp1p and of the Lsm1-7p complex to P-bodies, respectively. We also demonstrate that P-body assembly is redundant and no single known component of P-bodies is required for P-body assembly, although both Dcp2p and Pat1p contribute to P-body assembly. In addition, our results indicate that Pat1p can be a nuclear-cytoplasmic shuttling protein and acts early in P-body assembly. In contrast, the Lsm1-7p complex appears to primarily function in a rate limiting step after P-body assembly in triggering decapping. Taken together, these results provide insight both into the function of individual proteins involved in mRNA degradation and the mechanisms by which yeast P-bodies assemble.     

Morphological variation of the digestive tract: a feeding behaviour response in a freshwater fish species

Environmental Biology of Fishes - Plasticity of resource use represents an important strategy for fish species living in unstable freshwater environments. Trophic polymorphism (i.e. variation in...