Identifying quantitative operation principles in metabolic pathways: a systematic method for searching feasible enzyme activity patterns leading to cellular adaptive responses

<p>Abstract</p> <p>Background</p> <p>Optimization methods allow designing changes in a system so that specific goals are attained. These techniques are fundamental for metabolic engineering. However, they are not directly applicable for investigating the evolution of metabolic adaptation to environmental changes. Although biological systems have evolved by natural selection and result in well-adapted systems, we can hardly expect that actual metabolic processes are at the theoretical optimum that could result from an optimization analysis. More likely, natural systems are to be found in a feasible region compatible with global physiological requirements.</p> <p>Results</p> <p>We first present a new method for globally optimizing nonlinear models of metabolic pathways that are based on the Generalized Mass Action (GMA) representation. The optimization task is posed as a nonconvex nonlinear programming (NLP) problem that is solved by an outer-approximation algorithm. This method relies on solving iteratively reduced NLP slave subproblems and mixed-integer linear programming (MILP) master problems that provide valid upper and lower bounds, respectively, on the global solution to the original NLP. The capabilities of this method are illustrated through its application to the anaerobic fermentation pathway in <it>Saccharomyces cerevisiae</it>. We next introduce a method to identify the feasibility parametric regions that allow a system to meet a set of physiological constraints that can be represented in mathematical terms through algebraic equations. This technique is based on applying the outer-approximation based algorithm iteratively over a reduced search space in order to identify regions that contain feasible solutions to the problem and discard others in which no feasible solution exists. As an example, we characterize the feasible enzyme activity changes that are compatible with an appropriate adaptive response of yeast <it>Saccharomyces cerevisiae </it>to heat shock</p> <p>Conclusion</p> <p>Our results show the utility of the suggested approach for investigating the evolution of adaptive responses to environmental changes. The proposed method can be used in other important applications such as the evaluation of parameter changes that are compatible with health and disease states.</p

Free Radical Exposure Creates Paler Carotenoid-Based Ornaments: A Possible Interaction in the Expression of Black and Red Traits

Oxidative stress could be a key selective force shaping the expression of colored traits produced by the primary animal pigments in integuments: carotenoids and melanins. However, the impact of oxidative stress on melanic ornaments has only recently been explored, whereas its role in the expression of carotenoid-based traits is not fully understood. An interesting study case is that of those animal species simultaneously expressing both kinds of ornaments, such as the red-legged partridge (Alectoris rufa). In this bird, individuals exposed to an exogenous source of free radicals (diquat) during their development produced larger eumelanin-based (black) plumage traits than controls. Here, we show that the same red-legged partridges exposed to diquat simultaneously developed paler carotenoid-based ornaments (red beak and eye rings), and carried lower circulating carotenoid levels as well as lower levels of some lipids involved in carotenoid transport in the bloodstream (i.e., cholesterol). Moreover, partridges treated with a hormone that stimulates eumelanin production (i.e., alpha-melanocyte-stimulating hormone) also increased blood carotenoid levels, but this effect was not mirrored in the expression of carotenoid-based traits. The redness of carotenoid-based ornaments and the size of a conspicuous eumelanic trait (the black bib) were negatively correlated in control birds, suggesting a physiological trade-off during development. These findings contradict recent studies questioning the sensitivity of carotenoids to oxidative stress. Nonetheless, the impact of free radicals on plasma carotenoids seems to be partially mediated by changes in cholesterol metabolism, and not by direct carotenoid destruction/consumption. The results highlight the capacity of oxidative stress to create multiple phenotypes during development through differential effects on carotenoids and melanins, raising questions about evolutionary constraints involved in the production of multiple ornaments by the same organism

Non-Abelian T-duality and consistent truncations in type-II supergravity

For a general class of SO(4) symmetric backgrounds in type II-supergravity, we show that the action of non-Abelian T-duality can be described via consistent truncation to seven dimensional theories with seemingly massive modes. As such, any solution to these theories uplifts to both massive type IIA and IIB supergravities presenting an invertible map between the two. For supersymmetric backgrounds, we show that for spinors transforming under SO(4) the non-Abelian T-duality transformation breaks the original supersymmetry by half. We use these mappings to generate the non-Abelian T-duals of the maximally supersymmetric pp-wave, the Lin, Lunin, Maldacena geometries and spacetimes with Lifshitz symmetry.Comment: 41 pages, references added, published versio

Hepatic Radiofrequency Ablation Using Multiple Probes: Ex Vivo and In Vivo Comparative Studies of Monopolar versus Multipolar Modes

OBJECTIVE: We wanted to compare the efficiency of multipolar radiofrequency ablation (RFA) using three perfused-cooled electrodes with multiple overlapping and simultaneous monopolar techniques for creating an ablation zone in ex vivo bovine livers and in in vivo porcine livers. MATERIALS AND METHODS: In the ex vivo experiments, we used a 200 W generator (Valleylab, CC-3 model) and three perfused-cooled electrodes or internally cooled electrodes to create 30 coagulation zones by performing consecutive monopolar RFA (group A, n = 10), simultaneous monopolar RFA (group B, n = 10) or multipolar RFA (group C, n = 10) in explanted bovine livers. In the consecutive mode, three ablation spheres were created by sequentially applying 150 watts radiofrequency (RF) energy to the internally cooled electrodes for 12 minutes each for a total of 36 minutes. In the simultaneous monopolar and multipolar modes, RF energy was concurrently applied to the three perfused-cooled electrodes for 20 minutes at 150 watt with instillation of 6% hypertonic saline at 2 mL/min. During RFA, we measured the temperatures of the treated area at its center. The changes in impedance, the current and liver temperature during RFA, as well as the dimensions of the thermal ablation zones, were compared among the three groups. In the in vivo experiments, three coagulations were created by performing multipolar RFA in a pig via laparotomy with using same parameter as the ex vivo study. RESULTS: In the ex vivo experiments, the impedance was gradually decreased during the RFA in groups B and C, but in group A, the impedance was increased during RFA and this induced activation by the pulsed RF technique. In groups A, B and C, the mean final-temperature values were 80+/-10 degrees C, 69+/-18 degrees C and 79+/-12 degrees C, respectively (p < 0.05). The multipolar mode created a larger volume of ablation than did the other modes: 37.6+/-4.0 cm3 (group A); 44.9+/-12.7 cm3 (group B); and 78.9+/-6.9 cm3 (group C) (p < 0.05). In the in vivo experiment, the pig well tolerated the RFA procedure and no major complications occurred during the 4 days of the follow-up period. The mean volume of coagulations produced by multipolar RFA in the pig liver was 60.5+/-17.9 cm3. CONCLUSION: For the multiple probe RFA, the multipolar mode with hypertonic saline instillation was more efficient in generating larger areas of thermal ablation than either the consecutive or simultaneous monopolar modes.ope

Type IIB supergravity solutions with AdS5 from Abelian and non-Abelian T dualities

We present a large class of new backgrounds that are solutions of type IIB supergravity with a warped AdS${}_5$ factor, non-trivial axion-dilaton, $B$-field and three-form Ramond-Ramond flux but yet have no five-form flux. We obtain these solutions and many of their variations by judiciously applying non-Abelian and Abelian T-dualities, as well as coordinate shifts to AdS${}_5\times X_5$ IIB supergravity solutions with $X_5=S^5, T^{1,1}, Y^{p,q}$. We address a number of issues pertaining to charge quantization in the context of non-Abelian T-duality. We comment on some properties of the expected dual super conformal field theories by studying their CFT central charge holographically. We also use the structure of the supergravity Page charges, central charges and some probe branes to infer aspects of the dual super conformal field theories.Comment: 71 pages, one table. v2: References added, some normalizations corrected, results unchange

Cardiovascular, endocrine and behavioural responses to suckling and permanent separation in goats

<p>Abstract</p> <p>Background</p> <p>Suckling can be a peaceful or vulnerable event for goats and kids, whereas, separation is suggested as stressful. The aim of this study was to investigate physiology and behaviour in these two different situations in dairy goats.</p> <p>Methods</p> <p>Four studies were performed with seven goats kept with their first-born kid in individual boxes. The goats were videotaped and heart rate and arterial blood pressure were recorded every minute by telemetry from parturition until 24 hours after separation. One to two days after parturition, Study 1 was performed with analyses of heart rate and blood pressure around a suckling. In Study 2, performed 3-5 days after parturition, blood sampling was done before, during and after suckling. Study 3 was performed 4-6 days post partum, with blood sampling before and after a permanent goat and kid separation. In addition, vocalisations were recorded after separation. Blood samples were obtained from a jugular vein catheter and analysed for plasma cortisol, β-endorphin, oxytocin, and vasopressin concentrations. Study 4 was performed during the first (N1) and second nights (N2) after parturition and the nights after Study 2 (N3) and 3 (N4). Heart rate, blood pressure and time spent lying down were recorded.</p> <p>Results</p> <p>The kids suckled 2 ± 0.2 times per hour and each suckling bout lasted 43 ± 15 s. In Study 1, heart rate and blood pressure did not change significantly during undisturbed suckling. In Study 2, plasma cortisol (P ≤ 0.05 during suckling and P ≤ 0.01 five minutes after suckling) and β-endorphin (P ≤ 0.05) concentrations increased during suckling, but oxytocin and vasopressin concentrations did not change. In Study 3, the goats and kids vocalised intensively during the first 20 minutes after separation, but the physiological variables were not affected. In Study 4, heart rate and arterial blood pressure declined gradually after parturition and were lowest during N4 (P ≤ 0.05) when the goats spent longer time lying down than during earlier nights (P ≤ 0.01 during N1 and N3 and P ≤ 0.05 during N2).</p> <p>Conclusions</p> <p>Suckling elevated plasma cortisol and β-endorphin concentrations in the goats. The intensive vocalisation in the goats after separation, earlier suggested to indicate stress, was not accompanied by cardiovascular or endocrine responses.</p

Antioxidant enzymes and lipid peroxidation in endometrium of patients with polyps, myoma, hyperplasia and adenocarcinoma

<p>Abstract</p> <p>Background</p> <p>Oxidative stress and impaired antioxidant system have been proposed as a potential factors involved in the pathophysiology of diverse disease states, including carcinogenesis. In this study, we explored the lipid peroxidation levels and antioxidant enzyme activities in women diagnosed with different forms of gynecological diseases in order to evaluate the antioxidant status in endometrium of such patients.</p> <p>Methods</p> <p>Endometrial tissues of gynecological patients with different diagnoses were collected and subjected to assays for superoxide dismutase, catalase, glutathione peroxidase, glutathione reductase and lipid hydroperoxides.</p> <p>Results</p> <p>Superoxide dismutase activity was significantly decreased (50% in average) in hyperplastic and adenocarcinoma patients. Activities of both glutathione peroxidase and glutathione reductase were increased 60% and 100% on average, in hyperplastic patients, while in adenocarcinoma patients only glutathione reductase activity was elevated 100%. Catalase activity was significantly decreased in adenocarcinoma patients (47%). Lipid hydroperoxides level was negatively correlated to superoxide dismutase and catalase activities, and positively correlated to glutathione peroxidase and glutathione reductase activities.</p> <p>Conclusions</p> <p>This study provided the first comparison of antioxidant status and lipid peroxidation in endometrial tissues of patients with polyps, myoma, hyperplasia and adenocarcinoma. The results showed that patients with premalignant (hyperplastic) and malignant (adenocarcinoma) lesions had enhanced lipid peroxidation and altered uterine antioxidant enzyme activities than patients with benign uterine diseases, polyps and myoma, although the extent of disturbance varied with the diagnosis. Further investigation is needed to clarify the mechanisms responsible for the observed alterations and whether lipid hydroperoxide levels and antioxidant enzyme activities in uterus of gynecological patients might be used as additional parameter in clinical evaluation of gynecological disorders.</p