A comparison of stigmatellin conformations, free and bound to the photosynthetic reaction center and the cytochrome bc1 complex

We describe in detail the conformations of the inhibitor stigmatellin in its free form and bound to the ubiquinone-reducing (Q(B)) site of the reaction center and to the ubiquinol-oxidizing (Q(o)) site of the cytochrome bc(1) complex. We present here the first structures of a stereochemically correct stigmatellin in complexes with a bacterial reaction center and the yeast cytochrome bc1 complex. The conformations of the inhibitor bound to the two enzymes are not the same. We focus on the orientations of the stigmatellin side-chain relative to the chromone head group, and on the interaction of the stigmatellin side-chain with these membrane protein complexes. The different conformations of stigmatellin found illustrate the structural variability of the Q sites, which are affected by the same inhibitor. The free rotation about the chi1 dihedral angle is an essential factor for allowing stigmatellin to bind in both the reaction center and the cytochrome bc1 pocket.     

Whole plant response of Pongamia pinnata to drought stress tolerance revealed by morpho-physiological,biochemical and transcriptome analysis

Molecular Biology Reports - Pongamia is considered an important biofuel species worldwide. Drought stress in the early growth stages of Pongamia influences negatively on the germination and...     

Variations in fecundity over catchment scales: Implications for caddisfly populations spanning a thermal gradient

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The immediate wound‐induced oxidative burst of Saccharina latissima depends on light via photosynthetic electron transport

Reactive oxygen species (ROS) produced by an oxidative burst are an important component of the wound response in algae, vascular plants, and animals. In all taxa, ROS production is usually attributed solely to a defense‐related enzyme like NADPH‐oxidase (Nox). However, here we show that the initial, wound‐induced oxidative burst of the kelp Saccharina latissima depends on light and photosynthetic electron transport. We measured oxygen evolution and ROS production at different light levels and in the presence of a photosynthetic inhibitor, and we used spin trapping and electron paramagnetic resonance as an orthogonal method. Using an in vivo chemical probe, we provide data suggesting that wound‐induced ROS production in two distantly related and geographically isolated species of Antarctic macroalgae may be light dependent as well. We propose that electron transport chains are an important and as yet unaddressed component of the wound response, not just for photosynthetic organisms, but for animals via mitochondria as well. This component may have been obscured by the historic use of diphenylene iodonium, which inhibits not only Noxes but also photosynthetic and respiratory electron transport as well. Finally, we anticipate physiological and/or ecological consequences of the light dependence of macroalgal wound‐induced ROS since pathogens and grazers do not disappear in the dark.     

Population densities and density–area relationships in a community with advective dispersal and variable mosaics of resource patches

Many communities comprise species that select resources that are patchily distributed in an environment that is otherwise unsuitable or suboptimal. Effects of this patchiness can depend on the characteristics of patch arrays and animal movements, and produce non-intuitive outcomes in which population densities are unrelated to resource abundance. Resource mosaics are predicted to have only weak effects, however, where patches are ephemeral or organisms are transported advectively. The running waters of streams and benthic invertebrates epitomize such systems, but empirical tests of resource mosaics are scarce. We sampled 15 common macroinvertebrates inhabiting distinct detritus patches at four sites within a sand-bed stream, where detritus formed a major resource of food and living space. At each site, environmental variables were measured for 100 leaf packs; invertebrates were counted in 50 leaf packs. Sites differed in total abundance of detritus, leaf pack sizes and invertebrate densities. Multivariate analysis indicated that patch size was the dominant environmental variable, but invertebrate densities differed significantly between sites even after accounting for patch size. Leaf specialists showed positive and strong density–area relationships, except where the patch size range was small and patches were aggregated. In contrast, generalist species had weaker and variable responses to patch sizes. Population densities were not associated with total resource abundance, with the highest densities of leaf specialists in sites with the least detritus. Our results demonstrate that patchy resources can affect species even in communities where species are mobile, have advective dispersal, and patches are relatively ephemeral.     

Predicting breast cancer using an expression values weighted clinical classifier

Background

Clinical data, such as patient history, laboratory analysis, ultrasound parameters-which are the basis of day-to-day clinical decision support-are often used to guide the clinical management of cancer in the presence of microarray data. Several data fusion techniques are available to integrate genomics or proteomics data, but only a few studies have created a single prediction model using both gene expression and clinical data. These studies often remain inconclusive regarding an obtained improvement in prediction performance. To improve clinical management, these data should be fully exploited. This requires efficient algorithms to integrate these data sets and design a final classifier.LS-SVM classifiers and generalized eigenvalue/singular value decompositions are successfully used in many bioinformatics applications for prediction tasks. While bringing up the benefits of these two techniques, we propose a machine learning approach, a weighted LS-SVM classifier to integrate two data sources: microarray and clinical parameters.

Results

We compared and evaluated the proposed methods on five breast cancer case studies. Compared to LS-SVM classifier on individual data sets, generalized eigenvalue decomposition (GEVD) and kernel GEVD, the proposed weighted LS-SVM classifier offers good prediction performance, in terms of test area under ROC Curve (AUC), on all breast cancer case studies.

Conclusions

Thus a clinical classifier weighted with microarray data set results in significantly improved diagnosis, prognosis and prediction responses to therapy. The proposed model has been shown as a promising mathematical framework in both data fusion and non-linear classification problems.     

Inhibiting GPI anchor biosynthesis in fungi stresses the endoplasmic reticulum and enhances immunogenicity

In fungi, the anchoring of proteins to the plasma membrane via their covalent attachment to glycosylphosphatidylinositol (GPI) is essential and thus provides a valuable point of attack for the development of antifungal therapeutics. Unfortunately, studying the underlying biology of GPI-anchor synthesis is difficult, especially in medically relevant fungal pathogens because they are not genetically tractable. Compounding difficulties, many of the genes in this pathway are essential in Saccharomyces cerevisiae. Here, we report the discovery of a new small molecule christened gepinacin (for GPI acylation inhibitor) which selectively inhibits Gwt1, a critical acyltransferase required for the biosynthesis of fungal GPI anchors. After delineating the target specificity of gepinacin using genetic and biochemical techniques, we used it to probe key, therapeutically relevant consequences of disrupting GPI anchor metabolism in fungi. We found that, unlike all three major classes of antifungals in current use, the direct antimicrobial activity of this compound results predominantly from its ability to induce overwhelming stress to the endoplasmic reticulum. Gepinacin did not affect the viability of mammalian cells nor did it inhibit their orthologous acyltransferase. This enabled its use in co-culture experiments to examine Gwt1's effects on host-pathogen interactions. In isolates of Candida albicans, the most common fungal pathogen in humans, exposure to gepinacin at sublethal concentrations impaired filamentation and unmasked cell wall β-glucan to stimulate a pro-inflammatory cytokine response in macrophages. Gwt1 is a promising antifungal drug target, and gepanacin is a useful probe for studying how disrupting GPI-anchor synthesis impairs viability and alters host-pathogen interactions in genetically intractable fungi.     

MicroRNA MiR-214 Regulates Ovarian Cancer Cell Stemness by Targeting p53/Nanog

Previous studies have shown aberrant expression of miR-214 in human malignancy. Elevated miR-214 is associated with chemoresistance and metastasis. In this study, we identified miR-214 regulation of ovarian cancer stem cell (OCSC) properties by targeting p53/Nanog axis. Enforcing expression of miR-214 increases, whereas knockdown of miR-214 decreases, OCSC population and self-renewal as well as the Nanog level preferentially in wild-type p53 cell lines. Furthermore, we found that p53 is directly repressed by miR-214 and that miR-214 regulates Nanog through p53. Expression of p53 abrogated miR-214-induced OCSC properties. These data suggest the critical role of miR-214 in OCSC via regulation of the p53-Nanog axis and miR-214 as a therapeutic target for ovarian cancer.     

Nitric oxide-induced conversion of cellular chelatable iron into macromolecule-bound paramagnetic dinitrosyliron complexes

One of the most important biological reactions of nitric oxide (nitrogen monoxide, *NO) is its reaction with transition metals, of which iron is the major target. This is confirmed by the ubiquitous formation of EPR-detectable g=2.04 signals in cells, tissues, and animals upon exposure to both exogenous and endogenous *NO. The source of the iron for these dinitrosyliron complexes (DNIC), and its relationship to cellular iron homeostasis, is not clear. Evidence has shown that the chelatable iron pool (CIP) may be at least partially responsible for this iron, but quantitation and kinetic characterization have not been reported. In the murine cell line RAW 264.7, *NO reacts with the CIP similarly to the strong chelator salicylaldehyde isonicotinoyl hydrazone (SIH) in rapidly releasing iron from the iron-calcein complex. SIH pretreatment prevents DNIC formation from *NO, and SIH added during the *NO treatment "freezes" DNIC levels, showing that the complexes are formed from the CIP, and they are stable (resistant to SIH). DNIC formation requires free *NO, because addition of oxyhemoglobin prevents formation from either *NO donor or S-nitrosocysteine, the latter treatment resulting in 100-fold higher intracellular nitrosothiol levels. EPR measurement of the CIP using desferroxamine shows quantitative conversion of CIP into DNIC by *NO. In conclusion, the CIP is rapidly and quantitatively converted to paramagnetic large molecular mass DNIC from exposure to free *NO but not from cellular nitrosothiol. These results have important implications for the antioxidative actions of *NO and its effects on cellular iron homeostasis.     

Corticosterone manipulation reveals differences in hierarchical organization of multidimensional reproductive trade-offs in r-strategist and K-strategist females

Life history trade-offs are often hierarchical with decisions at one level affecting lower level trade-offs. We investigated trade-off structure in female side-blotched lizards (Uta stansburiana), which exhibit two evolved strategies: yellow-throated females are K-strategists and orange-throated are r-strategists. Corticosterone treatment was predicted to differentially organize these females' reproductive decisions. Corticosterone-treated yellow females suppressed reproduction but survived well, and augmented egg mass without decreasing clutch size. Conversely, corticosterone enhanced mortality and reproductive rates in orange females, and increased egg mass only after lengthy exposure. Corticosterone did not affect post-laying condition, suggesting that corticosterone increased egg mass through enhanced energy acquisition (income breeding). Corticosterone enhanced survival of lightweight females, but decreased survival of heavy females, introducing a foraging vs. predation trade-off. We conclude that rather than being a direct, functional relationship, observed trade-offs between offspring size and number represent evolved differences in hierarchical organization of multidimensional trade-offs, particularly in response to stress.