Multiple solvent crystal structures: probing binding sites, plasticity and hydration

Multiple solvent crystal structures (MSCS) of porcine pancreatic elastase were used to map the binding surface the enzyme. Crystal structures of elastase in neat acetonitrile, 95% acetone, 55% dimethylformamide, 80% 5-hexene-1,2-diol, 80% isopropanol, 80% ethanol and 40% trifluoroethanol showed that the organic solvent molecules clustered in the active site, were found mostly unclustered in crystal contacts and in general did not bind elsewhere on the surface of elastase. Mixtures of 40% benzene or 40% cyclohexane in 50% isopropanol and 10% water showed no bound benzene or cyclohexane molecules, but did reveal bound isopropanol. The clusters of organic solvent probe molecules coincide with pockets occupied by known inhibitors. MSCS also reveal the areas of plasticity within the elastase binding site and allow for the visualization of a nearly complete first hydration shell. The pattern of organic solvent clusters determined by MSCS for elastase is consistent with patterns for hot spots in protein-ligand interactions determined from database analysis in general. The MSCS method allows probing of hot spots, plasticity and hydration simultaneously, providing a powerful complementary strategy to guide computational methods currently in development for binding site determination, ligand docking and design.     

Signal-dependent control of gluconeogenic key enzyme genes through coactivator-associated arginine methyltransferase 1

Together with impaired glucose uptake in skeletal muscle, elevated hepatic gluconeogenesis is largely responsible for the hyperglycemic phenotype in type II diabetic patients. Intracellular glucocorticoid and cyclic adenosine monophosphate (cAMP)/protein kinase A-dependent signaling pathways contribute to aberrant hepatic glucose production through the induction of gluconeogenic enzyme gene expression. Here we show that the coactivator-associated arginine methyltransferase 1 (CARM1) is required for cAMP-mediated activation of rate-limiting gluconeogenic phosphoenolpyruvate carboxykinase (PEPCK; EC 4.1.1.32) and glucose-6-phosphatase genes. Mutational analysis showed that CARM1 mediates its effect via the cAMP-responsive element within the PEPCK promoter, which is identified here as a CARM1 target in vivo. In hepatocytes, endogenous CARM1 physically interacts with cAMP-responsive element binding factor CREB and is recruited to the PEPCK and glucose-6-phosphatase promoters in a cAMP-dependent manner associated with increased promoter methylation. CARM1 might, therefore, represent a critical component of cAMP-dependent glucose metabolism in the liver.     

Chlorophyll a fluorescence responses of temperate Phaeophyceae under submersion and emersion regimes: a comparison of rapid and steady-state light curves

The potential of algae to acclimate to environmental stress is commonly assessed using chlorophyll a fluorescence, with changes in parameters of photosynthesis versus irradiance (P/E) curves measured either as rapid light curves (RLC) or steady-state light curves (LC). Here, effects of emersion on primary photosynthesis of four brown macroalgae (Ascophyllum nodosum, Fucus serratus, Sargassum muticum, Laminaria digitata) were compared by applying both RLC and LC. When LC were used, photosynthetic performance was enhanced during emersion in A. nodosum and F. serratus as shown by increases in q_P, rETR_max and E _k. By contrast, emersion had no impact on photosynthetic parameters of S. muticum and L. digitata. Relative changes in the NPQ?CrETR relationship were reduced in A. nodosum, F. serratus and S. muticum, but remained unaffected in L. digitata. As none of the species developed their potential NPQ_max, corresponding values could not be determined from RLC. Using RLC, observed photosynthetic performance of F. serratus and L. digitata was reduced upon emersion, whilst values for NPQ_max were enhanced. Only results derived from LC provide evidence for a potential physiological adaptation of brown macroalgae to their natural habitat; it is recommended using the LC protocol to detect environmental impacts on photosynthesis.     

Composition of humic acid-degrading estuarine and marine bacterial communities

We examined the bacterial decomposition of humic acids (HA) in two flow-through culture experiments, one inoculated by marine and one by estuarine bacterial communities. In both experiments, the cultures were fed with HA media of salinities of 28 and 14, close to their ambient and a distinctly different, foreign salinity. HA were decomposed to >?60% of the initial concentration within 70?days, and the foreign salinity yielded the highest decomposition. A detrended correspondence analysis of denaturing gradient gel electrophoresis (DGGE) banding patterns showed that during incubation, the bacterial community composition underwent distinct changes. A phylogenetic analysis of DGGE bands excised and bacteria isolated at the end on HA as the sole carbon source showed that Alphaproteobacteria and Gammaproteobacteria largely dominated the communities in the marine flow-through cultures, whereas Gammaproteobacteria, Actinobacteria and Alphaproteobacteria dominated the estuarine communities. Eleven of 13 isolates obtained from both experiments were able to grow on HA as the sole carbon source, seven on phenol and three, affiliated to the Roseobacter clade, on various aromatic acids. The bacteria retrieved from the flow-through cultures were closely (96-99%) affiliated to organisms capable of degrading humic matter, aromatic and aliphatic compounds and also to other bacteria reported previously from the Wadden Sea and Weser estuary.     

Gentiana asclepiadea protects human cells against oxidation DNA lesions

The objectives of this study were to examine whether the methanolic and aqueous extracts from the haulm and flower of Gentiana asclepiadea exhibited free radical scavenging and protective (antigenotoxic) effect against DNA oxidation induced by H(2)O(2) in human lymphocytes and human embryonic kidney cells (HEK 293). All four extracts exhibited high scavenging effect on 1,1-diphenyl-2-picrylhydrazyl radicals at concentrations 2.5 and 25 mg ml(-1). The level of DNA damage was measured using the alkaline version of single-cell gel electrophoresis (comet assay). Challenge with H(2)O(2) shows that the pre-treatment of the cells with non-genotoxic doses of Gentiana extracts protected human DNA-either eliminated or significantly reduced H(2)O(2) induced DNA damage. The genotoxic activity of H(2)O(2) was most effectively decreased after 30 min of pre-incubation with 0.05 mg ml(-1) (range, 93.5%-96.3% of reduction in lymphocytes) and 0.25 mg ml(-1) (range, 59.5%-71.4% and 52.7%-66.4% of reduction in lymphocytes and HEK 293 cells, respectively) of G. asclepiadea extracts. These results suggest that the tested G. asclepiadea extracts could be considered as an effective natural antioxidant source.     

Poly(2-ethyl-2-oxazoline) as alternative for the stealth polymer poly(ethylene glycol): comparison of in vitro cytotoxicity and hemocompatibility

Limitations of PEG in drug delivery have been reported from clinical trials. PEtOx (0.4-40 kDa) as alternative is synthesized by a living, microwave-assisted polymerization, and is directly compared to PEG of similar molar mass regarding cytotoxicity and hemocompatibility. In short-term treatments, both types of polymers are well tolerated even at high concentrations. Moderate concentration and molar mass dependent cytotoxic effects occurred only after long-term incubation at concentrations higher than therapeutic doses. PEtOx possesses not only an easy route of synthesis and beneficial physicochemical characteristics such as low viscosity and high stability, which are advantageous over PEG, but additionally in vitro toxicology comparable to PEG.     

Comparative proteomic analysis to dissect differences in signal transduction in activating TSH receptor mutations in the thyroid

In the thyroid, cAMP controls both thyroid growth and function. Gain-of-function mutations in the thyroid-stimulating hormone receptor (TSHR) lead to constitutive cAMP formation and are a major cause of autonomous thyroid adenomas. The impact of activating TSHR mutations on the signal transduction network of the thyrocyte is not fully understood. To gain more insights into constitutive TSHR signaling, rat thyrocytes (FRTL-5 cells) with stable expression of three activating TSHR mutants (mutTSHR: A623I, L629F and Del613-621), which differ in their functional characteristics in vitro, were analyzed by a quantitative proteomic approach and compared to the wild-type TSHR (WT-TSHR). This study revealed (1) differences in the expression of Rab proteins suggesting an increased TSHR internalization in mutTSHR but not in the WT-TSHR; (2) differential stimulation of PI3K/Akt signaling in mutTSHR vs. WT-TSHR cells, (3) activation of Epac, impairing short-time Akt phosphorylation in both, mutTSHR and WT-TSHR cells. Based on the analysis of global changes in protein expression patterns, our findings underline the complexity of gain-of-function TSHR signaling in thyrocytes, which extends beyond pure cAMP and/or IP formation. Moreover, evidence for augmented endocytosis in the mutTSHR, adds to a new concept of TSHR signaling in thyroid autonomy. Further studies are required to clarify whether the observed differences in Rab, PI3K and Epac signaling may contribute to differences in the phenotypic presentation, i.e. stimulation of function and growth of thyroid autonomy in vivo.     

Mechanism of PP2A-mediated IKKβ dephosphorylation: a systems biological approach

Background  

Biological effects of nuclear factor-κB (NFκB) can differ tremendously depending on the cellular context. For example, NFκB induced by interleukin-1 (IL-1) is converted from an inhibitor of death receptor induced apoptosis into a promoter of ultraviolet-B radiation (UVB)-induced apoptosis. This conversion requires prolonged NFκB activation and is facilitated by IL-1 + UVB-induced abrogation of the negative feedback loop for NFκB, involving a lack of inhibitor of κB (IκBα) protein reappearance. Permanent activation of the upstream kinase IKKβ results from UVB-induced inhibition of the catalytic subunit of Ser-Thr phosphatase PP2A (PP2Ac), leading to immediate phosphorylation and degradation of newly synthesized IκBα.     

Isolation of ten tetranucleotide microsatellite loci in the Northern Wheatear (Oenanthe oenanthe)

We isolated 10 polymorphic microsatellite DNA loci from the Northern Wheatear (Oenanthe oenanthe) and optimized these for future studies in population genetics and behavioural ecology. The loci were screened for polymorphism using 107 individuals from one population in Germany. The primers amplified loci with high numbers of alleles ranging from two to 20 alleles per locus.     

Tomato-aphid-hoverfly: a tritrophic interaction incompatible for pest management

Trichome-based tomato resistance offers the potential to reduce pesticide use, but its compatibility with biological control remains poorly understood. We evaluated Episyrphus balteatus De Geer (Diptera, Syrphidae), an efficient aphidophagous predator, as a potential biological control agent of Myzus persicae Sulzer (Hemiptera, Aphididae) on trichome-bearing tomato cultivars. Episyrphus balteatus’ foraging and oviposition behavior, as well as larval mobility and aphid accessibility, were compared between two tomato cultivars (Lycopersicon esculentum Mill. ‘Moneymaker’ and ‘Roma’) and two other crop plants; broad bean (Vicia faba L.) and potato (Solanum tuberosum L.). Hoverfly adults landed and laid more eggs on broad beans than on three species of Solanaceae. Hoverfly larval movement was drastically reduced on tomato, and a high proportion of hoverfly larvae fell from the plant before reaching aphid prey. After quantifying trichome abundance on each of these four plants, we suggest that proprieties of the plant surface, specifically trichomes, are a key factor contributing to reduced efficacy of E. balteatus as a biological agent for aphid control on tomatoes. Handling editor: Stanislaw Gorb