Detection and characterization of xenon-binding sites in proteins by 129Xe NMR spectroscopy

Xenon-binding sites in proteins have led to a number of applications of xenon in biochemical and structural studies. Here we further develop the utility of 129Xe NMR in characterizing specific xenon-protein interactions. The sensitivity of the 129Xe chemical shift to its local environment and the intense signals attainable by optical pumping make xenon a useful NMR reporter of its own interactions with proteins. A method for detecting specific xenon-binding interactions by analysis of 129Xe chemical shift data is illustrated using the maltose binding protein (MBP) from Escherichia coli as an example. The crystal structure of MBP in the presence of 8atm of xenon confirms the binding site determined from NMR data. Changes in the structure of the xenon-binding cavity upon the binding of maltose by the protein can account for the sensitivity of the 129Xe chemical shift to MBP conformation. 129Xe NMR data for xenon in solution with a number of cavity containing phage T4 lysozyme mutants show that xenon can report on cavity structure. In particular, a correlation exists between cavity size and the binding-induced 129Xe chemical shift. Further applications of 129Xe NMR to biochemical assays, including the screening of proteins for xenon binding for crystallography are considered.     

Biogeographical history of cuckoo‐shrikes (Aves: Passeriformes): transoceanic colonization of Africa from Australo‐Papua

Aim Cuckoo‐shrikes and allies (Campephagidae) form a radiation of birds widely distributed in the Indo‐Pacific and Africa. Recent studies on the group have been hampered by poor taxon sampling, causing inferences about systematics and biogeography to be rather speculative. With improved taxon sampling and analyses within an explicit spatiotemporal framework, we elucidate biogeographical patterns of dispersal and diversification within this diverse clade of passerine birds. Location Africa, Asia, Australo‐Papua, the Pacific, the Philippines and Wallacea. Methods We use model‐based phylogenetic methods (Mr Bayes and garli ) to construct a phylogenetic hypothesis of the core Campephagidae (Campephagidae with the exclusion of Pericrocotus). The phylogeny is used to assess the biogeographical history of the group with a newly developed Bayesian approach to dispersal–vicariance analysis (Bayes‐diva) . We also made use of a partitioned beast analysis, with several calibration points taken from island ages, passerine mitochondrial substitution rates and secondary calibration points for passerine birds, to assess the timing of diversification and dispersal. Results We present a robust molecular phylogeny that includes all genera and 84% of the species within the core Campephagidae. Furthermore, we estimate divergence dates and ancestral area relationships. We demonstrate that Campephagidae originated in Australo‐Papua with a single lineage (Pericrocotus) dispersing to Asia early. Later, there was further extensive transoceanic dispersal from Australo‐Papua to Africa involving lineages within the core Campephagidae radiation. Main conclusions The phylogenetic relationships, along with the results of the ancestral area analysis and the timing of dispersal events, support a transoceanic dispersal scenario from Australo‐Papua to Africa by the core Campephagidae. The sister group to core Campephagidae, Pericrocotus, dispersed to mainland Asia in the late Oligocene. Asia remained uncolonized by the core Campephagidae until the Pliocene. Transoceanic dispersal is by no means an unknown phenomenon, but our results represent a convincing case of colonization over a significant water gap of thousands of kilometres from Australo‐Papua to Africa.     

Prophylactic neuroprotection by blueberry-enriched diet in a rat model of light-induced retinopathy

The role of anthocyanins is controversial in vision health. This study investigates the impact of a blueberry-enriched diet as neuroprotectant in a rat model of light-induced retinopathy. Thirty-eight albino Wistar rats and 25 pigmented Brown–Norway rats were fed by gavage with long (7 weeks) and short (2 weeks) intervention with fortified blueberry juice (1 ml; 2.8 mg cyanidin 3-glucoside equivalents) or with a placebo solution (7 weeks) that contained the abundant nonanthocyanin blueberry phenolic, namely, chlorogenic acid, before being submitted to 2 hours of intense light regimen (1.8×10⁴ lux). Retinal health was measured by fitting electroretinogram responses with the Naka–Rushton equation. The light-induced retinal damage was severe in the placebo groups, with the maximum amplitude of the electroretinogram being significantly reduced in both Wistar and Brown–Norway rats. The maximum amplitude of the electroretinogram was significantly protected from the light insult in the Wistar rats supplemented with blueberry juice for 7 or 2 weeks, and there was no significant difference between these two groups. The same dietary intervention in the Brown–Norway groups failed to protect the retina. Histological examination of retinal section confirmed the electroretinography results, showing protection of the outer nuclear layer of the retina in the Wistar rats fed with blueberries, while all placebo-fed rats and blueberry-fed Brown–Norway rats showed evidence of retinal damage concentrated in the superior hemiretina. The neuroprotective potential of anthocyanins in this particular model is discussed in terms of interaction with rhodopsin/phototransduction and in terms of antioxidative capacity.     

Expression of the IRT1 metal transporter is controlled by metals at the levels of transcript and protein accumulation

Iron, an essential nutrient, is not readily available to plants because of its low solubility. In addition, iron is toxic in excess, catalyzing the formation of hydroxyl radicals that can damage cellular constituents. Consequently, plants must carefully regulate iron uptake so that iron homeostasis is maintained. The Arabidopsis IRT1 gene is the major transporter responsible for high-affinity iron uptake from the soil. Here, we show that the steady state level of IRT1 mRNA was induced within 24 h after transfer of plants to iron-deficient conditions, with protein levels peaking 72 h after transfer. IRT1 mRNA and protein were undetectable 12 h after plants were shifted back to iron-sufficient conditions. Overexpression of IRT1 did not confer dominant gain-of-function enhancement of metal uptake. Analysis of 35S-IRT1 transgenic plants revealed that although IRT1 mRNA was expressed constitutively in these plants, IRT1 protein was present only in the roots when iron is limiting. Under these conditions, plants that overexpressed IRT1 accumulated higher levels of cadmium and zinc than wild-type plants, indicating that IRT1 is responsible for the uptake of these metals and that IRT1 protein levels are indeed increased in these plants. Our results suggest that the expression of IRT1 is controlled by two distinct mechanisms that provide an effective means of regulating metal transport in response to changing environmental conditions.     

A proton delivery pathway in the soluble fumarate reductase from Shewanella frigidimarina

The mechanism for fumarate reduction by the soluble fumarate reductase from Shewanella frigidimarina involves hydride transfer from FAD and proton transfer from the active-site acid, Arg-402. It has been proposed that Arg-402 forms part of a proton transfer pathway that also involves Glu-378 and Arg-381 but, unusually, does not involve any bound water molecules. To gain further insight into the importance of this proton pathway we have perturbed it by substituting Arg-381 by lysine and methionine and Glu-378 by aspartate. Although all the mutant enzymes retain measurable activities, there are orders-of-magnitude decreases in their k(cat) values compared with the wild-type enzyme. Solvent kinetic isotope effects show that proton transfer is rate-limiting in the wild-type and mutant enzymes. Proton inventories indicate that the proton pathway involves multiple exchangeable groups. Fast scan protein-film voltammetric studies on wild-type and R381K enzymes show that the proton transfer pathway delivers one proton per catalytic cycle and is not required for transporting the other proton, which transfers as a hydride from the reduced, protonated FAD. The crystal structures of E378D and R381M mutant enzymes have been determined to 1.7 and 2.1 A resolution, respectively. They allow an examination of the structural changes that disturb proton transport. Taken together, the results indicate that Arg-381, Glu-378, and Arg-402 form a proton pathway that is completely conserved throughout the fumarate reductase/succinate dehydrogenase family of enzymes.     

Helper requirements for generation of effector CTL to islet beta cell antigens

We have dissected the helper requirements for converting a tolerogenic CD8 T cell response into one capable of causing destruction of the pancreatic islets. Injection of naive OVA-specific CD8 T cells into transgenic mice expressing OVA in the pancreas only resulted in islet destruction when activated CD4 Th cells were coinjected. This requirement for activated CD4 T cell help for induction of primary CD8 T cell-mediated immunity to tissue Ags contrasts recent reports suggesting that help is only important for CTL memory. Our findings show that signaling of CD40 on the dendritic cell presenting to CD8 T cells is important, but not sufficient, for induction of diabetes. Furthermore, once helpers are activated, they need not recognize Ag on the dendritic cells they license. This provides insight into the helper requirements for adoptive transfer immunotherapy of tumors and suggests key points for inhibition of CTL-mediated autoimmunity.     

Hijacking mitochondria: bacterial toxins that modulate mitochondrial function

Bacterial infection has enormous global social and economic impacts stemming from effects on human health and agriculture. Although there are still many unanswered questions, decades of research has uncovered many of the pathogenic mechanisms at play. It is now clear that bacterial pathogens produce a plethora of proteins known as "toxins" and "effectors" that target a variety of physiological host processes during the course of infection. One of the targets of host targeted bacterial toxins and effectors are the mitochondria. The mitochondrial organelles are major players in many biological functions, including energy conversion to ATP and cell death pathways, which inherently makes them targets for bacterial proteins. We present a summary of the toxins targeted to mitochondria and for those that have been studied in finer detail, we also summarize what we know about the mechanisms of targeting and finally their action at the organelle.     

Gender-specific associations of marine n-3 fatty acids and fish consumption with 10-year incidence of stroke

Background

There is some evidence that the association of fish and marine fatty acids with stroke risk differs between men and women. We investigated the gender-specific associations of habitual intake of the marine fatty acids eicosapentaenoic acid (EPA) plus docosahexaenoic acid (DHA) and fish on incident stroke in a population-based study in the Netherlands.

Methods

We prospectively followed 20,069 men and women, aged 20–65 years, without cardiovascular diseases at baseline. Habitual diet was assessed with a validated 178-item food frequency questionnaire. Incidence of stroke was assessed through linkage with mortality and morbidity registers. Cox proportional hazards models were used to estimate multivariable-adjusted hazard ratios (HR) and 95% confidence intervals (95%CI).

Results

During 8–13 years of follow-up, 221 strokes occurred. In women, an inverse dose-response relation (P-trend = 0.02) was observed between EPA-DHA intake and incident stroke, with an HR of 0.49 (95% CI: 0.27–0.91) in the top quartile of EPA-DHA (median 225 mg/d) as compared to the bottom quartile (median 36 mg/d). In men, the HR (95%CI) for the top quartile of EPA-DHA intake was 0.87 (0.51–1.48) (P-trend = 0.36). Similar results were observed for fish consumption and stroke incidence.

Conclusion

A higher EPA-DHA and fish intake is related to a lower stroke risk in women, while for men an inverse association could not be demonstrated.