Generation of hydrogen peroxide by brain mitochondria: the effect of reoxygenation following postdecapitative ischemia

The hypothesis that mitochondria damaged during complete cerebral ischemia generate increased amounts of superoxide anion radical and hydrogen peroxide (H2O2) upon postischemic reoxygenation has been tested. In rat brain mitochondria, succinate supported H2O2 generation, whereas NADH-linked substrates, malate plus glutamate, did so only in the presence of respiratory chain inhibitors. Succinate-supported H2O2 generation was diminished by rotenone and the uncoupler carbonyl cyanide m-chlorphenylhydrazone and enhanced by antimycin A and increased oxygen tensions. When maximally reduced, the NADH dehydrogenase and the ubiquinone-cytochrome b regions of the electron transport chain are sources of H2O2. These studies suggest that a significant portion of H2O2 generation in brain mitochondria proceeds via the transfer of reducing equivalents from ubiquinone to the NADH dehydrogenase portion of the electron transport chain. Succinate-supported H2O2 generation by mitochondria isolated from rat brain exposed to 15 min of postdecapitative ischemia was 90% lower than that of control preparations. The effect of varying oxygen tensions on H2O2 generation by postischemic mitochondrial preparations was negligible compared with the increased H2O2 generation measured in control preparations. Comparison of the effects of respiratory chain inhibitors and oxygen tension on succinate-supported H2O2 generation suggests that the ability for reversed electron transfer is impaired during ischemia. These data do not support the hypothesis that mitochondrial free radical generation increases during postischemic reoxygenation.     

Assessing the genetic effects of rehabilitating harbor seals (<Emphasis Type="Italic">Phoca vitulina</Emphasis>) in the Wadden Sea using stochastic simulations

Rehabilitation of marine mammals with the intent of releasing them back into nature is carried out for several species. Rehabilitation can help supporting critically endangered species, increase public awareness, and serve scientific purposes, but rehabilitation also causes concern due to risk of introducing diseases into the wild populations and genetic changes from disruption of natural selection and host-pathogen co-evolution. In this study, we investigate another potential risk from rehabilitation that has not previously been considered, i.e., anthropogenic increase in population inbreeding level. For this purpose, we performed stochastic population viability analyses of the Wadden Sea harbor seal population using VORTEX. In the Wadden Sea, rehabilitation takes place in several rehabilitation centers, and many of the seals suffer from parasitic bronchopneumonia or are orphaned. Several studies have found a correlation between helminth infection and inbreeding level. Moreover, a relation between fitness traits such as pup survival and inbreeding has been demonstrated. On this basis, we assess the effects from rehabilitating relatively inbred seals on population size and genetic diversity. We find that releasing seals significantly affect population inbreeding level and to a lesser extent population size. The effect depends on the level of inbreeding in rehabilitated seals as well as the actual number of inbred seals released.     

Insights into lipid-protein interactions from computer simulations

Lipid-protein interactions play an important direct role in the function of many membrane proteins. We argue they are key players in membrane structure, modulate membrane proteins in more subtle ways than direct binding, and are important for understanding the mechanism of classes of hydrophobic drugs. By directly comparing membrane proteins from different families in the same, complex lipid mixture, we found a unique lipid environment for every protein. Extending this work, we identified both differences and similarities in the lipid environment of GPCRs, dependent on which family they belong to and in some cases their conformational state, with particular emphasis on the distribution of cholesterol. More recently, we have been studying modes of coupling between protein conformation and local membrane properties using model proteins. In more applied approaches, we have used similar methods to investigate specific hypotheses on interactions of lipid and lipid-like molecules with ion channels. We conclude this perspective with some considerations for future work, including a new more sophisticated coarse-grained force field (Martini 3), an interactive visual exploration framework, and opportunities to improve sampling.     

Introduction or reintroduction? Last resorts for the latest bird to become extinct in Europe, the Andalusian hemipode Turnix sylvatica sylvatica

The Andalusian hemipode (Turnix sylvatica sylvatica) (Order: Turniciformes, Family: Turnicidae), formerly distributed in several Mediterranean countries, is a critically endangered bird, if not already extinct. Subspecies of the T. sylvatica complex, in turn composed by nine subspecies are widely distributed in Africa and southern Asia. The last free-ranging Andalusian hemipodes were shot by hunters near Doñana National Park (Spain) in 1981. Therefore, this species could be the last bird species getting extinct in Iberia and Europe in the XXth century. This investigation deals with the phylogenetic relationships of the Andalusian hemipode with the supposedly congeneric T. varia , T. tanki , T. suscitator and T. pyrrhothorax, and with the supposedly conspecific T. sylvatica lepurana, which is the geographically nearest buttonquail population (occurring in central and southern Africa). A 606 bp long fragment of the cytochrome b gene (approx. 1140 bp) of the mitochondrial DNA was sequenced, using both museum skins (the only available source for T. s. sylvatica) or blood/tissue samples from contemporary individuals (remaining species and subspecies). Seven haplotypes were found: two each for T. varia and T. s. lepurana, and one each for T. tanki, T. suscitator, T. pyrrhothorax, and T. s. sylvatica. Sequence divergence values obtained from pairwise distances between the T. sylvatica group haplotypes and the other species, ranged from 19.4 to 25.9%. The low genetic divergence between T. s. sylvatica and T. s. lepurana (0.00–0.01%) confirmed that the current classification based on morphological characters is correct, and that these two taxa may should be considered as subspecies. This close relationship would permit an introduction T. sylvatica where the species was last seen in Spain (i.e., Doñana National Park). This area is now strictly protected and human persecution is no longer a problem.     

Genetic variability of central–western European pine marten (Martes martes) populations

Recent studies highlighted the potential role of cryptic glacial refugia for temperate taxa in Europe beyond the Mediterranean peninsulas. To further investigate phylogeographic features of the European pine marten (Martes martes) in previously identified cryptic refugia located in central–western Europe, we analysed the hyper-variable diagnostic fragment of the mitochondrial control region in a total of 134 specimens, allowing for reliable comparisons with previous genetic studies of the species. We included samples from eight different European countries in central–western Europe (Belgium, France, Luxembourg and the Netherlands), in south–western Europe (Spain), in north–central Europe (Denmark) and in central Europe (Germany and Poland). The sequences collapsed in 17 haplotypes, which allowed us to determine the genetic composition of the pine marten populations throughout central–western Europe. Overall, our results showed that the population genetic variation, estimated by the standardised haplotype diversity, was high (0.400?≤?Hs?≤?0.762), and it was considerably higher in Germany (0.762) and the Netherlands (0.722) compared to the other countries. The nucleotide diversity was relatively low (0.002?≤?π?≤?0.016) even in Germany and the Netherlands (0.016 and 0.014, respectively), suggesting relatively small, long-term effective population sizes or severe bottlenecks. Out of the 17 haplotypes found in our study area, 13 were unique and limited to a single country: one in Denmark, one in Spain, four in Poland and seven in the Netherlands. The pairwise genetic distance ranged from 0.001 to 0.032 and did not show any evident correlation with the geographic distances between the populations. A genealogical relationship network was constructed, which provided evidence for a recent origin of many of the unique haplotypes. Approximately 82 % of the samples analysed in this study belonged to haplotypes grouped into a previously identified central–northern European phylogroup of the species. Our results support previous findings, indicating low contribution of southern refugial populations to the postglacial recolonization of central–western Europe and a predominant contribution of pine marten populations that survived the Last Glacial Maxima in cryptic northern refugia.     

Brown hares on the edge: Genetic population structure of the Danish brown hare

Denmark lies on the edge of the distributional range of the brown hareLepus europaeus Pallas, 1778, where population differentiation is most likely to occur. A total of 369 brown hares from eight geographically distinct Danish European brown hare populations were used to study the genetic population structure. In all, 480bp of the mitochondrial D-loop were sequenced in both directions. Observed genetic diversity (π) was relatively low (π=0.41%) while haplotype diversity (h=0.808) and the number of unique haplotypes (19) were similar to levels found in other European brown hare populations. The observed population structure was pronounced (pairwise conventionalF _ST and ϕ _st ranged between 6.9–57% and 5–69.8%, respectively). There was no correlation between the geographic and the genetic distance. Population structure was influenced by genetic drift, anthropogenic effects (eg translocation and escapes from hare-farms) and by post-glacial recolonization from southern refuges or refuges north east of the Black Sea. Analysis of historical population expansion/fluctuation events indicated that the populations have experienced different demographic events in the recent past. Relatively high sequence divergence between some populations might be explained by multiple recolonization events after the last Pleistocene glaciations or by stocking effects. Colonization from southern refuges was supported by the observation that haplotype 2 in the Danish brown hare was identical to the central European ancestral haplotype c07.     

Conformational dynamics of Tetracenomycin aromatase/cyclase regulate polyketide binding and enzyme aggregation propensity

BackgroundThe N-terminal domain of Tetracenomycin aromatase/cyclase (TcmN), an enzyme derived from Streptomyces glaucescens, is involved in polyketide cyclization, aromatization, and folding. Polyketides are a diverse class of secondary metabolites produced by certain groups of bacteria, fungi, and plants with various pharmaceutical applications. Examples include antibiotics, such as tetracycline, and anticancer drugs, such as doxorubicin. Because TcmN is a promising enzyme for in vitro production of polyketides, it is important to identify conditions that enhance its thermal resistance and optimize its function.MethodsTcmN unfolding, stability, and dynamics were evaluated by fluorescence spectroscopy, circular dichroism, nuclear magnetic resonance ¹⁵N relaxation experiments, and microsecond molecular dynamics (MD) simulations.ResultsTcmN thermal resistance was enhanced at low protein and high salt concentrations, was pH-dependent, and denaturation was irreversible. Conformational dynamics on the μs-ms timescale were detected for residues in the substrate-binding cavity, and two predominant conformers representing opened and closed cavity states were observed in the MD simulations.ConclusionBased on the results, a mechanism was proposed in which the thermodynamics and kinetics of the TcmN conformational equilibrium modulate enzyme function by favoring ligand binding and avoiding aggregation.General significanceUnderstanding the principles underlying TcmN stability and dynamics may help in designing mutants with optimal properties for biotechnological applications.     

Proteolytic activity of Oidiodendron kalrai.

The physiochemical characteristics of the intracellular proteolytic enzymes of Oidiodendron kalari, a neuropathogenic fungus, were studied. The organism in the yeast phase was grown in a semisynthetic medium containing 1% tryptone, at 37 degrees C for 48 hr, on a gyrotory shaker. The crude extract was prepared by breaking the cells in a French pressure cell and the proteolytci activity was tested against biological substrates. The cell-free extract hydrolyzed casein, hemoglobin, lactalbumin, gelatin, elastin, collagen and purified rabbit renal basement membrane to various degrees. Optimal proteolytic activity was observed at pH 6 and at 32 degrees C. Calcium and EDTA did not affect the enzymatic activity; however, activity was partially inhibited by sulfhydryl-blocking agents and by heat-inactivated horse, calf, and human serum. The extract was totally inactivated by exposure to a temperature of 70 degrees C for 60 min. Storage at -76 degrees C or -15 degrees C for 6 months or at 4 degrees C for 4 weeks did not affect protease activity.