Isolation by distance in saproxylic beetles may increase with niche specialization

Species confined to temporally stable habitats are usually susceptible to habitat fragmentation, as living in long-lasting habitats is predicted to constrain evolution of dispersal ability. In Europe, saproxylic invertebrates associated with tree hollows are currently threatened due to the severe fragmentation of their habitat, but data on the population genetic consequences of such habitat decline are still scarce. By employing AFLP markers, we compared the spatial genetic structure of two ecologically and taxonomically related beetle species, Osmoderma barnabita and Protaetia marmorata (Cetoniidae). Both species are exclusively associated with tree hollows, but O. barnabita has a more restricted host preferences compared to P. marmorata. Analyses of spatial autocorrelation showed, in line with the predicted low dispersal potential of these saproxylic beetles, that both species are characterized by a strong kinship structure, which was more pronounced in the specialist O. barnabita than in the generalist P. marmorata. Individuals of both species sampled within single trees showed high relatedness (≈0.50 in O. barnabita and ≈0.15 in P. marmorata). Interestingly, groups of pheromone-emitting O. barnabita males sampled on the same tree trunk were found to be full brothers. Whether this result can be explained by kin selection to increase attraction of conspecific females for mating or by severe inbreeding of beetles within individual tree hollows needs further study. Although our studied populations were significantly inbred, our results suggest that the dispersal ability of Osmoderma beetles may be one order of magnitude greater than suggested by previous dispersal studies and acceptable levels of habitat fragmentation for metapopulation survival may be bigger than previously thought.     

Transition metal complexes IX. Nickel complexes with a chiral azaphosphole ligand

The reaction of (−)-(R)-myrtenal and (+)-(R)-phenylethylamine gave a Schiff base 1 which was reacted with MePBr₂ in the presence of a base to give under dehydrohalogenation of an intermediate McCormack product a salt 2. Treatment of 2 with sodium led to the formation of the azaphosphole 4. η³-C₃H₅NiCl and 4 gave a 1:1 adduct 5 and nickel(0) gave a 1:4 complex 6. Compounds 4–6 were characterized by NMR spectroscopy as well as by single crystal X-ray structure determination.     

Activation of DNA-PK by Ionizing Radiation Is Mediated by Protein Phosphatase 6

DNA-dependent protein kinase (DNA-PK) plays a critical role in DNA damage repair, especially in non-homologous end-joining repair of double-strand breaks such as those formed by ionizing radiation (IR) in the course of radiation therapy. Regulation of DNA-PK involves multisite phosphorylation but this is incompletely understood and little is known about protein phosphatases relative to DNA-PK. Mass spectrometry analysis revealed that DNA-PK interacts with the protein phosphatase-6 (PP6) SAPS subunit PP6R1. PP6 is a heterotrimeric enzyme that consists of a catalytic subunit, plus one of three PP6 SAPS regulatory subunits and one of three ankyrin repeat subunits. Endogenous PP6R1 co-immunoprecipitated DNA-PK, and IR enhanced the amount of complex and promoted its import into the nucleus. In addition, siRNA knockdown of either PP6R1 or PP6 significantly decreased IR activation of DNA-PK, suggesting that PP6 activates DNA-PK by association and dephosphorylation. Knockdown of other phosphatases PP5 or PP1γ1 and subunits PP6R3 or ARS-A did not reduce IR activation of DNA-PK, demonstrating specificity for PP6R1. Finally, siRNA knockdown of PP6R1 or PP6 but not other phosphatases increased the sensitivity of glioblastoma cells to radiation-induced cell death to a level similar to DNA-PK deficient cells. Our data demonstrate that PP6 associates with and activates DNA-PK in response to ionizing radiation. Therefore, the PP6/PP6R1 phosphatase is a potential molecular target for radiation sensitization by chemical inhibition.     

Induction of cytosolic NADPH-diaphorase/nitric oxide synthase in reactive microglia/macrophages after quinolinic acid lesions in the rat striatum: an electron and light microscopical study

Induction of nitric oxide synthase and increased production of nitric oxide in microglia may play a crucial role in neuronal damage and neurodegenerative disorders. In the present study we have used light and electron microscopical NADPH-diaphorase histochemistry as the visualization procedure for nitric oxide synthase to investigate the time-course and subcellular patterns of NADPH-diaphorase expression in microglia/macrophages of quinolinic acid-lesioned rat striatum. For light microscopy, NADPH-diaphorase histochemistry sections were stained with nitroblue tetrazolium, while for ultrastructural analysis the tetrazolium salt 2-(2-benzothiazolyl)-5-styryl-3(4-phthalhydrazidyl) tetrazolium chloride (BSPT) was applied. Light microscopical inspection revealed a progressively increasing number of positive cells with increasing intensity of NADPH-diaphorase staining in microglia/macrophages from day 1 after quinolinic acid injection onward. Electron microscopical examination revealed a membrane bound NADPH-diaphorase in quiescent microglia as well as in activated microglia/macrophages through all stages of the lesion studied. Predominantly membranes of the nuclear envelope and the endoplasmic reticulum were labeled with BSPT-formazan, while in advanced stages selective membrane portions of mitochondria, Golgi apparatus and plasmalemma were also stained. From day 5 onward after lesion induction, a very distinctive type of NADPH-diaphorase was observed, forming accumulations of electron-dense grains that were distributed differentially throughout cytoplasmic areas and phagocytic vacuoles. Dynamics of expression, unique cytosolic localization and occurrence exclusively in activated microglia/macrophages suggest that this particular NADPH-diaphorase activity probably reflects the inducible isoform of nitric oxide synthase, whereas the membrane-bound precipitate may represent the neuronal and/or the endothelial isoform of the enzyme.     

Codon bias and the folding dynamics of the cystic fibrosis transmembrane conductance regulator

Synonymous or silent mutations are often overlooked in genetic analyses for disease-causing mutations unless they are directly associated with potential splicing defects. More recent studies, however, indicate that some synonymous single polynucleotide polymorphisms (sSNPs) are associated with changes in protein expression, and in some cases, protein folding and function. The impact of codon usage and mRNA structural changes on protein translation rates and how they can affect protein structure and function is just beginning to be appreciated. Examples are given here that demonstrate how synonymous mutations alter the translational kinetics and protein folding and/or function. The mechanism for how this occurs is based on a model in which codon usage modulates the translational rate by introducing pauses caused by nonoptimal or rare codons or by introducing changes in the mRNA structure, and this in turn influences co-translational folding. Two examples of this include the multidrug resistance protein (p-glycoprotein) and the cystic fibrosis transmembrane conductance regulator gene (CFTR). CFTR is also used here as a model to illustrate how synonymous mutations can be examined using in silico predictive methods to identify which sSNPs have the potential to change protein structure. The methodology described here can be used to help identify “non-silent” synonymous mutations in other genes.     

Mycobacterium tuberculosis AtsG (Rv0296c), GlmU (Rv1018c) and SahH (Rv3248c) Proteins Function as the Human IL-8-Binding Effectors and Contribute to Pathogen Entry into Human Neutrophils

Mycobacterium tuberculosis is an extremely successful intracellular pathogen that has evolved a broad spectrum of pathogenic mechanisms that enable its manipulation of host defense elements and its survival in the hostile environment inside phagocytes. Cellular influx into the site of mycobacterial entry is mediated by a variety of chemokines, including interleukin-8 (IL-8), and the innate cytokine network is critical for the development of an adaptive immune response and infection control. Using affinity chromatography, liquid chromatography electrospray ionization tandem mass spectrometry and surface plasmon resonance techniques, we identified M. tuberculosis AtsG arylsulphatase, bifunctional glucosamine-1-phosphate acetyltransferase and N-acetylglucosamine-1-phosphate uridyl transferase (GlmU) and S-adenosyl-L-homocysteine hydrolase (SahH) as the pathogen proteins that bind to human IL-8. The interactions of all of the identified proteins (AtsG, GlmU and SahH) with IL-8 were characterized by high binding affinity with K_D values of 6.83x10^-6 M, 5.24x10^-6 M and 7.14x10^-10 M, respectively. Furthermore, the construction of Mtb mutant strains overproducing AtsG, GlmU or SahH allowed determination of the contribution of these proteins to mycobacterial entry into human neutrophils. The significantly increased number of intracellularly located bacilli of the overproducing M. tuberculosis mutant strains compared with those of “wild-type” M. tuberculosis and the binding interaction of AtsG, GlmU and SahH proteins with human IL-8 may indicate that these proteins participate in the modulation of the early events of infection with tubercle bacilli and could affect pathogen attachment to target cells.     

Modulation of SCF��-TrCP-dependent I��B�� Ubiquitination by Hydrogen Peroxide

Reactive oxygen species are known to participate in the regulation of intracellular signaling pathways, including activation of NF-κB. Recent studies have indicated that increases in intracellular concentrations of hydrogen peroxide (H₂O₂) have anti-inflammatory effects in neutrophils, including inhibition of the degradation of IκBα after TLR4 engagement. In the present experiments, we found that culture of lipopolysaccharide-stimulated neutrophils and HEK 293 cells with H₂O₂ resulted in diminished ubiquitination of IκBα and decreased SCF^β-TrCP ubiquitin ligase activity. Exposure of neutrophils or HEK 293 cells to H₂O₂ was associated with reduced binding between phosphorylated IκBα and SCF^β-TrCP but no change in the composition of the SCF^β-TrCP complex. Lipopolysaccharide-induced SCF^β-TrCP ubiquitin ligase activity as well as binding of β-TrCP to phosphorylated IκBα was decreased in the lungs of acatalasemic mice and mice treated with the catalase inhibitor aminotriazole, situations in which intracellular concentrations of H₂O₂ are increased. Exposure to H₂O₂ resulted in oxidative modification of cysteine residues in β-TrCP. Cysteine 308 in Blade 1 of the β-TrCP β-propeller region was found to be required for maximal binding between β-TrCP and phosphorylated IκBα. These findings suggest that the anti-inflammatory effects of H₂O₂ may result from its ability to decrease ubiquitination as well as subsequent degradation of IκBα through inhibiting the association between IκBα and SCF^β-TrCP.     

Searching for structural bias in particle swarm optimization and differential evolution algorithms

During the last two decades, a large number of metaheuristics have been proposed, leading to various studies that call for a deeper insight into the behaviour, efficiency and effectiveness of such methods. Among numerous concerns that are briefly reviewed in this paper, the presence of a structural bias (i.e. the tendency, not justified by the fitness landscape, to visit some regions of the search space more frequently than other regions) has recently been detected in simple versions of the genetic algorithm and particle swarm optimization. As of today, it remains unclear how frequently such a behaviour occurs in population-based swarm intelligence and evolutionary computation methods, and to what extent structural bias affects their performance. The present study focuses on the search for structural bias in various variants of particle swarm optimization and differential evolution algorithms, as well as in the traditional direct search methods proposed by Nelder–Mead and Rosenbrock half a century ago. We found that these historical direct search methods are structurally unbiased. However, most tested new metaheuristics are structurally biased, and at least some presence of structural bias can be observed in almost all their variants. The presence of structural bias seems to be stronger in particle swarm optimization algorithms than in differential evolution algorithms. The relationships between the strength of the structural bias and the dimensionality of the search space, the number of allowed function calls and the population size are complex and hard to generalize. For 14 algorithms tested on the CEC2011 real-world problems and the CEC2014 artificial benchmarks, no clear relationship between the strength of the structural bias and the performance of the algorithm was found. However, at least for artificial benchmarks, such old and structurally unbiased methods like Nelder–Mead algorithm performed relatively well. This is a warning that the presence of structural bias in novel metaheuristics may hamper their search abilities.