Optimization of the All-D Peptide D3 for Aβ Oligomer Elimination

The aggregation of amyloid-β (Aβ) is postulated to be the crucial event in Alzheimer’s disease (AD). In particular, small neurotoxic Aβ oligomers are considered to be responsible for the development and progression of AD. Therefore, elimination of thesis oligomers represents a potential causal therapy of AD. Starting from the well-characterized d-enantiomeric peptide D3, we identified D3 derivatives that bind monomeric Aβ. The underlying hypothesis is that ligands bind monomeric Aβ and stabilize these species within the various equilibria with Aβ assemblies, leading ultimately to the elimination of Aβ oligomers. One of the hereby identified d-peptides, DB3, and a head-to-tail tandem of DB3, DB3DB3, were studied in detail. Both peptides were found to: (i) inhibit the formation of Thioflavin T-positive fibrils; (ii) bind to Aβ monomers with micromolar affinities; (iii) eliminate Aβ oligomers; (iv) reduce Aβ-induced cytotoxicity; and (v) disassemble preformed Aβ aggregates. The beneficial effects of DB3 were improved by DB3DB3, which showed highly enhanced efficacy. Our approach yielded Aβ monomer-stabilizing ligands that can be investigated as a suitable therapeutic strategy against AD.     

Sequestosome-1/p62 Is the Key Intracellular Target of Innate Defense Regulator Peptide

Innate defense regulator-1 (IDR-1) is a synthetic peptide with no antimicrobial activity that enhances microbial infection control while suppressing inflammation. Previously, the effects of IDR-1 were postulated to impact several regulatory pathways including mitogen-activated protein kinase (MAPK) p38 and CCAAT-enhancer-binding protein, but how this was mediated was unknown. Using a combined stable isotope labeling by amino acids in cell culture-proteomics methodology, we identified the cytoplasmic scaffold protein p62 as the molecular target of IDR-1. Direct IDR-1 binding to p62 was confirmed by several biochemical binding experiments, and the p62 ZZ-type zinc finger domain was identified as the IDR-1 binding site. Co-immunoprecipitation analysis of p62 molecular complexes demonstrated that IDR-1 enhanced the tumor necrosis factor α-induced p62 receptor-interacting protein 1 (RIP1) complex formation but did not affect tumor necrosis factor α-induced p62-protein kinase ζ complex formation. In addition, IDR-1 induced p38 MAPK activity in a p62-dependent manner and increased CCAAT-enhancer-binding protein β activity, whereas NF-κB activity was unaffected. Collectively, these results demonstrate that IDR-1 binding to p62 specifically affects protein-protein interactions and subsequent downstream events. Our results implicate p62 in the molecular mechanisms governing innate immunity and identify p62 as a potential therapeutic target in both infectious and inflammatory diseases.     

Effects of drought and N level on the interactions of the root hemiparasite Rhinanthus alectorolophus with a combination of three host species

• Increasing nitrogen deposition and more frequent drought events are likely to change plant interactions in natural grasslands. Both factors may also influence the interactions between hemiparasitic plants, regarded as keystone species in many grasslands, and their host species.
• We grew a combination of three suitable hosts, a grass, a forb and a legume, with and without the hemiparasite Rhinanthus alectorolophus at three levels of nitrogen (N) and two levels of water availability in a factorial design.
• Biomass of the hemiparasite and host community increased with N level and was reduced by drought to a similar degree. Larger plants in fertilised pots started to wilt earlier, and the presence of a hemiparasite further increased drought sensitivity. The hemiparasite strongly reduced biomass of the host community and overall productivity, and affected the competitive balance among host plants because it particularly reduced biomass of the dominant grass. These effects were the opposite of those of high N. The hemiparasite increased the root mass fraction of the hosts at all levels of N and water availability, indicating that the effect of the hemiparasite on the hosts was mainly due to loss of belowground resources.
• Our results indicate that hemiparasites will not always respond more strongly to increased N availability and drought than autotrophic plants, and that hemiparasites can have similarly strong effects on grassland communities as soil fertility and drought. By preferentially attacking dominant species the hemiparasites might alleviate the negative effects of nutrient enrichment on grassland diversity.

     

Spread of a Distinct Stx2-Encoding Phage Prototype among Escherichia coli O104:H4 Strains from Outbreaks in Germany, Norway, and Georgia

Shiga toxin 2 (Stx2)-producing Escherichia coli (STEC) O104:H4 caused one of the world's largest outbreaks of hemorrhagic colitis and hemolytic uremic syndrome in Germany in 2011. These strains have evolved from enteroaggregative E. coli (EAEC) by the acquisition of the Stx2 genes and have been designated enteroaggregative hemorrhagic E. coli. Nucleotide sequencing has shown that the Stx2 gene is carried by prophages integrated into the chromosome of STEC O104:H4. We studied the properties of Stx2-encoding bacteriophages which are responsible for the emergence of this new type of E. coli pathogen. For this, we analyzed Stx bacteriophages from STEC O104:H4 strains from Germany (in 2001 and 2011), Norway (2006), and the Republic of Georgia (2009). Viable Stx2-encoding bacteriophages could be isolated from all STEC strains except for the Norwegian strain. The Stx2 phages formed lysogens on E. coli K-12 by integration into the wrbA locus, resulting in Stx2 production. The nucleotide sequence of the Stx2 phage P13374 of a German STEC O104:H4 outbreak was determined. From the bioinformatic analyses of the prophage sequence of 60,894 bp, 79 open reading frames were inferred. Interestingly, the Stx2 phages from the German 2001 and 2011 outbreak strains were found to be identical and closely related to the Stx2 phages from the Georgian 2009 isolates. Major proteins of the virion particles were analyzed by mass spectrometry. Stx2 production in STEC O104:H4 strains was inducible by mitomycin C and was compared to Stx2 production of E. coli K-12 lysogens.     

Identification of phenylalkane derivatives when Mycobacterium neoaurum and Rhodococcus erythropolis were cultured in the presence of various phenylalkanes

Phenylalkanes are ubiquitously found in nature as pollutants originating from oil, gas oil and petrol. Rising commercial demand for mineral oil fractions has led to the increased prevalence of environmental contamination, whereby these particular hydrocarbons are encountered by bacteria which have subsequently developed sophisticated metabolic routes for purposes of degradation. Herein a detailed analysis of these metabolic pathways in the degradation of phenylalkanes by Mycobacterium neoaurum and Rhodococcus erythropolis highlighted preponderance for the formation of certain metabolites of which 17 were identified and whereby striking differences were noticed depending specifically upon the length of the substrate’s alkyl chain. Although the degradation of even-numbered phenylalkane substrates was assumed to result in the generation of phenylacetic acid formed due to substrate terminal oxidation and subsequent β-oxidation, cultures of M. neoaurum and R. erythropolis were determined in an extracellular accumulation of odd-numbered acidic metabolites, suggesting a simultaneous presence of sub-terminal degradation mechanisms. However, results obtained from biotransformation assays containing even-chained phenylalkanoic acid intermediates as substrates revealed exclusive β-oxidative mechanisms and no generation of odd-numbered degradation products. R. erythropolis in contrast to M. neoaurum also proved viable for hydroxylation of the aromatic ring of metabolites. Interestingly, the generation of phenylacetic acid and subsequently 2-hydroxyphenyl acetic acid was monitored and entailed the presence of the lactone intermediate 2-coumaranone. These results enhance our understanding of the degradation of phenylalkanes and illustrate the potential application of such species in the bioremediation of these common environmental pollutants and in the strains’ diverse abilities to transform mineral oil compounds to new valuable products.     

Proteohistography--direct analysis of tissue with high sensitivity and high spatial resolution using ProteinChip technology.

On the proteomic level, all tissues, tissue constituents, or even single cells are heterogeneous, but the biological relevance of this cannot be adequately investigated with any currently available technique. The analysis of proteins of small tissue areas by any proteomic approach is limited by the number of required cells. Increasing the number of cells only serves to lower the spatial resolution of expressed proteins. To enhance sensitivity and spatial resolution we developed Proteohistography. Laser microdissection was used to mark special areas of interest on tissue sections attached to glass slides. These areas were positioned under microscopic control directly on an affinity chromatographic ProteinChip Array so that cells were lysed and their released proteins bound on a spatially defined point. The ProteinChip System, surface enhanced laser desorption/ionization time-of-flight mass spectrometry (SELDI-TOF-MS), allows the laser to be steered to up to 215 distinct positions across the surface of the spot, enabling a high spatial resolution of measured protein profiles for the analyzed tissue area. Protein profiles of the single positions were visually plotted over the used tissue section to visualize distribution proteohistologically. Results show that the spatial distribution of detectable proteins could be used as a Proteohistogram for a given tissue area. Consequently, this procedure can provide additional information to both a matrix-assisted laser desorption/ionization (MALDI)-based approach and immunohistochemistry, as it is more sensitive, highly quantitative, and no specific antibody is needed. Hence, proteomic heterogeneity can be visualized even if proteins are not known or identified.     

Induction of reactive oxygen species and cell survival in the presence of advanced glycation end products and similar structures

Advanced glycation end products (AGEs) that arise from the reaction of sugars with protein side chains and the terminal amino group are supposed to be involved in the pathogenesis of several diseases and therefore the effects of AGEs on cells are the objective of numerous investigations. The effects of AGEs on cells are commonly assumed to be transduced via the receptor for AGEs (RAGE) but there are also other receptors known to interact with AGEs and they are likely to be involved in signal transduction. The primary cellular effect of AGEs on cultured cells was found to be the formation of reactive oxygen species (ROS). For the present study one murine and three human cell lines were used. The effects of a set of different highly modified AGEs and AGE-like compounds derived from the incubation of different modifiers with BSA were tested for their effects on these cells. Almost all AGEs tested induced the production of reactive oxygen species (ROS) in the different cell lines although the intensity of the detected signals varied considerably between the cell lines and are strongly dependent on the AGE used for cell activation. The most highly modified BSA-species were shown to inhibit cell growth in all cell lines, whereas a moderately modified glucose derived BSA-AGE and BSA-GA(red) did not show any inhibitory effect on cell growth even when a high ROS formation was detected.     

The selective COX-2 inhibitor celecoxib modulates sphingolipid synthesis

Sphingolipids such as ceramides (Cers) play important roles in cell proliferation, apoptosis, and cell cycle regulation. An increased Cer level is linked to the cytotoxic effects of several chemotherapeutics. Various selective cyclooxygenase-2 (COX-2) inhibitors induce anti-proliferative effects in tumor cells. We addressed the possible interaction of the selective COX-2 inhibitors, coxibs, with the sphingolipid pathway as an explanation of their anti-proliferative effects. Sphingolipids were measured using liquid chromatography tandem mass spectrometry. Treatment of various cancer cell lines with celecoxib significantly increased sphinganine, C(16:0)-, C(24:0)-, C(24:1)-dihydroceramide (dhCer) and led to a depletion of C(24:0)-, C(24:1)-Cer in a time- and concentration-dependent manner, whereas other coxibs had no effect. Using (13)C,(15)N-labeled l-serine, we demonstrated that the augmented dhCers after celecoxib treatment originate from de novo synthesis. Celecoxib inhibited the dihydroceramide desaturase (DEGS) in vivo with an IC(50) of 78.9 +/- 1.5 muM and increased total Cer level about 2-fold, indicating an activation of sphingolipid biosynthesis. Interestingly, inhibition of the sphingolipid biosynthesis by specific inhibitors of l-serine palmitoyltransferase diminished the anti-proliferative potency of celecoxib. In conclusion, induction of de novo synthesis of sphingolipids and inhibition of DEGS contribute to the anti-proliferative effects of celecoxib.     

Insights into succession processes using temporally repeated habitat models: results from a long‐term study in a post‐mining landscape

Questions: The early phases of primary succession are governed by chance events and dispersal‐related processes in an environment that is largely free of competition. Thus, the predictability of vegetation patterns using environmental site factors can be expected to be low and spatial autocorrelation to be high. We asked whether the match between vegetation and environment becomes better in the course of succession, and whether vegetation types shift their realized niche with time. Location: Lignite mining region in Central Germany, the post‐mining landscape “Goitzsche” (Saxony‐Anhalt). Methods: Vegetation types were mapped in a 10‐m grid (total area 4.8 ha), starting in 1995, at 3‐year intervals until 2007. We used a temporal comparison of habitat models. We applied: GLS regression to partition the variation in coverage of vegetation types into environmental (soil pH) and spatial components; logistic regression to model the presence/absence of vegetation types along a soil acidity gradient; and autologistic regression allowing for soil acidity and neighbourhood effects. Results: For most vegetation types, the proportion of variation explained by space was high but declined during succession. The outcome of autologistic models suggests that soil acidity often plays a minor role compared to neighbourhood effects in the earlier phase of succession than 12 years later. For four vegetation types, the pH range in which the type was expected to be dominant clearly became smaller with time. These trends support the view that the role of processes related to chance and dispersal decrease with time, while those related to environmental filtering mediated by biotic interactions increase. Conclusions: We conclude that temporal comparisons of spatially explicit habitat models provide insights into changing biotic community processes and their effects on habitat specificity of species or their communities. Thus, this approach may be particularly important for analysis of ecological systems that are not in equilibrium with their environmental drivers.