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  • 1
    Publication Date: 1990-04-01
    Print ISSN: 0956-540X
    Electronic ISSN: 1365-246X
    Topics: Geosciences
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  • 2
    Publication Date: 2016-05-12
    Description: Wood-rotting fungi possess remarkably diverse extracellular oxidation mechanisms, including enzymes, such as laccase and peroxidases, and Fenton chemistry. The ability to biologically drive Fenton chemistry by the redox cycling of quinones has previously been reported to be present in both ecologically diverging main groups of wood-rotting basidiomycetes. Therefore, we investigated whether it is even more widespread among fungal organisms. Screening of a diverse selection of a total of 18 ascomycetes and basidiomycetes for reduction of the model compound 2,6-dimethoxy benzoquinone revealed that all investigated strains were capable of reducing it to its corresponding hydroquinone. In a second step, depolymerization of the synthetic polymer polystyrene sulfonate was used as a proxy for quinone-dependent Fenton-based biodegradation capabilities. A diverse subset of the strains, including environmentally ubiquitous molds, white-rot fungi, as well as peatland and aquatic isolates, caused substantial depolymerization indicative for the effective employment of quinone redox cycling as biodegradation tool. Our results may also open up new paths to utilize diverse fungi for the bioremediation of recalcitrant organic pollutants.
    Keywords: Environmental Microbiology
    Print ISSN: 0378-1097
    Electronic ISSN: 1574-6968
    Topics: Biology
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  • 3
    Publication Date: 2018
    Description: 〈span〉〈div〉Summary〈/div〉The correct estimation of site-specific attenuation is crucial for the assessment of seismic hazard. Downhole instruments provide in this context valuable information to constrain attenuation directly from data. In this study, we apply an interferometric approach to this problem by deconvolving seismic motions recorded at depth with those recorded at the surface. In doing so, incident and surface-reflected waves can be separated. We apply this technique not only to earthquake data but also to recordings of ambient vibrations. We compute the transfer function between incident and surface-reflected waves in order to infer frequency dependent quality factors for S-waves. The method is applied to a 87 m deep borehole sensor and a co-located surface instrument situated at a hard-rock site in West Bohemia/Vogtland, Germany. We show that the described method provides comparable attenuation estimates using either earthquake data or ambient noise for frequencies between 5-15 Hz. Moreover, a single hour of noise recordings seems to be sufficient to yield stable deconvolution traces and quality factors, thus, offering a fast and easy way to derive attenuation estimates from borehole recordings even in low to mid seismicity regions.〈/span〉
    Print ISSN: 2051-1965
    Electronic ISSN: 1365-246X
    Topics: Geosciences
    Published by Oxford University Press on behalf of The Deutsche Geophysikalische Gesellschaft (DGG) and the Royal Astronomical Society (RAS).
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  • 4
    Publication Date: 2016-02-24
    Description: Genetic diseases constitute the most important cause for end-stage renal disease in children and adolescents. Mutations in the ACTN4 gene, encoding the actin-binding protein α-actinin-4, are a rare cause of autosomal dominant familial focal segmental glomerulosclerosis (FSGS). Here, we report the identification of a novel, disease-causing ACTN4 mutation (p.G195D, de novo ) in a sporadic case of childhood FSGS using next generation sequencing. Proteome analysis by quantitative mass spectrometry (MS) of patient-derived urinary epithelial cells indicated that ACTN4 levels were significantly decreased when compared with healthy controls. By resolving the peptide bearing the mutated residue, we could proof that the mutant protein is less abundant when compared with the wild-type protein. Further analyses revealed that the decreased stability of p.G195D is associated with increased ubiquitylation in the vicinity of the mutation site. We next defined the ACTN4 interactome, which was predominantly composed of cytoskeletal modulators and LIM domain-containing proteins. Interestingly, this entire group of proteins, including several highly specific ACTN4 interactors, was globally decreased in the patient-derived cells. Taken together, these data suggest a mechanistic link between ACTN4 instability and proteome perturbations of the ACTN4 interactome. Our findings advance the understanding of dominant effects exerted by ACTN4 mutations in FSGS. This study illustrates the potential of genomics and complementary, high-resolution proteomics analyses to study the pathogenicity of rare gene variants.
    Print ISSN: 0964-6906
    Electronic ISSN: 1460-2083
    Topics: Biology , Medicine
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  • 5
    Publication Date: 2012-01-20
    Description: SUMMARY Tsunami early warning (TEW) is a challenging task as a decision has to be made within few minutes on the basis of incomplete and error-prone data. Deterministic warning systems have difficulties in integrating and quantifying the intrinsic uncertainties. In contrast, probabilistic approaches provide a framework that handles uncertainties in a natural way. Recently, we have proposed a method using Bayesian networks (BNs) that takes into account the uncertainties of seismic source parameter estimates in TEW. In this follow-up study, the method is applied to 10 recent large earthquakes offshore Sumatra and tested for its performance. We have evaluated both the general model performance given the best knowledge we have today about the source parameters of the 10 events and the corresponding response on seismic source information evaluated in real-time. We find that the resulting site-specific warning level probabilities represent well the available tsunami wave measurements and observations. Difficulties occur in the real-time tsunami assessment if the moment magnitude estimate is severely over- or underestimated. In general, the probabilistic analysis reveals a considerably large range of uncertainties in the near-field TEW. By quantifying the uncertainties the BN analysis provides important additional information to a decision maker in a warning centre to deal with the complexity in TEW and to reason under uncertainty.
    Print ISSN: 0956-540X
    Electronic ISSN: 1365-246X
    Topics: Geosciences
    Published by Oxford University Press on behalf of The Deutsche Geophysikalische Gesellschaft (DGG) and the Royal Astronomical Society (RAS).
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  • 6
    Publication Date: 2012-06-28
    Description: Regulation of the positive transcription elongation factor, P-TEFb, plays a major role in controlling mammalian transcription and this is accomplished in part by controlled release of P-TEFb from the 7SK snRNP that sequesters the kinase in an inactive state. We demonstrate here that a similar P-TEFb control system exists in Drosophila . We show that an RNA previously suggested to be a 7SK homolog is, in fact, associated with P-TEFb, through the action of a homolog of the human HEXIM1/2 proteins (dHEXIM). In addition, a Drosophila La related protein (now called dLARP7) is shown to be the functional homolog of human LARP7. The Drosophila 7SK snRNP (d7SK snRNP) responded to treatment of cells with P-TEFb inhibitors and to nuclease treatment of cell lysates by releasing P-TEFb. Supporting a critical role for the d7SK snRNP in Drosophila development, dLARP7 and dHEXIM were found to be ubiquitously expressed throughout embryos and tissues at all stages. Importantly, knockdown of dHEXIM was embryonic lethal, and reduction of dHEXIM in specific tissues led to serious developmental defects. Our results suggest that regulation of P-TEFb by the d7SK snRNP is essential for the growth and differentiation of tissues required during Drosophila development.
    Print ISSN: 0305-1048
    Electronic ISSN: 1362-4962
    Topics: Biology
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  • 7
    Publication Date: 2012-08-08
    Description: Myelin is essential for the rapidity of saltatory nerve conduction, and also provides trophic support for axons to prevent axonal degeneration. Two critical determinants of myelination are SOX10 and EGR2/KROX20. SOX10 is required for specification of Schwann cells from neural crest, and is required at every stage of Schwann cell development. Egr2/Krox20 expression is activated by axonal signals in myelinating Schwann cells, and is required for cell cycle arrest and myelin formation. To elucidate the integrated function of these two transcription factors during peripheral nerve myelination, we performed in vivo ChIP-Seq analysis of myelinating peripheral nerve. Integration of these binding data with loss-of-function array data identified a range of genes regulated by these factors. In addition, although SOX10 itself regulates Egr2/Krox20 expression, leading to coordinate activation of several major myelin genes by the two factors, there is a large subset of genes that are activated independent of EGR2. Finally, the results identify a set of SOX10-dependent genes that are expressed in early Schwann cell development, but become subsequently repressed by EGR2/KROX20.
    Print ISSN: 0305-1048
    Electronic ISSN: 1362-4962
    Topics: Biology
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  • 8
    Publication Date: 2016-11-01
    Description: DNA polymerase (Pol) is a unique A-family polymerase that is essential for alternative end-joining (alt-EJ) of double-strand breaks (DSBs) and performs translesion synthesis. Because Pol is highly expressed in cancer cells, confers resistance to ionizing radiation and chemotherapy agents, and promotes the survival of homologous recombination (HR) deficient cells, it represents a promising new cancer drug target. As a result, identifying substrates that are selective for this enzyme is a priority. Here, we demonstrate that Pol efficiently and selectively incorporates into DNA large benzo-expanded nucleotide analogs (dxAMP, dxGMP, dxTMP, dxAMP) which exhibit canonical base-pairing and enhanced base stacking. In contrast, functionally related Y-family translesion polymerases exhibit a severely reduced ability to incorporate dxNMPs, and all other human polymerases tested from the X, B and A families fail to incorporate them under the same conditions as Pol. We further find that Pol is inhibited after multiple dxGMP incorporation events, and that Pol efficiency for dxGMP incorporation approaches that of native dGMP. These data demonstrate a unique function for Pol in incorporating synthetic large-sized nucleotides and suggest the future possibility of the use of dxG nucleoside or related prodrug analogs as selective inhibitors of Pol activity.
    Print ISSN: 0305-1048
    Electronic ISSN: 1362-4962
    Topics: Biology
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  • 9
    Publication Date: 2014-07-05
    Description: Lewy bodies, a pathological hallmark of Parkinson's disease (PD), contain aggregated alpha-synuclein (αSyn), which is found in several modified forms and can be discovered phosphorylated, ubiquitinated and truncated. Aggregation-prone truncated species of αSyn caused by aberrant cleavage of this fibrillogenic protein are hypothesized to participate in its sequestration into inclusions subsequently leading to synaptic dysfunction and neuronal death. Here, we investigated the role of calpain cleavage of αSyn in vivo by generating two opposing mouse models. We crossed into human [A30P]αSyn transgenic (i) mice deficient for calpastatin, a calpain-specific inhibitor, thus enhancing calpain activity (SynCAST(–)) and (ii) mice overexpressing human calpastatin leading to reduced calpain activity (SynCAST(+)). As anticipated, a reduced calpain activity led to a decreased number of αSyn-positive aggregates, whereas loss of calpastatin led to increased truncation of αSyn in SynCAST(–). Furthermore, overexpression of calpastatin decreased astrogliosis and the calpain-dependent degradation of synaptic proteins, potentially ameliorating the observed neuropathology in [A30P]αSyn and SynCAST(+) mice. Overall, our data further support a crucial role of calpains, particularly of calpain 1, in the pathogenesis of PD and in disease-associated aggregation of αSyn, indicating a therapeutic potential of calpain inhibition in PD.
    Print ISSN: 0964-6906
    Electronic ISSN: 1460-2083
    Topics: Biology , Medicine
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  • 10
    Publication Date: 2018-03-29
    Print ISSN: 0035-8711
    Electronic ISSN: 1365-2966
    Topics: Physics
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