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Lerch S.,Max Planck Institute for Polymer Research | Ritz S.,Max Planck Institute for Polymer Research | Ritz S.,Institute of Molecular Biology IMB gGmbH | Bley K.,Max Planck Institute for Polymer Research | And 8 more authors.
Nanomedicine: Nanotechnology, Biology, and Medicine | Year: 2015

Many nanoparticular drug delivery approaches rely on a detailed knowledge of the acidification process during intracellular trafficking of endocytosed nanoparticles (NPs). Therefore we produced a nanoparticular pH sensor composed of the fluorescent pH-sensitive dual wavelength dye carboxy seminaphthorhodafluor-1 (carboxy SNARF-1) coupled to the surface of amino-functionalized polystyrene NPs (SNARF-1-NP). By applying a calibration fit function to confocal laser scanning microscopy (CLSM) images, local pH values were determined. The acidification and ripening process of endo/lysosomal compartments containing nanoparticles was followed over time and was found to progress up to 6. h to reach an equilibrium pH distribution (maximum pH. 5.2 [±. 0.2]). The SNARF-1-NP localization in endo/lysosomal compartments was confirmed by transmission electron microscopy (TEM) and quantitative co-localization analysis with fluorescent endolysosomal marker Rab-proteins by confocal laser scanning microscopy (CLSM). The herein described nanoparticular pH-sensor is a versatile tool to monitor dynamic pH processes inside the endolysosomal compartments. From the Clinical Editor: In this interesting article, the authors elegantly designed a nanoparticular pH sensor with fluorescence probe with the capability to measure intracellular and intravesicular pH changes. The application of this method would enable the further understanding of nanoparticle uptake and intracellular physiology. © 2015 Elsevier Inc.

Casas-Vila N.,Institute of Molecular Biology IMB gGmbH | Scheibe M.,Institute of Molecular Biology IMB gGmbH | Freiwald A.,Institute of Molecular Biology IMB gGmbH | Kappei D.,National University of Singapore | Butter F.,Institute of Molecular Biology IMB gGmbH
BMC Genomics | Year: 2015

Background: To date, telomere research in fungi has mainly focused on Saccharomyces cerevisiae and Schizosaccharomyces pombe, despite the fact that both yeasts have degenerated telomeric repeats in contrast to the canonical TTAGGG motif found in vertebrates and also several other fungi. Results: Using label-free quantitative proteomics, we here investigate the telosome of Neurospora crassa, a fungus with canonical telomeric repeats. We show that at least six of the candidates detected in our screen are direct TTAGGG-repeat binding proteins. While three of the direct interactors (NCU03416 [ncTbf1], NCU01991 [ncTbf2] and NCU02182 [ncTay1]) feature the known myb/homeobox DNA interaction domain also found in the vertebrate telomeric factors, we additionally show that a zinc-finger protein (NCU07846) and two proteins without any annotated DNA-binding domain (NCU02644 and NCU05718) are also direct double-strand TTAGGG binders. We further find two single-strand binders (NCU02404 [ncGbp2] and NCU07735 [ncTcg1]). Conclusion: By quantitative label-free interactomics we identify TTAGGG-binding proteins in Neurospora crassa, suggesting candidates for telomeric factors that are supported by phylogenomic comparison with yeast species. Intriguingly, homologs in yeast species with degenerated telomeric repeats are also TTAGGG-binding proteins, e.g. in S. cerevisiae Tbf1 recognizes the TTAGGG motif found in its subtelomeres. However, there is also a subset of proteins that is not conserved. While a rudimentary core TTAGGG-recognition machinery may be conserved across yeast species, our data suggests Neurospora as an emerging model organism with unique features. © 2015 Casas-Vila et al.

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