HumboldtUniversity Berlin

Berlin, Germany

HumboldtUniversity Berlin

Berlin, Germany
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Carzino R.,Italian Institute of Technology | Pignatelli F.,Italian Institute of Technology | Farina D.,Italian Institute of Technology | Torre B.,Italian Institute of Technology | And 10 more authors.
Nanotechnology | Year: 2014

Exploiting the intrinsic photosensitivity of TiO2nanoparticles, we demonstrated how ultraviolet (UV) pulsed laser irradiation of acrylate polymer nanocomposite solutions can separate the initial clusters of these colloidal semiconductor nanorods into clearly distinct units. From the irradiated solutions, optically clear nanocomposite films are obtained which exhibit enhanced optical properties with respect to the nanocomposites obtained without previous UV treatment. © 2014 IOP Publishing Ltd.

Engelhard C.,Free University of Berlin | Wang X.,University Paris - Sud | Robles D.,University Paris - Sud | Moldt J.,University of Marburg | And 6 more authors.
Plant Cell | Year: 2014

Cryptochromes are blue light receptors with multiple signaling roles in plants and animals. Plant cryptochrome (cry1 and cry2) biological activity has been linked to flavin photoreduction via an electron transport chain comprising three evolutionarily conserved tryptophan residues known as the Trp triad. Recently, it has been reported that cry2 Trp triad mutants, which fail to undergo photoreduction in vitro, nonetheless show biological activity in vivo, raising the possibility of alternate signaling pathways. Here, we show that Arabidopsis thaliana cry2 proteins containing Trp triad mutations indeed undergo robust photoreduction in living cultured insect cells. UV/Vis and electron paramagnetic resonance spectroscopy resolves the discrepancy between in vivo and in vitro photochemical activity, as small metabolites, including NADPH, NADH, and ATP, were found to promote cry photoreduction even in mutants lacking the classic Trp triad electron transfer chain. These metabolites facilitate alternate electron transfer pathways and increase light-induced radical pair formation. We conclude that cryptochrome activation is consistent with a mechanism of light-induced electron transfer followed by flavin photoreduction in vivo. We further conclude that in vivo modulation by cellular compounds represents a feature of the cryptochrome signaling mechanism that has important consequences for light responsivity and activation. © 2014 American Society of Plant Biologists. All rights reserved.

Toenjes R.,University of Potsdam | Sokolov I.M.,HumboldtUniversity Berlin | Postnikov E.B.,Kursk State University
European Physical Journal B | Year: 2014

We present a detailed analysis of the eigenfunctions of the Fokker-Planck operator forthe Lévy-Ornstein-Uhlenbeck process, their asymptotic behavior and recurrence relations,explicit expressions in coordinate space for the special cases of the Ornstein-Uhlenbeckprocess with Gaussian and with Cauchy white noise and for the transformation kernel, whichmaps the fractional Fokker-Planck operator of the Cauchy-Ornstein-Uhlenbeck process to thenon-fractional Fokker-Planck operator of the usual Gaussian Ornstein-Uhlenbeck process. Wealso describe how non-spectral relaxation can be observed in bounded random variables ofthe Lévy-Ornstein-Uhlenbeck process and their correlation functions. © 2014, EDP Sciences, SIF, Springer-Verlag Berlin Heidelberg.

Wandelt S.,HumboldtUniversity Berlin | Starlinger J.,HumboldtUniversity Berlin | Bux M.,HumboldtUniversity Berlin | Leser U.,HumboldtUniversity Berlin
Proceedings of the VLDB Endowment | Year: 2013

Until recently, genomics has concentrated on comparing sequences between species. However, due to the sharply falling cost of sequencing technology, studies of populations of individuals of the same species are now feasible and promise advances in areas such as personalized medicine and treatment of genetic diseases. A core operation in such studies is read mapping, i.e., finding all parts of a set of genomes which are within edit distance k to a given query sequence (k-approximate search). To achieve sufficient speed, current algorithms solve this problem only for one to-be-searched genome and compute only approximate solutions, i.e., they miss some kapproximate occurrences. We present RCSI, Referentially Compressed Search Index, which scales to a thousand genomes and computes the exact answer. It exploits the fact that genomes of different individuals of the same species are highly similar by first compressing the to-be-searched genomes with respect to a reference genome. Given a query, RCSI then searches the reference and all genome-specific individual differences. We propose efficient data structures for representing compressed genomes and present algorithms for scalable compression and similarity search. We evaluate our algorithms on a set of 1092 human genomes, which amount to approx. 3 TB of raw data. RCSI compresses this set by a ratio of 450:1 (26:1 including the search index) and answers similarity queries on a mid-class server in 15 ms on average even for comparably large error thresholds, thereby significantly outperforming other methods. Furthermore, we present a fast and adaptive heuristic for choosing the best reference sequence for referential compression, a problem. © 2013 VLDB Endowment.

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