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End date: 2011 × Start date: 2011 × DDC: 570 × Type: Text ×

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Now showing 1 - 8 of 8
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    Unraveling gene regulatory networks from time-resolved gene expression data - a measures comparison study
    (London : BioMed Central, 2011) Hempel, Sabrina; Koseska, Aneta; Nikoloski, Zoran; Kurths, Jürgen; Walther, Dirk
    Background Inferring regulatory interactions between genes from transcriptomics time-resolved data, yielding reverse engineered gene regulatory networks, is of paramount importance to systems biology and bioinformatics studies. Accurate methods to address this problem can ultimately provide a deeper insight into the complexity, behavior, and functions of the underlying biological systems. However, the large number of interacting genes coupled with short and often noisy time-resolved read-outs of the system renders the reverse engineering a challenging task. Therefore, the development and assessment of methods which are computationally efficient, robust against noise, applicable to short time series data, and preferably capable of reconstructing the directionality of the regulatory interactions remains a pressing research problem with valuable applications. Results Here we perform the largest systematic analysis of a set of similarity measures and scoring schemes within the scope of the relevance network approach which are commonly used for gene regulatory network reconstruction from time series data. In addition, we define and analyze several novel measures and schemes which are particularly suitable for short transcriptomics time series. We also compare the considered 21 measures and 6 scoring schemes according to their ability to correctly reconstruct such networks from short time series data by calculating summary statistics based on the corresponding specificity and sensitivity. Our results demonstrate that rank and symbol based measures have the highest performance in inferring regulatory interactions. In addition, the proposed scoring scheme by asymmetric weighting has shown to be valuable in reducing the number of false positive interactions. On the other hand, Granger causality as well as information-theoretic measures, frequently used in inference of regulatory networks, show low performance on the short time series analyzed in this study. Conclusions Our study is intended to serve as a guide for choosing a particular combination of similarity measures and scoring schemes suitable for reconstruction of gene regulatory networks from short time series data. We show that further improvement of algorithms for reverse engineering can be obtained if one considers measures that are rooted in the study of symbolic dynamics or ranks, in contrast to the application of common similarity measures which do not consider the temporal character of the employed data. Moreover, we establish that the asymmetric weighting scoring scheme together with symbol based measures (for low noise level) and rank based measures (for high noise level) are the most suitable choices.
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    Charge isomers of myelin basic protein: Structure and interactions with membranes, nucleotide analogues, and calmodulin
    (San Francisco, CA : Public Library of Science, 2011) Wang, C.; Neugebauer, U.; Bürck, J.; Myllykoski, M.; Baumgärtel, P.; Popp, J.; Kursula, P.
    As an essential structural protein required for tight compaction of the central nervous system myelin sheath, myelin basic protein (MBP) is one of the candidate autoantigens of the human inflammatory demyelinating disease multiple sclerosis, which is characterized by the active degradation of the myelin sheath. In this work, recombinant murine analogues of the natural C1 and C8 charge components (rmC1 and rmC8), two isoforms of the classic 18.5-kDa MBP, were used as model proteins to get insights into the structure and function of the charge isomers. Various biochemical and biophysical methods such as size exclusion chromatography, calorimetry, surface plasmon resonance, small angle X-ray and neutron scattering, Raman and fluorescence spectroscopy, and conventional as well as synchrotron radiation circular dichroism were used to investigate differences between these two isoforms, both from the structural point of view, and regarding interactions with ligands, including calmodulin (CaM), various detergents, nucleotide analogues, and lipids. Overall, our results provide further proof that rmC8 is deficient both in structure and especially in function, when compared to rmC1. While the CaM binding properties of the two forms are very similar, their interactions with membrane mimics are different. CaM can be used to remove MBP from immobilized lipid monolayers made of synthetic lipids - a phenomenon, which may be of relevance for MBP function and its regulation. Furthermore, using fluorescently labelled nucleotides, we observed binding of ATP and GTP, but not AMP, by MBP; the binding of nucleoside triphosphates was inhibited by the presence of CaM. Together, our results provide important further data on the interactions between MBP and its ligands, and on the differences in the structure and function between MBP charge isomers.
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    Bioinspired pressure actuated adhesive system
    (Saarbrücken : Leibniz-Institut für Neue Materialien, 2011) Paretkar, Dadhichi R.; Kamperman, Marleen; Schneider, Andreas S.; Arzt, Eduard
    We developed a dry snythetic adhesive system inspired by gecko feet that can switch reversibly from adhesion to non-adhesion with applied pressure as external stimulus. Micropatterned polydimethylsiloxane (PDMS) surfaces with pillars of 30 µm length and 10 µm diameter were fabricated using photolithography and moulding. Adhesion properties were determined with a flat probe as a function of preload. For low and moderate applied compressive preloads, measured adhesion was 7.5 times higher on the patterned surfaces than on flat controls whereas for high preloads adhesion dropped to very low values. In situ imaging showed that the increased preload caused the pillars to deform by bending and/or buckling and to lose their adhesive contact. The elasticity of PDMS aids the pillar recovery to the upright position upon removal of preload enabling repeatability of the switch. Such systems have promising properties e.g. for industrial pick-and-carry operations.
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    Biological materials - bioinspiration on different length scales
    (Saarbrücken : Leibniz-Institut für Neue Materialien, 2011) Weiss, Ingrid
    This article investigates nacre and peacock feather rachis from a molecular and structural point of view, in addition to unifying principles in nature that may control hierarchical functions. This biological material serves as an example for deciphering basic principles in nature that may subsequently be used to design new artificial materials and structures.
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    The intracellular localization of inorganic engineered versus biogenic materials: a comparison
    (Saarbrücken : Leibniz-Institut für Neue Materialien, 2011) Kucki, Melanie; Kraegeloh, Annette
    The uptake of engineered nanoobjects into cells is assumed to significantly account for their potential toxicity. By internalisation, nanoparticles are at least temporarily trapped in the confined volume of a single cell and come into close contact with cellular components, like organelles, structural proteins, enzymes or signalling molecules. As cells are highly structured entities, exhibiting various types of chemically and biologically distinct compartments, first of all the uptake mechanism determines which types of molecules are encountered. In this review, an introduction into the compartmentalisation of cells as well as some uptake processes is given. The localisation of engineered materials within cells of human and animal origin is exemplified. On the other hand, many living organisms are known for their ability to intracellularly precipitate inorganic structures. Some of these biogenic materials are chemically and structurally similar to artificially generated nanostructures. Therefore, the localisation of some biogenic structures within cells is also illustrated. Finally, the relevance of the specific cellular localisation for toxicity is discussed.
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    "Gecko-Workshop 2010" - INM initiates new worldwide conference series
    (Saarbrücken : Leibniz-Institut für Neue Materialien, 2011) Kamperman, Marleen; Arzt, Eduard
    In July 2010, scientists from all over the world gathered at INM to discuss gecko inspired adhesion at a workshop entitled "Bioinspired adhesion: from geckos to new products". The talks covered a range of current issues, including natural attachment systems, developments in artificial gecko-mimics, advances in mechanical models and possible products. This was the first dedicated workshop on this topic. The attendees unanimously agreed to create an international workshop series based on the INM example.
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    Smart skin patterns protect springtails
    (San Francisco, CA : Public Library of Science, 2011) Helbig, R.; Nickerl, J.; Neinhuis, C.; Werner, C.
    Springtails, arthropods who live in soil, in decaying material, and on plants, have adapted to demanding conditions by evolving extremely effective and robust anti-adhesive skin patterns. However, details of these unique properties and their structural basis are still unknown. Here we demonstrate that collembolan skin can resist wetting by many organic liquids and at elevated pressures. We show that the combination of bristles and a comb-like hexagonal or rhombic mesh of interconnected nanoscopic granules distinguish the skin of springtails from anti-adhesive plant surfaces. Furthermore, the negative overhang in the profile of the ridges and granules were revealed to be a highly effective, but as yet neglected, design principle of collembolan skin. We suggest an explanation for the non-wetting characteristics of surfaces consisting of such profiles irrespective of the chemical composition. Many valuable opportunities arise from the translation of the described comb-like patterns and overhanging profiles of collembolan skin into man-made surfaces that combine stability against wear and friction with superior non-wetting and anti-adhesive characteristics.
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    Compomics-utilities: An open-source Java library for computational proteomics
    (London : BioMed Central, 2011) Barsnes, Harald; Vaudel, Marc; Helsens, Kenny; Sickmann, Albert; Walther, Dirk; Berven, Frode S.
    The growing interest in the field of proteomics has increased the demand for software tools and applications that process and analyze the resulting data. And even though the purpose of these tools can vary significantly, they usually share a basic set of features, including the handling of protein and peptide sequences, the visualization of (and interaction with) spectra and chromatograms, and the parsing of results from various proteomics search engines. Developers typically spend considerable time and effort implementing these support structures, which detracts from working on the novel aspects of their tool.