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Bio Systems 05/2011; 105(2):107-8. · 1.27 Impact Factor
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ERCIM News. 01/2011; 2011:27-28.
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Comp. Int. and Neurosc. 01/2011; 2011.
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Membrane Computing - 12th International Conference, CMC 2011, Fontainebleau, France, August 23-26, 2011, Revised Selected Papers; 01/2011
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ABSTRACT: Although the number of reconstructed metabolic networks is steadily growing, experimental data integration into these networks is still challenging. Based on elementary flux mode analysis, we combine sequence information with metabolic pathway analysis and include, as a novel aspect, circadian regulation. While minimizing the need of assumptions, we are able to predict changes in the metabolic state and can hypothesise on the physiological role of circadian control in nitrogen metabolism of the green alga Chlamydomonas reinhardtii.
PLoS ONE 01/2011; 6(8):e23026. · 4.09 Impact Factor
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ABSTRACT: Exploration of chronobiological systems emerges as a growing research field within bioinformatics focusing on various applications in medicine, agriculture, and material sciences. From a systems biological perspective, the question arises whether biological control systems for regulation of oscillatory signals and their technical counterparts utilise similar mechanisms. If so, modelling approaches and parameterisation adopted from building blocks can help to identify general components for frequency control in circadian clocks along with gaining insight into mechanisms of clock synchronisation to external stimuli like the daily rhythm of sunlight and darkness. Phase-locked loops could be an interesting candidate in this context. Both, biology and engineering, can benefit from a unified view resulting from systems modularisation. In a first experimental study, we analyse a model of coupled repressilators. We demonstrate its ability to synchronise clock signals in a monofrequential manner. Several oscillators initially deviate in phase difference and frequency with respect to explicit reaction and diffusion rates. Accordingly, the duration of the synchronisation process depends on dedicated reaction and diffusion parameters whose settings still lack to be sufficiently captured analytically.
Computational Intelligence and Neuroscience 01/2011; 2011:262189.
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ABSTRACT: The evaluation of signal transduction networks is a constantly advancing challenge, which requires the use
of the latest modelling techniques to capture system dynamics and properties. State of the art modelling
techniques are drawn from a highly diverse range of different research areas, e.g., mathematics, computer
science, statistics, etc. As a result, the selection of appropriate modelling techniques for a certain research
area has become an arduous task (Heinrich & Schuster, 1996; Hinze & Sturm, 2004; Klipp et al., 2006).
07/2010: pages 227-257; , ISBN: 78-0980733044
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Membrane Computing, 10th International Workshop, WMC 2009, Curtea de Arges, Romania, August 24-27, 2009. Revised Selected and Invited Papers; 01/2009
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Melanie Schmidt,
Gunther Gessner,
Matthias Luff, Ines Heiland,
Volker Wagner,
Marc Kaminski,
Stefan Geimer,
Nicole Eitzinger,
Tobias Reissenweber,
Olga Voytsekh,
Monika Fiedler,
Maria Mittag,
Georg Kreimer
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ABSTRACT: Flagellate green algae have developed a visual system, the eyespot apparatus, which allows the cell to phototax. To further understand the molecular organization of the eyespot apparatus and the phototactic movement that is controlled by light and the circadian clock, a detailed understanding of all components of the eyespot apparatus is needed. We developed a procedure to purify the eyespot apparatus from the green model alga Chlamydomonas reinhardtii. Its proteomic analysis resulted in the identification of 202 different proteins with at least two different peptides (984 in total). These data provide new insights into structural components of the eyespot apparatus, photoreceptors, retina(l)-related proteins, members of putative signaling pathways for phototaxis and chemotaxis, and metabolic pathways within an algal visual system. In addition, we have performed a functional analysis of one of the identified putative components of the phototactic signaling pathway, casein kinase 1 (CK1). CK1 is also present in the flagella and thus is a promising candidate for controlling behavioral responses to light. We demonstrate that silencing CK1 by RNA interference reduces its level in both flagella and eyespot. In addition, we show that silencing of CK1 results in severe disturbances in hatching, flagellum formation, and circadian control of phototaxis.
The Plant Cell 09/2006; 18(8):1908-30. · 8.99 Impact Factor
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ABSTRACT: The unicellular flagellated green alga Chlamydomonas reinhardtii has emerged as a model organism for the study of a variety of cellular processes. Posttranslational control via protein phosphorylation plays a key role in signal transduction, regulation of gene expression, and control of metabolism. Thus, analysis of the phosphoproteome of C. reinhardtii can significantly enhance our understanding of various regulatory pathways. In this study, we have grown C. reinhardtii cultures in the presence of an inhibitor of Ser/Thr phosphatases to increase the phosphoprotein pool. Phosphopeptides from these cells were enriched by immobilized metal-ion affinity chromatography and analyzed by nano-liquid chromatography-electrospray ionization-mass spectrometry (MS) with MS-MS as well as neutral-loss-triggered MS-MS-MS spectra. In this way, we were able to identify 360 phosphopeptides from 328 different phosphoproteins of C. reinhardtii, thus providing new insights into a variety of cellular processes, including metabolic and signaling pathways. Comparative analysis of the phosphoproteome also yielded new functional information on proteins controlled by redox regulation (thioredoxin target proteins) and proteins of the chloroplast 70S ribosome, the centriole, and especially the flagella, for which 32 phosphoproteins were identified. The high yield of phosphoproteins of the latter correlates well with the presence of several flagellar kinases and indicates that phosphorylation/dephosphorylation represents one of the key regulatory mechanisms of eukaryotic cilia. Our data also provide new insights into certain cilium-related mammalian diseases.
Eukaryotic Cell 04/2006; 5(3):457-68. · 3.60 Impact Factor
