901 research outputs found
Microbial networks for bioremediation of chlorinated ethenes
Full text linkWesterhoff, H.V. [Promotor]Boogerd, F.C. [Copromotor]Röling, W.F.M. [Copromotor
Introduction to systems biology
No full textThe developments in the molecular biosciences have made possible a shift to combined molecular and system-level approaches to biological research under the name of Systems Biology. It integrates many types of molecular knowledge, which can best be achieved by the synergistic use of models and experimental data. Many different types of modeling approaches are useful depending on the amount and quality of the molecular data available and the purpose of the model. Analysis of such models and the structure of molecular networks have led to the discovery of principles of cell functioning overarching single species. Two main approaches of systems biology can be distinguished. Top-down systems biology is a method to characterize cells using system-wide data originating from the Omics in combination with modeling. Those models are often phenomenological but serve to discover new insights into the molecular network under study. Bottom-up systems biology does not start with data but with a detailed model of a molecular network on the basis of its molecular properties. In this approach, molecular networks can be quantitatively studied leading to predictive models that can be applied in drug design and optimization of product formation in bioengineering. In this chapter we introduce analysis of molecular network by use of models, the two approaches to systems biology, and we shall discuss a number of examples of recent successes in systems biology
Nodulation of groundnut by Bradyrhizobium: a simple infection process by crack entry
No full textInfection of legumes by rhizobia may occur by immediate intercellular penetration of root cells (crack entry) as an alternative mode to the more elaborate infection through infection threads. The intercellular spreading mode of infection is exemplified through a comprehensive description of root infection by Bradyrhizobium and nodule organogenesis in Arachis hypogaea (groundnut). The role of axillary root hairs and the processes of p ant penetration and intercellular spreading, of internalization and intracellular multiplication and of bacteroid differentiation are described. Then flavonoids and phytoalexins, Nod factors, lectins, and surface poly(oligo)saccharides pass in review. The roles of these various (macro)molecules in the chemical communication between the two symbionts are discussed. Attention is given to special features of groundnut nodules; the presence and functions of oleosomas and other bodies, the presence and functions of nodule lectins, and the evidence for the export of amides from the nodules are discussed. Finally, a speculative model for the groundnut infection process is presented
Modelling nitrogen assimilation of Escherichia coli at low ammonium concentration.
No full textModelling is an important methodology in systems biology research. In this paper, we presented a kinetic model for the complex ammonium assimilation regulation system of Escherichia coli. Based on a previously published model, the new model included AmtB mediated ammonium transport and AmtB regulation by GlnK. Protein concentrations and several parameter values were determined or refined based on new experimental data. Steady state analysis of the model showed that the expression of AmtB increased the ammonium assimilation rate 4-5-fold at external ammonium concentrations as low as 5 μM. Model analysis also suggested that AmtB and GS levels were coupled to maximize the assimilation flux and to avoid a possible negative ammonia diffusion flux. In addition, model simulation of the short term dynamic response to increased external ammonium concentrations implied that the maximal rate for GlnB/GlnK uridylylation/deuridylylation might be higher for a quick response to environmental changes. © 2009 Elsevier B.V. All rights reserved
- …
