From systems biology to systems biomedicine

Systems Biology is about combining theory, technology, and targeted experiments in a way that drives not only data accumulation but knowledge as well. The challenge in Systems Biomedicine is to furthermore translate mechanistic insights in biological systems to clinical application, with the central aim of improving patients' quality of life. The challenge is to find theoretically well-chosen models for the contextually correct and intelligible representation of multi-scale biological systems. In this review, we discuss the current state of Systems Biology, highlight the emergence of Systems Biomedicine, and highlight some of the topics and views that we think are important for the efficient application of Systems Theory in Biomedicine.     

Fast Reconstruction of Compact Context-Specific Metabolic Network Models

Systemic approaches to the study of a biological cell or tissue rely increasingly on the use of context-specific metabolic network models. The reconstruction of such a model from high-throughput data can routinely involve large numbers of tests under different conditions and extensive parameter tuning, which calls for fast algorithms. We present fastcore, a generic algorithm for reconstructing context-specific metabolic network models from global genome-wide metabolic network models such as Recon X. fastcore takes as input a core set of reactions that are known to be active in the context of interest (e.g., cell or tissue), and it searches for a flux consistent subnetwork of the global network that contains all reactions from the core set and a minimal set of additional reactions. Our key observation is that a minimal consistent reconstruction can be defined via a set of sparse modes of the global network, and fastcore iteratively computes such a set via a series of linear programs. Experiments on liver data demonstrate speedups of several orders of magnitude, and significantly more compact reconstructions, over a rival method. Given its simplicity and its excellent performance, fastcore can form the backbone of many future metabolic network reconstruction algorithms.     

CLEAN WATER: water detoxification using innovative photocatalysts

Environmental pollution abatement and especially the growing demand for clean water pose one of the most severe challenges worldwide. Besides the scarcity of water resources, the presence of hazardous chemicals with serious adverse health effects, even at extremely low concentrations, impose serious considerations for the quality of drinking water. The rapid evolution of nanoscale science and technology has dramatically expanded the materials’ application potential towards radically new or multifunctional properties rendering nanotechnology an indispensable component in shaping modern environmental science. The nanoscale-perspective maintaining the integrity of the environment is currently the stimulus for the development of innovative and cost-effective functional materials and sustainable processes for water treatment and purification. The CLEAN WATER (EU FP7 collaborative project) aims at the development of an innovative and efficient water detoxification technology exploiting solar energy and nano-engineered titania photocatalysts in combination with nanofiltration membranes. In this approach, nanostructured titania with high UV–visible response will be synthesized and stabilized on nanotubular membranes of controlled pore size and retention efficiency as well as on carbon nanotubes exploiting their high surface area to achieve photocatalytically active nanocomposite membranes. Comparative evaluation of the UV–visible and solar light efficiency of the modified titania photocatalysts for water detoxification will be intensively investigated on various target pollutants ranging from classical water contaminants such us phenols, pesticides and azo-dyes to the extremely hazardous cyanobacterial toxins and emerging endocrine disrupting compounds in order to evaluate/optimize the materials performance and validate their competence on water treatment. Particular efforts will be devoted to the analysis and quantification of degradation products as well as their toxicity. All these will be the crucial components for the fabrication of innovative continuous flow photocatalytic-disinfection-membrane reactors for the implementation of sustainable and cost effective water treatment technologies based on nano-engineered materials.