Efficient Reconstruction of Metabolic Pathways by Bidirectional Chemical Search

One of the main challenges in systems biology is the establishment of the metabolome: a catalogue of the metabolites and biochemical reactions present in a specific organism. Current knowledge of biochemical pathways as stored in public databases such as KEGG, is based on carefully curated genomic evidence for the presence of specific metabolites and enzymes that activate particular biochemical reactions. In this paper, we present an efficient method to build a substantial portion of the artificial chemistry defined by the metabolites and biochemical reactions in a given metabolic pathway, which is based on bidirectional chemical search. Computational results on the pathways stored in KEGG reveal novel biochemical pathways

Close-up of primary and secondary asteroseismic CoRoT targets and the ground-based follow-up observations

To optimise the science results of the asteroseismic part of the CoRoT satellite mission a complementary simultaneous ground-based observational campaign is organised for selected CoRoT targets. The observations include both high-resolution spectroscopic and multi-colour photometric data. We present the preliminary results of the analysis of the ground-based observations of three targets. A line-profile analysis of 216 high-resolution FEROS spectra of the delta Sct star HD 50844 reveals more than ten pulsation frequencies in the frequency range 5-18 c/d, including possibly one radial fundamental mode (6.92 c/d). Based on more than 600 multi-colour photometric datapoints of the beta Cep star HD180642, spanning about three years and obtained with different telescopes and different instruments, we confirm the presence of a dominant radial mode nu1=5.48695 c/d, and detect also its first two harmonics. We find evidence for a second mode nu2=0.3017 c/d, possibly a g-mode, and indications for two more frequencies in the 7-8 c/d domain. From Stromgren photometry we find evidence for the hybrid delta Sct/gamma Dor character of the F0 star HD 44195, as frequencies near 3 c/d and 21 c/d are detected simultaneously in the different filters.Comment: 7 pages, 6 figures, HELAS II International Conference "Helioseismology, Asteroseismology and MHD Connections", 2008, J.Phys.: Conf. Ser. 118, 01207

Membrane fluidity matters: Hyperthermia from the aspects of lipids and membranes

Hyperthermia is a promising treatment modality for cancer in combination both with radio- and chemotherapy. In spite of its great therapeutic potential, the underlying molecular mechanisms still remain to be clarified. Due to lipid imbalances and 'membrane defects' most of the tumour cells possess elevated membrane fluidity. However, further increasing membrane fluidity to sensitise to chemo-or radiotherapy could have some other effects. In fact, hyperfluidisation of cell membrane induced by membrane fluidiser initiates a stress response as the heat shock protein response, which may modulate positively or negatively apoptotic cell death. Overviewing some recent findings based on a technology allowing direct imaging of lipid rafts in live cells and lipidomics, novel aspects of the intimate relationship between the 'membrane stress' of tumour cells and the cellular heat shock response will be highlighted. Our findings lend support to both the importance of membrane remodelling and the release of lipid signals initiating stress protein response, which can operate in tandem to control the extent of the ultimate cellular thermosensitivity. Overall, we suggest that the fluidity variable of membranes should be used as an independent factor for predicting the efficacy of combinational cancer therapies

Graph Transformation in Molecular Biology

In the beginning, one of the main fields of application of graph transformation was biology, and more specifically morphology. Later, however, it was like if the biological applications had been left aside by the graph transformation community, just to be moved back into the mainstream these very last years with a new interest in molecular biology. In this paper, we review several fields of application of graph grammars in molecular biology, including: the modeling higherdimensional structures of biomolecules, the description of biochemical reactions, the analysis of metabolic pathways, and their potential use in computational systems biology

Portal supply and venous drainage of the caudate lobe in the healthy human liver. Virtual three-dimensional computed tomography volume study

Objective The venous vascular anatomy of the caudate lobe is exceptional. The purpose of this study was to assess portal inflow and venous outflow volumes of the caudate lobe. Methods Extrahepatic (provided by the first-order branches) versus intrahepatic (provided by the second- to third-order branches) portal inflow, as well as direct (via Spieghel veins) versus indirect (via hepatic veins) venous drainage patterns were analyzed in virtual 3-D liver maps in 140 potential live liver donors. Results The caudate lobe has a greater intrahepatic than extrahepatic portal inflow volume (mean 55 ± 26 vs. 45 ± 26%: p = 0.0763), and a greater extrahepatic than intrahepatic venous drainage (mean 54–61 vs. 39–46%). Intrahepatic drainage based on mean estimated values showed the following distribution: middle > inferior (accessory) > right > left hepatic vein. Conclusions Sacrifice of extrahepatic caudate portal branches can be compensated by the intrahepatic portal supply. The dominant outflow via Spieghel veins and the negligible role of left hepatic vein in caudate venous drainage may suggest reconstruction of caudate outflow via Spieghel veins in instances of extended left hemiliver live donation not inclusive of the middle hepatic vein. The anatomical data and the real implication for living donors must be further verified by clinical studies