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

Effect of molecular and electronic structure on the light harvesting properties of dye sensitizers

The systematic trends in structural and electronic properties of perylene diimide (PDI) derived dye molecules have been investigated by DFT calculations based on projector augmented wave (PAW) method including gradient corrected exchange-correlation effects. TDDFT calculations have been performed to study the visible absorbance activity of these complexes. The effect of different ligands and halogen atoms attached to PDI were studied to characterize the light harvesting properties. The atomic size and electronegativity of the halogen were observed to alter the relaxed molecular geometries which in turn influenced the electronic behavior of the dye molecules. Ground state molecular structure of isolated dye molecules studied in this work depends on both the halogen atom and the carboxylic acid groups. DFT calculations revealed that the carboxylic acid ligands did not play an important role in changing the HOMO-LUMO gap of the sensitizer. However, they serve as anchor between the PDI and substrate titania surface of the solar cell or photocatalyst. A commercially available dye-sensitizer, ruthenium bipyridine (RuBpy), was also studied for electronic and structural properties in order to make a comparison with PDI derivatives for light harvesting properties. Results of this work suggest that fluorinated, chlorinated, brominated, and iyodinated PDI compounds can be useful as sensitizers in solar cells and in artificial photosynthesis.Comment: Single pdf file, 14 pages with 7 figures and 4 table

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

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

Étude de l’efficacité des agents mucolytiques sur l’élimination du macroagrégat

Les auteurs ont étudié sur des rats les possibilités de l'élimination de l’organisme, sous l’effet de l’inhalation d’aérosols mucolytiques, du macroagrégat de l’albumine sérique humaine marquée à 131I, utilisé en scintigraphie pulmonaire. De tous les aérosols mucolytiques mis à l’épreuve, la N-acétyl-L-cystéine (Mucosolvin) réduit la radioactivité des poumons et du foie dans une mesure importante à la suite d’une inhalation de 40 min (diamètre des particules : 3 µm). La solution alcoolique de diméthyl-polysiloxane (Sicol) s’est avérée moins efficace en ce qui concerne la réduction de la radioactivité des poumons, mais a également accéléré l’élimination du macroagrégat. Aucun résultat n’a été obtenu avec le Tacholiquin dont la substance active est un détergent. Les auteurs montrent l’importance de l’inhalation d’aérosols mucolytiques après examen scintigraphique en vue de réduire la charge corporelle due au radionucléide

Continuous monitoring of radiotherapy through infrared image processing

Abstract Radiation therapy (radiotherapy) is a valuable technique used in medicine cancer treatment. It is a fact that many of the incidents and accidents involve only partial body irradiation and the extremities are the most frequently injured parts of the body. As it is still not general practice to use infrared (IR) thermographic imaging for the more precise diagnosis of local injuries, the availability of these techniques is very rarely mentioned in the publications. In this paper attention is drawn to what was introduced more than a decade ago, namely the use of IR thermographic procedures in diagnosing local radiation injuries. Further justification for introducing these techniques is that, in the relevant cases, the assesment of absorbed radiation dose through the widely known biological indicators or biological dosimetry assays is not always possible

Explicit collision simulation of chemical reactions in a graph based artificial chemistry

A Toy Model of an artificial chemistry that treats molecules as graphs was implemented based on a simple Extended Hückel Theory method. Here we describe an extension of the model that models chemical reactions as the result of “collisions”. In order to avoid a possible bias arising from prescribed generic reaction mechamisms, the reactions are simulated in a way that treats the formation and breakage of individual chemical bonds as elementary operations