TissueDistributionDBs: a repository of organism-specific tissue-distribution profiles

Tissue-distribution profiles are crucial for understanding the characteristics of cells and tissues in terms of their differential expression of genes. Most of the currently available resources for tissue-distribution profiles are either specialized for a few particular organisms, tissue types and disease stages or do not consider the “tissue ontology” levels for the calculation of the tissue-distribution profiles. Therefore, we have developed “TissueDistributionDBs”, a repository of tissue-distribution profiles based on the expressed sequence tags (ESTs) data extracted from the UniGene database by employing “Tissue Ontology” available at BRENDA. To overcome the occurrence of the natural language variations in the EST’s source tissue-type terms, we have generated a “tissue synonym library” and standardized these tissue-type terms by cross-referencing to the controlled vocabulary for tissue-type terms available at BRENDA “Tissue Ontology”. Furthermore, we have provided a quantitative expression for genes among the tissue types at various anatomical levels by constructing “tissue slims”. Concurrently, the expression among tissue types is used for tissue-distribution calculations. The resulting output profiles can be queried by the Sequence Retrieval System (SRS) and are currently available for 20 different model organisms. We benchmarked our database system against the Swissprot database using a set of 40 different tissue types. This database system is useful for the understanding of the tissue-specific expression patterns of genes, which have implications for the identification of possible new therapeutic drug targets, in gene discovery, and in the design and analysis of micro-arrays. TissueDistributionDBs can be accessed via the World Wide Web (www) at http://genius.embnet.dkfz-heidelberg.de/menu/tissue_db/.     

Rationalizing perhydrolase activity of aryl-esterase and subtilisin Carlsberg mutants by molecular dynamics simulations of the second tetrahedral intermediate state

The perhydrolysis reaction in hydrolases is an important example of catalytic promiscuity and has many potential industrial applications. The mechanisms of perhydrolase activity of a subtilisin Carlsberg mutant and of an aryl-esterase mutant have been investigated using classical molecular dynamics simulations of the second tetrahedral intermediate (TI) state. The simulations demonstrated that hydrogen bonding between the second TI of the perhydrolysis reaction is possible in the mutants but not wild type. The stabilization by hydrogen bonds was specific for the perhydrolysis intermediate and either no hydrogen bonding or only weakened hydrogen bonding to the second TI state of the hydrolysis reaction was observed. Furthermore, a significant hindrance to the formation of the catalytically important hydrogen bond between His64 and Ser221 in the catalytic triad by competing hydrogen bonds was found for the subtilisin mutant but not wild type enzyme in case of the hydrolysis intermediate. The opposite was observed in case of the perhydrolysis intermediate. The result offers a qualitative explanation for the overall reduced hydrolysis activity of the subtilisin mutant. In addition, the simulations also explain qualitatively the perhydrolysis activity of the enzyme variants and may be helpful for designing enzyme mutants with further improved perhydrolysis activity.     

Theoretical analysis of an optimal control problem of conductive–convective–radiative heat transfer

The problem of optimal heat removal from a three-dimensional domain is considered. The specific of the study consist in accounting for the radiative heat transfer. The so-called P₁ approximation of the radiative heat transfer equation is used, which reduces the model to a nonlinear elliptic system. A problem of optimal boundary control of this system is considered. The solvability of the control problem is proved, and necessary optimality conditions of first order are derived. Examples of non-singularity of these conditions are given.     

Adsorption of hydrogen and of oxygen on an open metal surface-HREELS investigation at Ni(311)

The adsorption behavior of hydrogen and oxygen on the stepped Ni(311) surface has been investigated by HREELS. A series of metastable phases was found for hydrogen adsorption at low temperatures with a succession of different adsorption sites indicated by the following loss peaks: 55 and 149 meV for the threefold site, shifting with higher coverage to 65 and 155 meV, respectively; 40 and 90 meV for the fourfold site, shifting to 35 and 85 meV with coverage; and 110 and 124 meV for an additional site between close packed rows. Room temperature adsorption of hydrogen leads to the reconstruction of the surface with occupation of three- and fourfold sites, represented by loss peaks at 60 and 145 meV for the threefold site and 74 meV for the fourfold site. This phase is the thermodynamically stable one. Oxygen is most likely initially adsorbed on a bridge site (loss peak at 66 meV). The stepped surface is already oxidized at very low exposures to oxygen, as seen by the characteristic vibration for oxide islands at 55 meV and later by the Fuchs-Kliewer mode of NiO at 68 meV.     

Classes caractéristiques pour les cônes projectifs et homologie d'intersection

Sans résumé En hommage à Jean Louis Verdier