TRANSPATH® is a database about signal transduction events. It provides information about signaling molecules, their reactions and the pathways these reactions constitute. The representation of signaling molecules is organized in a number of orthogonal hierarchies reflecting the classification of the molecules, their species-specific or generic features, and their post-translational modifications. Reactions are similarly hierarchically organized in a three-layer architecture, differentiating between reactions that are evidenced by individual publications, generalizations of these reactions to construct species-independent ‘reference pathways’ and the ‘semantic projections’ of these pathways. A number of search and browse options allow easy access to the database contents, which can be visualized with the tool PathwayBuilder™. The module PathoSign adds data about pathologically relevant mutations in signaling components, including their genotypes and phenotypes. TRANSPATH® and PathoSign can be used as encyclopaedia, in the educational process, for vizualization and modeling of signal transduction networks and for the analysis of gene expression data. TRANSPATH® Public 6.0 is freely accessible for users from non-profit organizations under .
TRANSPATH is a database system about gene regulatory networks that combines encyclopedic information on signal transduction with tools for visualization and analysis. The integration with TRANSFAC, a database about transcription factors and their DNA binding sites, provides the possibility to obtain complete signaling pathways from ligand to target genes and their products, which may themselves be involved in regulatory action. As of July 2002, the TRANSPATH Professional release 3.2 contains about 9800 molecules, >1800 genes and >11 400 reactions collected from approximately 5000 references. With the ArrayAnalyzer, an integrated tool has been developed for evaluation of microarray data. It uses the TRANSPATH data set to identify key regulators in pathways connected with up- or down-regulated genes of the respective array. The key molecules and their surrounding networks can be viewed with the PathwayBuilder, a tool that offers four different modes of visualization. More information on TRANSPATH is available at http://www.biobase.de/pages/products/databases.html.
Background: Currently, there is a gap between purely theoretical studies of the topology of large bioregulatory networks and the practical traditions and interests of experimentalists. While the theoretical approaches emphasize the global characterization of regulatory systems, the practical approaches focus on the role of distinct molecules and genes in regulation. To bridge the gap between these opposite approaches, one needs to combine 'general' with 'particular' properties and translate abstract topological features of large systems into testable functional characteristics of individual components. Here, we propose a new topological parameter -the pairwise disconnectivity index of a network's element -that is capable of such bridging.
A flexible, low-cost energy-harvesting device based on the magnetoelectric (ME) effect was designed using Fe 64 Co 17 Si 7 B 12 as amorphous magnetostrictive ribbons and polyvinylidene fluoride (PVDF) as the piezoelectric element. A 3 cm-long sandwich-type laminated composite was fabricated by gluing the ribbons to the PVDF with an epoxy resin. A voltage multiplier circuit was designed to produce enough voltage to charge a battery. The power output and power density obtained were 6.4 μW and 1.5 mW cm −3 , respectively, at optimum load resistance and measured at the magnetomechanical resonance of the laminate. The effect of the length of the ME laminate on power output was also studied: the power output exhibited decays proportionally with the length of the ME laminate. Nevertheless, good performance was obtained for a 0.5 cm-long device working at 337 KHz within the low radio frequency (LRF) range.
The importance of 2'-OH groups of codons for binding of cognate tRNAs to ribosomal P and A sites was analyzed applying the following strategy. An mRNA of 41 nucleotides was synthesized with the structure C16-GAA-UUC-GUC-C16 coding for glutamic acid (E), phenylalanine (F) and valine (V), respectively, in the middle (EFV-mRNA). A second template, the E(dF)V-mRNA, was identical except that it carried a deoxyribo-codon-dUdUdC- for phenylalanine. tRNA binding to the P site is totally insensitive to the presence or absence of the 2'-OH group of the P-site codon, and tRNA binding to the P site is also not affected if the A-site codon lacks the 2'-OH groups. However, binding is impaired if the deoxy-codon is present at the E site. In sharp contrast, the A-site binding of Ac-aminoacyl-tRNA was severely reduced in the presence of the deoxy-codon at the A site as well as at the P site. The results demonstrate that the correctness of base pairing is also "sensed" via a correct sugar structure of the codon, e.g. positioning of the sugar pucker (2'-OH), during the decoding process at the A site (elongation) but not during the decoding at the P site (initiation).
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