Genetic Network Analyzer: qualitative simulation of genetic regulatory networks

MOTIVATION: The study of genetic regulatory networks has received a major impetus from the recent development of experimental techniques allowing the measurement of patterns of gene expression in a massively parallel way. This experimental progress calls for the development of appropriate computer tools for the modeling and simulation of gene regulation processes. RESULTS: We present Genetic Network Analyzer (GNA), a computer tool for the modeling and simulation of genetic regulatory networks. The tool is based on a qualitative simulation method that employs coarse-grained models of regulatory networks. The use of GNA is illustrated by a case study of the network of genes and interactions regulating the initiation of sporulation in Bacillus subtilis. AVAILABILITY: GNA and the model of the sporulation network are available at http://www-helix.inrialpes.fr/gna.     

13C-NMR spectroscopic investigation of α- and β-1,4-D-glucose homooligomers

A complete, unambiguous assignment of all the ¹³C signals of cellobiose and maltose has been achieved using methods such as selective proton decoupling, ¹³C selective spin labeling, and isotopic chemical shift induced by deuterium. The chemical-shift variation of the ¹³C signals with the degree of polymerization in each α or β (1 → 4) series is discussed. The chemical-shift dependence on temperature and solvent in these two series is shown and interpreted in terms of modifications of the solvation and of the conformation.     

Children's competition in a natural setting: evidence for the ideal free distribution

Little is known of the foraging abilities of children in modern cultures, especially when children forage in groups. Here we present a test of optimal foraging theory in groups of street children working for money. The children we observed were selling bottles of water to drivers distributed in two lanes at a crossroad of Istanbul, Turkey. As predicted by the ideal free distribution (a model of optimal group foraging), the ratio of children working in the two lanes was sensitive to the ratio of cars (and therefore the ratio of potential buyers) present in each lane. Deviations from the ideal free model arose largely from numerical restrictions on the set of possible ratios compatible with a small group size. When these constraints were taken into account, optimal behavior emerged as a robust aspect of the children's group distribution. Our results extend to human children aspects of group foraging that were previously tested in human adults or other animal species.     

Increased activin levels in cerebrospinal fluid of rabbits with bacterial meningitis are associated with activation of microglia

Activin, a member of the transforming growth factor superfamily, is upregulated in a number of inflammatory episodes such as septicemia and rheumatoid arthritis. In the CNS, activin has been predominantly assessed in terms of a neuroprotective role. In this report we characterized the activin response in the CNS in a rabbit model of meningitis. In normal animals, cerebrospinal fluid (CSF) activin levels were higher than those in serum, indicating an intracranial secretion of this cytokine. Following intracisternal inoculation with Streptococcus pneumoniae, activin in CSF was unchanged for the first 12 h and then rose progressively; levels were increased approximately 15-fold within 24 h. Activin levels were correlated positively with CSF protein content and with the number of apoptotic neurons in the dentate gyrus. No apparent correlation was observed between CSF activin concentrations and bacterial titer, lactate concentrations or leukocyte density. Using immunohistochemistry, activin staining was localized to epithelial cells of the choroid plexus, cortical neurons and the CA3 region of the hippocampus, with similar staining intensities in both normal and meningitic brains. However, in meningitic brains there was also strong staining in activated microglia and infiltrating macrophages. Taken together, these results demonstrate that activin forms part of the CNS response to immune challenge and may be an important mediator to modulate inflammatory processes in the brain.