METANNOGEN: compiling features of biochemical reactions needed for the reconstruction of metabolic networks

Background  

One central goal of computational systems biology is the mathematical modelling of complex metabolic reaction networks. The first and most time-consuming step in the development of such models consists in the stoichiometric reconstruction of the network, i. e. compilation of all metabolites, reactions and transport processes relevant to the considered network and their assignment to the various cellular compartments. Therefore an information system is required to collect and manage data from different databases and scientific literature in order to generate a metabolic network of biochemical reactions that can be subjected to further computational analyses.     

Overexpression of DNA polymerase beta: a genomic instability enhancer process.

DNA polymerase beta (Pol beta) is the most inaccurate of the six DNA polymerases found in mammalian cells. In a normal situation, it is expressed at a constant low level and its role is believed to be restricted to repair synthesis in the base excision repair pathway participating to the genome stability. However, excess of Pol beta, found in some human tumors, could confer an increase in spontaneous mutagenesis and result in a highly mutagenic tolerance phenotype toward bifunctional DNA cross-linking anticancer drugs. Here, we present a hypothesis on the mechanisms used by Pol beta to be a genetic instability enhancer through its overexpression. We hypothesize that an excess of Pol beta perturbs the well-defined specific functions of DNA polymerases developed by the cell and propose Pol beta-mediated gap fillings during DNA transactions like repair, replication, or recombination pathways as key processes to introduce illegitimate deoxyribonucleotides or mutagenic base analogs like those produced by intracellular oxidative processes. These mechanisms may predominate during cellular nonproliferative phases in the absence of DNA replication.     

Structural characterization of the transmembrane and cytoplasmic domains of human CD4

Cluster determinant 4 (CD4) is a type I transmembrane glycoprotein of 58 kDa. It consists of an extracellular domain of 370 amino acids, a short transmembrane region, and a cytoplasmic domain of 40 amino acids at the C-terminal end. We investigated the structure of the 62 C-terminal residues of CD4, comprising its transmembrane and cytoplasmic domains. The five cysteine residues of this region have been replaced with serine and histidine residues in the polypeptide CD4mut. Uniformly 15N and 13C labeled protein was recombinantly expressed in E. coli and purified. Functional binding activity of CD4mut to protein VpU of the human immunodeficiency virus type 1 (HIV-1) was verified. Close to complete NMR resonance assignment of the 1H, 13C, and 15N spins of CD4mut was accomplished. The secondary structure of CD4mut in membrane simulating dodecylphosphocholine (DPC) micelles was characterized based on secondary chemical shift analysis, NOE-based proton-proton distances, and circular dichroism spectroscopy. A stable transmembrane helix and a short amphipathic helix in the cytoplasmic region were identified. The fractional helicity of the cytoplasmic helix appears to be stabilized in the presence of DPC micelles, although the extension of this helix is reduced in comparison to previous studies on synthetic peptides in aqueous solution. The role of the amphipathic helix and its potentially variable length is discussed with respect to the biological functions of CD4.     

Low diversity and high levels of population genetic structuring in introduced eastern mosquitofish (<Emphasis Type="Italic">Gambusia holbrooki</Emphasis>) in the greater Melbourne area,Australia

Eastern mosquitofish (Gambusia holbrooki) were introduced into Australia in 1925 and released to control mosquitoes. Gambusia holbrooki rapidly became invasive in recipient environments and now threaten native fauna. In this study, we used five polymorphic microsatellite loci and sequence from two mitochondrial genes, cytochrome b and cytochrome oxidase I, to evaluate genetic variation, colonisation and movement patterns of introduced G. holbrooki in the greater Melbourne area, and to assist in identifying the feasibility of local eradication. Microsatellite variation was consistently low within populations and there was evidence of bottleneck events for several populations. Populations displayed significant structuring associated with river basins rather than geographic distance, suggesting that habitat connectivity is important for dispersal. However, a few populations within river basins were more closely related to populations in other river basins than within their own basin, most likely reflecting a role of human-assisted dispersal in population establishment. Mitochondrial sequencing revealed only a single haplotype and suggested all populations were founded by individuals from a common source. These genetic data help delineate boundaries for local management strategies.     

A simplified method for the determination of nitric oxide in biological solutions.

A new simplified procedure for determination of nitric oxide (NO) in biological solutions is described utilizing a new reducing system of nitric oxide prior to chemiluminescence. Advantages of the new method makes heating of the reducing solution unnecessary and avoids cooling and condensation of generated vapors. Only traces of acid with a high boiling point are used. The method permits analysis of small sample volumes (200 microL). The basal production of nitric oxide by freshly harvested endothelial cells ranged from 100 to 880 picomoles.     

Tissue slice cultures from humans or rodents: a new tool to evaluate biological effects of heavy ions

The aim of this interdisciplinary project is to establish slice culture preparations from rodents and humans as a new model system for studying effects of X-rays and heavy ions within normal and tumor tissues. The advantage of such slice cultures relies on the conservation of an organotypic environment, the easy treatment and observation by live-imaging microscopy, and the independence from genetic immortalization strategies used to generate cell lines. Rat brains as well as human tumors were cut into 300-μm-thick sections and cultivated in an incubator in a humidified atmosphere at 37°C. This is realized by a membrane-based culture system with a liquid–air interface. With this system, it is possible to keep rodent slices viable for several months. Human brain tumor slices remained vital for at least 21 days. Slices were irradiated with X-rays at the radiation facility of the University Hospital in Frankfurt/Main at doses up to 40 Gy. Heavy ion irradiations were performed at GSI (Darmstadt) with different ions, energies, and doses. The irradiated slices were analyzed by 3D-confocal microscopy following immunostaining for DNA damage, microglia, and proliferation markers. The phosphorylated histone γH2AX proved to be suitable for the detection of ion traversals in this system.     

Cell Penetrating Apidaecin Peptide Interactions with Biomimetic Phospholipid Membranes

Apidaecin peptides from Apis mellifera hemolymph are believed to attack intracellular bacterial targets. Our in vivo results for apidaecins 1a and 1b confirm that bacterial activity is non-lytic, however, the manner in which these peptides pass through the cell membrane to exert this activity is unknown. These data are combined with fluorescence (dye leakage) and quartz crystal microbalance studies to investigate the membrane interaction for these two wildtype peptides. It was found that the peptides penetrate the membrane in a trans-membrane manner. The amount of peptide uptake by the membrane is proportional to the concentration of the peptide, however, this appears to be a dynamic equilibrium which can be almost completely reversed by addition of buffer medium. Interestingly, a small residual mass remains within the membrane and the amount of peptide remaining in the membrane is a function of the buffer-salt concentration viz. in high salt, the residual peptide mass remaining is small whereas at low salt concentration, a larger mass of peptide remains bound. These results support a direct membrane penetration mechanism by the wild type apidaecins 1a and 1b. In both cases the peptide–membrane interaction has a negligible effect on the membrane, although, in high salt a permanent change in the membrane does occur at the highest peptide concentration which does not recover following peptide removal. Stefania Piantavigna and Patricia Czihal contributed equally to this article.     

Age-specific patterns in honeydew production and honeydew composition in the aphid Metopeurum fuscoviride: implications for ant-attendance

The intensity of the mutualistic relationship between aphids and ants depends mainly on the composition and amount of honeydew. We used the model system Tanacetum vulgare-Metopeurum fuscoviride to study age-related differences in honeydew production and composition and its effect on the mutualism between M. fuscoviride and the ant Lasius niger. First and second instar larvae of M. fuscoviride produced only half of the amount of honeydew as older larvae or adults. There were, however, no differences between age classes in the total honeydew sugar concentration, which averaged approx. 80 μg sugar/μl honeydew. Honeydew sugar composition also did not differ between age classes, and melezitose was the dominant sugar (59% in all classes). The amino acid concentration, by contrast, increased significantly with aphid age, reaching 22.6 nmol per μl honeydew in adult M. fuscoviride. This increase was mainly caused by asparagine and glutamine, while there were no differences in the concentrations of the five other regularly detected amino acids and cystine, respectively. The intensity of ant-attendance was significantly lower in colonies of first and second instar larvae than in colonies of older age classes. Ant-attendance correlated with the amount of honeydew produced, and not with the total amino acid concentration.