Subnetwork hierarchies of biochemical pathways

MOTIVATION: The vastness and complexity of the biochemical networks that have been mapped out by modern genomics calls for decomposition into subnetworks. Such networks can have inherent non-local features that require the global structure to be taken into account in the decomposition procedure. Furthermore, basic questions such as to what extent the network (graph theoretically) can be said to be built by distinct subnetworks are little studied. RESULTS: We present a method to decompose biochemical networks into subnetworks based on the global geometry of the network. This method enables us to analyze the full hierarchical organization of biochemical networks and is applied to 43 organisms from the WIT database. Two types of biochemical networks are considered: metabolic networks and whole-cellular networks (also including for example information processes). Conceptual and quantitative ways of describing the hierarchical ordering are discussed. The general picture of the metabolic networks arising from our study is that of a few core-clusters centred around the most highly connected substances enclosed by other substances in outer shells, and a few other well-defined subnetworks. AVAILABILITY: An implementation of our algorithm and other programs for analyzing the data is available from http://www.tp.umu.se/forskning/networks/meta/ SUPPLEMENTARY INFORMATION: Supplementary material is available at http://www.tp.umu.se/forskning/networks/meta/     

Influence of pre-ovulatory insemination and early pregnancy on the infiltration by cells of the immune system in the sow endometrium

The aim of this study was to investigate the distribution of leukocytes in the sow endometrium following insemination and during early pregnancy. Cross-bred multiparous sows (Swedish Landrace x Swedish Yorkshire) were artificially inseminated (AI) once at 20-15 h before ovulation. Blood samples were collected from the jugular vein 1 h before slaughter for analyses of oestradiol-17beta and progesterone levels. The sows were slaughtered at 5-6 h (group I, n = 4) after AI or at different times after ovulation: 20-25 h (group II, n = 4), 70 h (group III, n = 4), day 11 (group IV, n = 3; first day of standing oestrus = day 1) and day 19 (group V, n = 3). Uterine horns were flushed to control for the presence of spermatozoa and neutrophils (groups I-IV) and/or for recovery of oocytes and/or embryos (groups II-IV, control of pregnancy). Mesometrial uterine samples were fixed, embedded in plastic resin and stained with toluidine blue. The surface and glandular epithelia as well as subepithelial and glandular connective tissue layers were examined by light microscopy. A marked number of neutrophils and spermatozoa were observed in the flushings from the uterine horns of sows slaughtered at 5-6 h after insemination. All animals slaughtered after ovulation were pregnant but no morphological effect of pregnancy was observed until day 11. In the surface epithelium, the largest numbers of intraepithelial lymphocytes were found in groups II and III, the smallest number was found in group V. The largest number of lymphocytes within the glandular epithelium was found in group III. The largest number of macrophages within the surface and glandular epithelia were found in group I. Neutrophils were found within the surface epithelium only in groups I and II. In the subepithelial connective tissue layer, a high infiltration of neutrophils was found in groups I and II while the largest number of eosinophils was found in group IV. The largest number of lymphocytes was observed in group V. In conclusion, this study showed a variation in the infiltration and distribution of neutrophils, lymphocytes, macrophages, eosinophils and plasma cells in the endometrium following insemination and during different stages of early pregnancy. Particularly, the pattern of lymphocyte presence on day 19 of pregnancy, indicate that the lymphocyte function may play a role during embryonic attachment in the pig.     

Carbon and nitrogen distribution in the green algal lichens<Emphasis Type="Italic"> Hypogymnia physodes</Emphasis> and<Emphasis Type="Italic"> Platismatia glauca</Emphasis> in relation to nutrient supply

With the aim of understanding how some lichens can survive intensive fertilization we investigated two green algal ( Trebouxia) lichens, Hypogymnia physodes (L.) Nyl. and Platismatia glauca (L.) W. Culb., and compared control (Ctr), and intensively fertilized (F) thalli. We measured total N, proteins and amino acids to assess lichen N status. Chlorophyll a indicated photosynthetic capacity and photobiont mass, ergosterol the metabolic demands of the fungus, and chitin the fungal biomass. For carbon status we measured glucose, the photobiont ( Trebouxia) export product ribitol, and the mycobiont-specific carbohydrates arabitol and mannitol. The F-thalli had 2-3 times higher protein and N concentrations, 5-10 times higher chlorophyll a concentrations, while ergosterol and chitin were doubled. The ribitol concentrations were 4-5 times higher in the F-thalli, while the fungal carbohydrates did not increase to the same extent. The amino acid arginine had increased 60-fold. The F-thalli also had a relatively higher N investment in the photobiont in relation to mycobiont tissue compared to the Ctr-thalli, probably resulting in an increased capacity for carbon assimilation, most possibly required for maintaining the higher nutrient status of the F-thalli. Arginine accumulation possibly avoided toxic effects of accumulated NH4+, albeit binding a significant fraction of assimilated carbon.     

Roles for asparagine endopeptidase in class II MHC-restricted antigen processing

The adaptive immune response depends on the creation of suitable peptides from foreign antigens for display on MHC molecules to T lymphocytes. Similarly, MHC-restricted display of peptides derived from self proteins results in the elimination of many potentially autoreactive T cells. Different proteolytic systems are used to generate the peptides that are displayed as T cell epitopes on class I compared with class II MHC molecules. In the case of class II MHC molecules, the proteases that reside within the endosome/lysosome system of antigen-presenting cells are responsible; surprisingly, however, there are relatively few data on which enzymes are involved. Recently we have asked whether proteolysis is required simply in a generic sense, or whether the action of particular enzymes is needed to generate specific class II MHC-associated T cell epitopes. Using the recently identified mammalian asparagine endopeptidase as an example, we review recent evidence that individual enzymes can make clear and non-redundant contributions to MHC-restricted peptide display.     

Determination of ximelagatran,an oral direct thrombin inhibitor,its active metabolite melagatran,and the intermediate metabolites,in biological samples by liquid chromatography-mass spectrometry

Analytical methods for the determination of ximelagatran, an oral direct thrombin inhibitor, its active metabolite melagatran, and intermediate metabolites, melagatran hydroxyamidine and melagatran ethyl ester, in biological samples by liquid chromatography (LC) positive electrospray ionization mass spectrometry (MS) using selected reaction monitoring are described. Isolation from human plasma was achieved by solid-phase extraction on octylsilica. Analytes and isotope-labelled internal standards were separated by LC utilising a C(18) analytical column and a mobile phase comprising acetonitrile-4 mmol/l ammonium acetate (35:65, v/v) containing 0.1% formic acid, at a flow-rate of 0.75 ml/min. Absolute recovery was approximately 80% for ximelagatran, approximately 60% for melagatran ethyl ester and >90% for melagatran and melagatran hydroxyamidine. Limit of quantification was 10 nmol/l, with a relative standard deviation <20% for each analyte and <5% above 100 nmol/l. Procedures for determination of these analytes in human urine and breast milk, plus whole blood from rat and mouse are also described.     

5-Hydroxytryptamine2B receptors stimulate Ca2+ increases in cultured astrocytes from three different brain regions

The expression of 5-hydroxytryptamine-2B (5-HT2B) receptor mRNA has recently been shown in cultured astrocytes. Here the expression of functional 5-HT2B receptors has been studied in cultured astrocytes from rat cerebral cortex, hippocampus, and brain stem. Fluo-3- and fura-2-based microspectrofluorometry was used for measuring changes in intracellular free calcium concentrations ([Ca2+]i). The 5-HT2B agonist alpha-methyl 5-HT (40 nM) produced rapid transient increases in [Ca2+]i in astrocytes from all three brain regions studied, and these responses were blocked by the selective 5-HT2B antagonist rauwolscine (1 microM). The specificity of the responses to alpha-methyl 5-HT was further demonstrated by the failure of 4-(4-fluorobenzoyl)-1-(4-phenylbutyl)-piperidine oxalate (1 microM), a specific 5-HT2A/5-HT2C antagonist, to block these responses. The 5-HT2B-induced increases in [Ca2+]i persisted in Ca2+-free buffer, indicating that the increase in [Ca2+]i results from mobilization of intracellular Ca2+ stores. The expression of 5-HT2B receptors on astroglial cells was further verified immunohistochemically and by Western blot analysis. These results provide evidence of the existence of 5-HT2B receptors on astrocytes in primary culture.     

Site-selective dephosphorylation of the platelet-derived growth factor beta-receptor by the receptor-like protein-tyrosine phosphatase DEP-1

Ligand stimulation of PDGF beta-receptors leads to autophosphorylation of the regulatory tyrosine 857 and of tyrosine residues that in their phosphorylated form serve as docking sites for Src homology 2 domain-containing proteins. Regulation of the PDGF beta-receptor by protein-tyrosine phosphatases is poorly understood. We have investigated PDGF beta-receptor dephosphorylation by receptor-like protein-tyrosine phosphatase DEP-1 using a cell line with inducible DEP-1 expression and by characterizing in vitro dephosphorylation of the PDGF beta-receptor and of receptor-derived phosphopeptides by DEP-1. After DEP-1 induction PDGF beta-receptor.DEP-1 complexes and reduced receptor tyrosine phosphorylation were observed. Phosphopeptide analysis of the PDGF beta-receptors from DEP-1-expressing cells and of the receptors dephosphorylated in vitro by DEP-1 demonstrated that dephosphorylation of autophosphorylation sites of the receptor differed and revealed that the regulatory Tyr(P)(857) was not a preferred site for DEP-1 dephosphorylation. When dephosphorylation of synthetic receptor-derived peptides was analyzed, the selectivity was reproduced, indicating that amino acid sequence surrounding the phosphorylation sites is the major determinant of selectivity. This notion is supported by the observation that the poorly dephosphorylated Tyr(P)(562) and Tyr(P)(857), in contrast to other analyzed phosphorylation sites, are surrounded by basic amino acid residues at positions -4 and +3 relative to the tyrosine residue. Our study demonstrates that DEP-1 dephosphorylation of the PDGF beta-receptor is site-selective and may lead to modulation, rather than general attenuation, of signaling.