Evolving a lingua franca and associated software infrastructure for computational systems biology: the Systems Biology Markup Language (SBML) project

Biologists are increasingly recognising that computational modelling is crucial for making sense of the vast quantities of complex experimental data that are now being collected. The systems biology field needs agreed-upon information standards if models are to be shared, evaluated and developed cooperatively. Over the last four years, our team has been developing the Systems Biology Markup Language (SBML) in collaboration with an international community of modellers and software developers. SBML has become a de facto standard format for representing formal, quantitative and qualitative models at the level of biochemical reactions and regulatory networks. In this article, we summarise the current and upcoming versions of SBML and our efforts at developing software infrastructure for supporting and broadening its use. We also provide a brief overview of the many SBML-compatible software tools available today.     

Phylogenetic analysis of Glomeromycota by partial LSU rDNA sequences

We analyzed the large subunit ribosomal RNA (rRNA) gene [LSU ribosomal DNA (rDNA)] as a phylogenetic marker for arbuscular mycorrhizal (AM) fungal taxonomy. Partial LSU rDNA sequences were obtained from ten AM fungal isolates, comprising seven species, with two new primers designed for Glomeromycota LSU rDNA. The sequences, together with 58 sequences available from the databases, represented 31 AM fungal species. Neighbor joining and parsimony analyses were performed with the aim of evaluating the potential of the LSU rDNA for phylogenetic resolution. The resulting trees indicated that Archaeosporaceae are a basal group in Glomeromycota, Acaulosporaceae and Gigasporaceae belong to the same clade, while Glomeraceae are polyphyletic. The results support data obtained with the small subunit (SSU) rRNA gene, demonstrating that the LSU rRNA gene is a useful molecular marker for clarifying taxonomic and phylogenetic relationships in Glomeromycota.     

Synthesis, tuberculosis inhibitory activity, and SAR study of N-substituted-phenyl-1,2,3-triazole derivatives

The aim of this work was to describe the synthesis, the in vitro anti-Mycobacterium tuberculosis profile, and the structure–activity relationship (SAR) study of new N-substituted-phenyl-1,2,3-triazole-4-carbaldehydes (3a–l). The reactions of aromatic amine hydrochlorides with diazomalonaldehyde (1) produced several N-substituted-phenyl-1,2,3-triazole-4-carbaldehydes (3a–l) in moderate-to-good yields. In order to investigate the influence of the difluoromethylene group on the anti-Mycobacterium activity of these compounds, fluorination of triazoles with DAST converted the corresponding carbaldehyde compounds into new difluoromethyl derivatives (4a–l) in excellent yield. Characterization of all compounds was achieved by spectroscopic means and additional for 1-(4-methylphenyl)-1,2,3-triazole-4-carbaldehyde, 3k by X-ray crystallography. Compounds (3a–l) and (4a–l) have been screened for the inhibitory activity against Mycobacterium tuberculosis H37Rv strain (ATCC 27294) and all of them were able to inhibit the growth of the bacterium. Interestingly, 3a and 3k exhibited the best inhibition with MIC values of 2.5 μg/mL, similar to pharmaceuticals currently used in the treatment of tuberculosis. Our SAR study indicated the importance of the hydrogen bond acceptor subunit (3a–l), the position in the aromatic ring, the planarity of triazole and phenyl rings in these compounds, and a correlation between the uniform HOMO coefficient distribution and the anti-tubercular activity. The significant activity of 3a and 3k pointed them as promising lead molecules for further synthetic and biological exploration.     

DIFFERENCES BETWEEN IN VIVO ABSORPTION AND FLUORESCENCE EXCITATION SPECTRA IN NATURAL SAMPLES OF PHYTOPLANKTON

The fluorescence excitation spectrum of live phytoplankton cells represents the portion of light absorbed that has been effectively transferred to chlorophyll a of photosystem II, whereas light absorbed by photoprotective pigments will not lead to fluorescence. Therefore, the in vivo fluorescence excitation spectrum of phytoplankton has been used as a proxy for the action spectrum of phytoplankton in computations of primary production in the ocean. The distribution of chlorophyll a between photosystems, as well as variations in the pathway of energy inside the photosynthetic membrane, can also influence the fluorescence excitation spectrum. In this study, we investigated the contribution of photoprotective pigments to the differences found between in vivo absorption and fluorescence excitation spectra of phytoplankton measured during two cruises: one from Las Islas Canarias to Nova Scotia and another in the Labrador Sea. A comparison of normalized fluorescence excitation and absorption spectra showed high variability in the difference between absorption and fluorescence in the blue region of the spectrum for samples from the two cruises. This difference was not entirely correlated with the concentration of photoprotective carotenoids. In this paper, results are interpreted in terms of differences in pigment composition and known patterns of energy distribution in the photosystems of different algal groups.     

Phosphotyrosyl-protein phosphatase. Specific inhibition by Zn

Epidermal growth factor stimulates a cyclic AMP-independent protein kinase associated with membrane vesicles derived from human epidermoid carcinoma cells (Carpenter, G., King, L., Jr., and Cohen, S. (1979) J. Biol. Chem. 254,. 4884-4891). The kinase specifically phosphorylates tyrosyl residues in a Mr = 150,000 membrane protein (Ushiro, H., and Cohen, S. (1980) J. Biol. Chem. 255, 8363-8365). We show that the reverse reaction, catalyzed by a phosphotyrosyl-protein phosphatase associated with the membrane, is inhibited by Zn2+. Dephosphorylation of phosphotyrosyl residues in the Mr = 150,000 protein is completely inhibited by Zn2+ at concentrations as low as 10 microM, whereas other divalent cations have no substantial effect. Inhibition of the phosphatase was reversed by EDTA and the activity in membrane preparations was increased by EDTA or fluoride, agents commonly thought to be phosphatase inhibitors. Acid hydrolysis of the membrane proteins followed by analysis of phosphoamino acids by two-dimensional electrophoresis revealed that the phosphatase hydrolyzed phosphotyrosyl in preference to phosphoseryl residues. The specific inhibition of this phosphatase activity by low concentrations of Zn2+ may be indicative of the physiological importance of Zn2+ in the regulation of cellular phosphotyrosyl-protein levels.     

Serial Observations on Patterns of Growth, Myelin Formation, Maintenance and Degeneration in Cultures of New-Born Rat and Kitten Cerebellum

New-born rat and kitten cerebellum may be maintained for prolonged periods (over 5 months) in the Maximow assembly if explanted on to a coverslip previously coated with a thin gel of reconstituted rat tail collagen and fed a glucose-enriched "natural" medium. After a 2 week period of adjustment and early outgrowth, most cultures exhibit myelin formation. Axons located within the surrounding neuroglial sheet of the explant area myelinate. The sheaths are first evident as long, unsegmented, smooth, parallel, refractile lines. Simultaneously, neuronal nuclei tend to assume central positions and powdery granules of Nissl substance and lipoid materials begin to accumulate within the cytoplasm. During prolonged maintenance, axons may increase in width and the myelin may thicken. Some exhibit transient irregularities and swellings. Degeneration of some axons occurs manifested either by (a) progressive swellings and distortions of the myelin sheath and thinning of intervening portions of the axons which finally yield, leaving the swellings as myelin bodies, or by (b) small aneurysm-like distortions of myelin sheaths on thinning axons which become dull, irregular, and thread-like filaments beaded by the former herniations. The observations are compared with previous studies of in vitro and in vivo myelin formation with particular reference to neuronal-neuroglial relationships.     

A strongly fluorescing abnormal chromosome in a malformed child

Summary The case of a sexchromatin negative girl with multiple malformations is presented. A small metacentric chromosome was found to replace her second X chromosome, half of which was strongly fluorescing after staining with Quinacrinedihydrochloride, and late replicating after labelling with tritiated thymidine. The chromosome was interpreted as a translocation chromosome between the long arms of a Y and a partially trisomic autosome.