KEGGconverter: a tool for the in-silico modelling of metabolic networks of the KEGG Pathways database

Background  

The KEGG Pathway database is a valuable collection of metabolic pathway maps. Nevertheless, the production of simulation capable metabolic networks from KEGG Pathway data is a challenging complicated work, regardless the already developed tools for this scope. Originally used for illustration purposes, KEGG Pathways through KGML (KEGG Markup Language) files, can provide complete reaction sets and introduce species versioning, which offers advantages for the scope of cellular metabolism simulation modelling. In this project, KEGGconverter is described, implemented also as a web-based application, which uses as source KGML files, in order to construct integrated pathway SBML models fully functional for simulation purposes.     

Composition and distribution of carrabiose moieties in hybrid kappa-/iota-carrageenans using carrageenases

Hybrid kappa/iota-carrageeans extracted from Gigartina skottsbergii, Chondracanthus chamisso?, and Chondrus crispus were incubated with Pseudoalteromonas carrageenovora kappa-carrageenase and Alteromonas fortis iota-carrageenase. The degradation products as well as the resistant fraction were fully characterized by chromatography, NMR, and mass spectrometry. The low percentage of degradation observed after treatment by the iota-carrageenase suggests that long segments of iota-carrabiose or block of iota-carrageenan are low in abundance. The degradation products of the kappa-carrageenase allow discriminating three modes of kappa-carrabiose distribution: blocks of kappa-carrabiose, kappa-carrabiose rich fraction containing iota-carrabiose units probably randomly distributed, and iota-carrabiose rich fraction which corresponds to the resistant fraction. The proportions of each fraction were related to the botanical origin as well as the place of growth of the seaweed.     

Antioxidant Properties of Fruits and Vegetables Shots and Juices: An Electron Paramagnetic Resonance Study

The antioxidant activity of some commercially available fruit and vegetable juices was evaluated with regard to their radical scavenging activity against the stable free radical 4-hydroxy-2,2,6,6-tetramethyl-l-piperidinyloxy (TEMPOL) monitored by electron paramagnetic resonance (EPR) spectroscopy. TEMPOL is a stable nitroxide free radical characterized by a well-defined EPR spectrum consisting of three peaks. The integral intensity of the EPR spectra of TEMPOL was decreased upon juice addition, and the decrease was dose dependent. EPR spectroscopy using stable free radicals provides a simple, rapid, and sensitive method for the determination of antioxidant activity of fruit and vegetable juices. The method was standardized by using the standard antioxidant compound Trolox, and the antioxidant activity of the juices was expressed as Trolox equivalents. When concentrated juices of fruits and vegetables (shots) were considered, the evaluated antioxidant activity was almost twofold higher than that of the conventional, non-concentrated ones. Fruits and vegetables shots also showed very good stability during storage. This finding indicates that natural antioxidant compounds contained in commercially available concentrated juices are not eliminated or inactivated when the juices are kept refrigerated according to the instructions of the manufacturer.     

An immunogold evaluation of cortical actin reorganization in pubertal Sertoli cells in vitro after PMA treatment

The aim of the present study was to investigate stress fibers and cortical actin reorganization in pubertal Sertoli cells in vitro after PMA treatment. Actin was studied by means of immunogold labeling, using the 'Progressive Lowering of Temperature' technique (PLT). Actin rearrangement was evaluated by a quantitative analysis of the gold label distribution. Eight hours after addition of 10(-7) M PMA, rearrangement of cortical actin was minimal, but stress fiber perturbation was significant as shown by immunogold labeling distribution measurements. PMA-mediated F-actin reorganization and redistribution in non-neoplastic cells is discussed, since these phenomena have been closely linked with cell transformation.     

Prognostic significance of metallothionein expression in renal cell carcinoma

BACKGROUND: Metallothionein (MT) protein expression deficiency has been implicated in carcinogenesis while MT over expression in tumors is indicative of tumor resistance to anti-cancer treatment. The purpose of the study was to examine the expression of MT expression in human renal cell carcinoma (RCC) and to correlate MT positivity, the pattern and extent of MT expression with tumor histologic cell type and nuclear grade, pathologic stage and patients' survival. PATIENTS AND METHODS: The immunohistochemical expression of MT was determined in 43 formalin-fixed and paraffin-embedded RCC specimens, using a mouse monoclonal antibody that reacts with both human MT-I and MT-II. Correlation was sought between immunohistochemical (MT positivity, intensity and extension of staining) and clinico-pathological data (histological cell type, tumor nuclear grade, pathologic stage and patients' survival). RESULTS: Positive MT staining was present in 21 cases (49%), being mild/moderate and intense in 8 and 13 cases, respectively. The pattern was cytoplasmic in 7 cases and was both cytoplasmic and nuclear in 14 cases. MT expression in a percentage of up to 25% of tumor cells (negative MT staining included) was observed in 31 cases, in a percentage 25-50% of tumor cells in 7 cases, and in a percentage of 50-75% of tumor cells in 5 cases. There was no significant correlation of MT intensity of staining to histological type, stage and patients' survival, while it was inversely correlated to higher tumor nuclear grade. MT extent of staining did not correlate with histological type, nuclear grade, and pathologic stage while a statistically significant association was found with patients' survival. CONCLUSIONS: The inverse correlation between MT staining intensity and tumor nuclear grade in RCC suggests a role of MT in tumor differentiation process. Since extent of MT expression is inversely correlated with survival it may be possibly used as a clinical prognostic parameter.     

Low-Protein Diet Induces IRE1α-Dependent Anticancer Immunosurveillance

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Gene ARMADA: an integrated multi-analysis platform for microarray data implemented in MATLAB

Background  

The microarray data analysis realm is ever growing through the development of various tools, open source and commercial. However there is absence of predefined rational algorithmic analysis workflows or batch standardized processing to incorporate all steps, from raw data import up to the derivation of significantly differentially expressed gene lists. This absence obfuscates the analytical procedure and obstructs the massive comparative processing of genomic microarray datasets. Moreover, the solutions provided, heavily depend on the programming skills of the user, whereas in the case of GUI embedded solutions, they do not provide direct support of various raw image analysis formats or a versatile and simultaneously flexible combination of signal processing methods.