BioArray Software Environment (BASE): a platform for comprehensive management and analysis of microarray data

The microarray technique requires the organization and analysis of vast amounts of data. These data include information about the samples hybridized, the hybridization images and their extracted data matrices, and information about the physical array, the features and reporter molecules. We present a web-based customizable bioinformatics solution called BioArray Software Environment (BASE) for the management and analysis of all areas of microarray experimentation. All software necessary to run a local server is freely available.     

The vasodilator-stimulated phosphoprotein promotes actin polymerisation through direct binding to monomeric actin

Glucocorticoid induced tumor necrosis factor receptor (GITR) is a new member of the tumor necrosis factor-nerve growth factor receptor superfamily of which the function has not been well studied. The extracellular domain of GITR was produced in Escherichia coli and purified as a single band of predicted M(r) of 18.0 kDa. GITR and GITR ligand were expressed constitutively on the surface of Raw 264.7 macrophage cell line and murine peritoneal macrophages. An extracellular domain of GITR can activate murine macrophages to express inducible nitric oxide synthase and to generate nitric oxide in a dose- and time-dependent manner.     

Absorption and CD spectroscopy and modeling of various LH2 complexes from purple bacteria

The absorption (OD) and circular dichroism (CD) spectra of LH2 complexes from various purple bacteria have been measured and modeled. Based on the lineshapes of the spectra we can sort the LH2 complexes into two distinguishable groups: "acidophila"-like (type 1) and "molischianum"-like (type 2). Starting from the known geometric structures of Rhodopseudomonas (Rps.) acidophila and Rhodospirillum (Rsp.) molischianum we can model the OD and CD spectra of all species by just slightly varying some key parameters: the interaction strength, the energy difference of alpha- and beta-bound B850 bacteriochlorophylls (BChls), the orientation of the B800 and B850 BChls, and the (in)homogeneous broadening. Although the ring size can vary, the data are consistent with all the LH2 complexes having basically very similar structures.     

Essential oil constituents of Valeriana italica and Valeriana tuberosa. Stereochemical and conformational study of 15-acetoxyvaleranone

The chemical composition of the essential oils obtained by hydrodistillation of roots, stems with leaves and inflorescences of Valeriana italica Lam. and Valeriana tuberosa L. were studied by GC/MS. Seventy-three and forty-one constituents were identified from each plant, respectively. The major constituent of the oil obtained from the roots of V. italica was isolated and identified as 15-acetoxyvaleranone. Its stereochemistry and conformation has been studied using NMR spectroscopy and molecular modelling. The oils obtained from V. tuberosa completely lacked the characteristic valerane or kessane sesquiterpenes.     

The metabolism of sulindac enhances its scavenging activity against reactive oxygen and nitrogen species

Sulindac is a sulfoxide prodrug that, in vivo, is converted to the metabolites sulindac sulfide and sulindac sulfone. It is therapeutically used as an anti-inflammatory and analgesic in the symptomatic treatment of acute and chronic rheumatoid arthritis, osteoarthritis, and ankylosing spondylitis. In addition to its anti-inflammatory properties, sulindac and its metabolites have been shown to have an important role in the prevention of colonic carcinogenesis. Although the inhibition of prostaglandin synthesis constitutes the primary mechanism of action of sulindac, it is well known that reactive oxygen species (ROS) and reactive nitrogen species (RNS) are implicated in the pathophysiology of inflammation and cancer. Thus, the aim of this study was to evaluate the scavenging activity of sulindac and its sulfone and sulfide metabolites for an array of ROS (HO*, O2(*-), and HOCl) and RNS (*NO and ONOO-) using in vitro systems. The results we obtained demonstrate that the metabolism of sulindac increases its scavenging activity for all RNS and ROS studied, notably with regard to the scavenging of HOCl. These effects may strongly contribute to the anti-inflammatory and anticarcinogenic efficacy that has been shown for sulindac.     

Etanercept versus etanercept plus methotrexate: a registry-based study suggesting that the combination is clinically more efficacious

Etanercept can be used both as monotherapy and in combination with methotrexate (MTX), but direct comparisons of these two options have not yet been reported. In order to compare the results seen in actual practice between these two options, clinical data on 97 patients followed in the Stockholm TNFα Follow-Up Registry were analysed. In 57 of these patients etanercept was added to previously started MTX while the others were treated with etanercept alone. The two groups had similar levels of disease activity at baseline. After 3 months, a significantly lower mean disease activity score (28-joint count-based disease activity score) was attained by the patients on etanercept plus MTX. In this group, the number of patients achieving European League Against Rheumatism-defined remission was also significantly greater. Other disease outcomes showed non-significant trends in the same direction. These data suggest that the combination of etanercept plus MTX is clinically more efficacious than etanercept alone.