A sequence-oriented comparison of gene expression measurements across different hybridization-based technologies

Over the last decade, gene expression microarrays have had a profound impact on biomedical research. The diversity of platforms and analytical methods available to researchers have made the comparison of data from multiple platforms challenging. In this study, we describe a framework for comparisons across platforms and laboratories. We have attempted to include nearly all the available commercial and 'in-house' platforms. Using probe sequences matched at the exon level improved consistency of measurements across the different microarray platforms compared to annotation-based matches. Generally, consistency was good for highly expressed genes, and variable for genes with lower expression values as confirmed by quantitative real-time (QRT)-PCR. Concordance of measurements was higher between laboratories on the same platform than across platforms. We demonstrate that, after stringent preprocessing, commercial arrays were more consistent than in-house arrays, and by most measures, one-dye platforms were more consistent than two-dye platforms.     

The Grafting of Universal T-Helper Epitopes Enhances Immunogenicity of HIV-1 Tat Concurrently Improving Its Safety Profile

Extracellular Tat (eTat) plays an important role in HIV-1 pathogenesis. The presence of anti-Tat antibodies is negatively correlated with disease progression, hence making Tat a potential vaccine candidate. The cytotoxicity and moderate immunogenicity of Tat however remain impediments for developing Tat-based vaccines. Here, we report a novel strategy to concurrently enhance the immunogenicity and safety profile of Tat. The grafting of universal helper T-lymphocyte (HTL) epitopes, Pan DR Epitope (PADRE) and Pol₇₁₁ into the cysteine rich domain (CRD) and the basic domain (BD) abolished the transactivation potential of the Tat protein. The HTL-Tat proteins elicited a significantly higher titer of antibodies as compared to the wild-type Tat in BALB/c mice. While the N-terminal epitope remained immunodominant in HTL-Tat immunizations, an additional epitope in exon-2 was recognized with comparable magnitude suggesting a broader immune recognition. Additionally, the HTL-Tat proteins induced cross-reactive antibodies of high avidity that efficiently neutralized exogenous Tat, thus blocking the activation of a Tat-defective provirus. With advantages such as presentation of multiple B-cell epitopes, enhanced antibody response and importantly, transactivation-deficient Tat protein, this approach has potential application for the generation of Tat-based HIV/AIDS vaccines.     

K-252a and Staurosporine Promote Choline Acetyltransferase Activity in Rat Spinal Cord Cultures

Abstract: The protein kinase inhibitor K-252a increased choline acetyltransferase (ChAT) activity in rat embryonic spinal cord cultures in a dose-dependent manner (EC₅₀ of ∼100 n M ) with maximal stimulatory activity at 300 n M resulting in as much as a fourfold increase. A single application of K-252a completely prevented the marked decline in ChAT activity occurring over a 5-day period following culture initiation. Of 11 kinase inhibitors, only the structurally related inhibitor Staurosporine also increased ChAT activity (EC₅₀ of ∼0.5 n M ). Effective concentrations of K-252a were not cytotoxic or mitogenic and did not alter the total protein content of treated cultures. Insulin-like growth factor I, basic fibroblast growth factor, ciliary neurotrophic factor, and leukemia inhibitory factor yielded dose-dependent increases in ChAT activity in spinal cord cultures. The combination of K-252a with insulin-like growth factor-l or basic fibroblast growth factor increased ChAT activity up to eightfold over that of untreated controls, which was greater than that observed with each compound alone. K-252a combined with ciliary neurotrophic factor or leukemia inhibitory factor demonstrated no additive or synergistic effects on ChAT activity. These results suggest that there are multiple mechanisms for the regulation of ChAT activity in spinal cord cultures. The enhancement of spinal cord ChAT activity by K-252a and Staurosporine defines a new neurotrophic activity for these small organic molecules and raises the possibility that they may activate some regulatory elements in common with the ciliary neurotrophic factor and leukemia inhibitory factor family of neurotrophic proteins.     

Rhinosporidiosis in Delhi, North India: Case Series from a Non-endemic Area and Mini-review

We report three cases of rhinosporidiosis from migrant population of Delhi. Three male patients had sino-nasopharyngeal, nasopharyngeal and nasal rhinosporidiosis, respectively. One patient gave a history of bathing in stagnant water. The diagnosis was made by clinical presentation and microscopic observation of characteristic sporangia of Rhinosporidium seebri in mycological and histopathological investigations. All the patients were successfully treated with complete surgical excision of lesions and cauterization of base. There were no recurrences.     

WISP-3 functions as a ligand and promotes superoxide dismutase activity

WISP-3 (Wnt1 inducible secreted protein-3) mutations have been linked to the connective tissue diseases progressive pseudorheumatoid dysplasia and polyarticular juvenile idiopathic arthritis, both of which are accompanied by disorders in cartilage maintenance/homeostasis. The molecular mechanism of WISP-3 mediated effects in the sustenance of cartilage has not been described in detail. Our previous study illustrates the potential role of WISP-3 in regulating the expression of cartilage-specific molecules that sustain chondrocyte growth and cartilage integrity. The present study was conducted to investigate the mode of action of WISP-3 in greater detail. Experimental results depicted here suggest that WISP-3 can function as a ligand and signal via autocrine and/or paracrine modes upon being secreted by chondrocytes. Furthermore, apart from regulating collagen II and aggrecan expression, WISP-3 may also promote superoxide dismutase expression and activity in chondrocytes.     

Spectroscopic characterization and photobleaching kinetics of hypericin-N-methyl pyrrolidone formulations.

Hypericin (HY) is a promising photosensitizer in photodynamic therapy (PDT). It was recently reported that appropriate use of N-methyl pyrrolidone (NMP) enhanced in vivo PDT efficacy of HY and enhanced in vivo delivery of HY. This present study further investigates the use of NMP and other known non-toxic pharmaceutical additives, polyvinylpyrrolidone (PVP, K29/32) and copolyvidonum (S630), for formulating HY to enhance its delivery with photodynamic activity as a goal in mind. Hence, the first objective of this study was to characterize the solubilization of HY by NMP, K29/32 and S630. Thermodynamic considerations were used to explain the solvation process. Photobleaching is another important property of photosensitizers. There is no report on the photostability of HY in pharmaceutical formulations used for PDT. Therefore, the second objective of this study was to investigate the photobleaching of HY in these formulations. The fluorescence of HY was found to increase significantly in higher concentrations of NMP or when 5% of polymer was co-mixed with 5% of NMP solution. The photobleaching of HY in these formulations followed first-order kinetics. The loss of fluorescence paralleled to the loss of absorption of HY. The formulation of HY with 40% NMP was found to be the most stable.