Discovering study-specific gene regulatory networks

Microarrays are commonly used in biology because of their ability to simultaneously measure thousands of genes under different conditions. Due to their structure, typically containing a high amount of variables but far fewer samples, scalable network analysis techniques are often employed. In particular, consensus approaches have been recently used that combine multiple microarray studies in order to find networks that are more robust. The purpose of this paper, however, is to combine multiple microarray studies to automatically identify subnetworks that are distinctive to specific experimental conditions rather than common to them all. To better understand key regulatory mechanisms and how they change under different conditions, we derive unique networks from multiple independent networks built using glasso which goes beyond standard correlations. This involves calculating cluster prediction accuracies to detect the most predictive genes for a specific set of conditions. We differentiate between accuracies calculated using cross-validation within a selected cluster of studies (the intra prediction accuracy) and those calculated on a set of independent studies belonging to different study clusters (inter prediction accuracy). Finally, we compare our method's results to related state-of-the art techniques. We explore how the proposed pipeline performs on both synthetic data and real data (wheat and Fusarium). Our results show that subnetworks can be identified reliably that are specific to subsets of studies and that these networks reflect key mechanisms that are fundamental to the experimental conditions in each of those subsets.

2-Cys peroxiredoxin responds to low temperature and other cues in Caragana jubata, a plant species of cold desert of Himalaya

A 2-Cys peroxiredoxin cDNA (CjPrx) was isolated and characterized from Caragana jubata, a temperate/alpine plant species of high altitude cold desert of Himalaya and Eurasia. The cDNA obtained was 1,064 bp long consisting of an open reading frame of 789 bp encoding 262 amino acids. The calculated molecular mass of the mature protein was 28.88 kDa and pI was 5.84. Deduced amino acid sequence of CjPrx shared a high degree homology with 2-CysPrx proteins from other plants. CjPrx had both the PRX_type 2-Cys domain and thioredoxin-like superfamily domains. CjPrx contained 26.72% α-helices, 6.87% β-turns, 20.61% extended strands and 45.80% random coils, and was a hydrophilic protein. Expression of CjPrx was modulated by low temperature, methyl jasmonate (MJ), salicylic acid and drought stress, but no significant change was observed in response to abscisic acid treatment. Among all the treatments, a strong up-regulation of CjPrx was observed in response to MJ treatment.

Src and Syk are targeted to an anti-inflammatory ethanol extract of Aralia continentalis

ETHNOPHARMACOLOGICAL RELEVANCE

Aralia continentalis Kitagawa (Araliaceae) is a representative ethnomedicinal herbal plant traditionally prescribed in Korea to relieve various inflammatory symptoms. However, the exact molecular mechanism of its anti-inflammatory activity has not been fully investigated.

MATERIALS AND METHODS

The effect of the ethanol extract from the roots of this plant (Ac-EE) on the production of the inflammatory mediator nitric oxide (NO) was studied in RAW264.7 cells. Its effect on inflammatory symptoms (gastritis and hepatitis) in mice was also examined. In particular, the molecular inhibitory mechanism was analysed by measuring the activation of transcription factors and their upstream signalling and the kinase activity of target enzymes.

RESULTS

Ac-EE dose-dependently suppressed NO production in lipopolysaccharide (LPS)-activated RAW264.7 cells. This extract also displayed curative activity against EtOH/HCl-induced gastritis and LPS-induced hepatitis in mice. Ac-EE-mediated anti-inflammatory activity was found to be at the transcriptional level, as it blocked the activation of the nuclear factor (NF)-κB pathway composed of Syk and Src, according to immunoblotting and immunoprecipitation analyses and a kinase assay with whole and nucleus lysates from RAW264.7 cells and mice.

CONCLUSION

Ac-EE may be developed as a functional herbal remedy targeting Syk- and Src-mediated anti-inflammatory mechanisms. Future work using pre-clinical studies will be needed to investigate this possibility.

8-(Tosylamino)quinoline inhibits macrophage-mediated inflammation by suppressing NF-κB signaling

AIM

The macrophage-mediated inflammatory response may contribute to the development of cancer, diabetes, atherosclerosis and septic shock. This study was to characterize several new compounds to suppress macrophage-mediated inflammation.

METHODS

Peritoneal macrophages from C57BL/6 male mice and RAW264.7 cells were examined. Anti-inflammatory activity was evaluated in the cells exposed to lipopolysaccharide (LPS). The mechanisms of the anti-inflammatory activity were investigated via measuring transcription factor activation in response to specific signals and via assaying the activities of the target kinases.

RESULTS

Of 7 candidate compounds tested, 8-(tosylamino)quinoline (8-TQ, compound 7) exhibited the strongest activities in suppressing the production of NO, TNF-α, and PGE(2) in LPS-activated RAW264.7 cells and peritoneal macrophages (the IC(50) values=1-5 μmol/L). This compound (1.25-20 μmol/L) dose-dependently suppressed the expression of the pro-inflammatory genes for iNOS, COX-2, TNF-α, and the cytokines IL-1β and IL-6 at the level of transcription in LPS-activated RAW264.7 cells. 8-TQ (20 μmol/L) significantly suppressed the activation of NF-κB and its upstream signaling elements, including inhibitor of κB (IκBα), IκBα kinase (IKK) and Akt in LPS-activated RAW264.7 cells. In in vivo experiments, oral administration of 20 and 40 mg/kg 8-TQ for 3 d significantly alleviated the signs of LPS-induced hepatitis and HCl/EtOH-induced gastritis, respectively, in ICR mice.

CONCLUSION

8-TQ (compound 7) exerts significant anti-inflammatory activity through the inhibition of the Akt/NF-κB pathway, thus may be developed as a novel anti-inflammatory drug.