Hypoxia-induced changes in intragenic DNA methylation correlate with alternative splicing in breast cancer

The tumor microenvironment is marked by gradients in the level of oxygen and nutrients, with oxygen levelsreaching a minimum at the core of the tumor, a condition known as tumor hypoxia. Mediated by members of theHIF family of transcription factors, hypoxia leads to a more aggressive tumor phenotype by transactivation ofseveral genes as well as reprogramming of pre-mRNA splicing. Intragenic DNA methylation, which is known toaffect alternative splicing in cancer, could be one of several reasons behind the changes in splicing patterns underhypoxia. Here, we have tried to establish a correlation between intragenic DNA methylation and alternative usageof exons in tumor hypoxia. First, we have generated a custom hypoxia signature consisting of 34 genes that are upregulated under hypoxia and are direct targets of HIF-1a. Using this gene expression signature, we have successfully stratified publicly available breast cancer patient samples into hypoxia positive and hypoxia negativegroups followed by mining of differentially spliced isoforms between these groups. The Hypoxia Hallmarksignature from MSigDB was also used independently to stratify the same tumor samples into hypoxic andnormoxic. We found that 821 genes were showing differential splicing between samples stratified using a customsignature, whereas, 911 genes were showing differential splicing between samples stratified using the MSigDBsignature. Finally, we performed multiple correlation tests between the methylation levels (b) of microarrayprobes located within 1 kilo base pairs of isoform-specific exons using those exons’ expression levels in the samepatient samples in which the methylation level was recorded. We found that the expression level of one of theexons of DHX32 and BICD2 significantly correlated with the methylation levels, and we were also able to predictpatient survival (p-value: 0.02 for DHX32 and 0.0024 for BICD2). Our findings provide new insights into thepotential functional role of intragenic DNA methylation in modulating alternative splicing during hypoxia.

Treatment of rayon grade pulp drain effluent by upflow anaerobic fixed packed bed reactor (UAFPBR).

The Rayon grade pulp (RGP) drain effluent of pulp and paper mill was studied to find out pollutant loading and its control measures by low cost and efficient treatment method. Upflow anaerobic fixed packed bed reactor (UAFPBR) with brick ballasts as packing material was used for this purpose. This was compared with conventional anaerobic treatment method. The digested slurry was taken as inoculum from the active cow dung biogas plant. After stabilization of the reactors the reduction in pollutant loading was found to be higher in UAFPBR than conventional anaerobic reactor (CAR). Hydraulic retention time (HRT) of 12 hr was optimum for the treatment of effluent when 74.5% COD and 81% BOD reduction was obtained. 30% inoculum concentration was best for the anaerobic treatment of RGP colour drain effluent. The maximum biogas production (1.37 l l-1 of effluent) was when the effluent was inoculated with 30% seeding material. Thus, UAFPBR system was very efficient in terms of BOD, COD, TSS and TDS removal from RGP drain of paper mills in ambient environmental conditions.

Effect of carbon and nitrogen source amendment on synthetic dyes decolourizing efficiency of white-rot fungus, Phanerochaete chrysosporium.

Decolourization activity of Phanerochaete chrysosporium for three synthetic dyes viz., congo red, malachite green and crystal violet and impact of additional carbon and nitrogen supply on decolourization capacity of fungus were investigated. Maximum decolourizing capacity was observed up to 15 ppm. Addition of urea as nitrogen source and glucose as carbon source significantly enhanced decolourizing capacity (up to 87%) of fungus. In all the cases, both colour and COD were reduced more in non-sterilized treatments as compared to sterilized ones. Significant reductions in COD content of dye solutions (79-84%) were recorded by fungus supplied with additional carbon and nitrogen. A highly significant correlation (r = 0.78, p < 0.001) between colour and COD of dye solutions was recorded. Thus, a readily available carbon and nitrogen source is imperative to enhance the bioremediation activity of this fungus which has been the most suitable for synthetic dyes and textile industry wastewater treatment.