A Genome Wide Meta-Analysis Study for Identification of Common Variation Associated with Breast Cancer Prognosis

Objective

Genome wide association studies (GWAs) of breast cancer mortality have identified few potential associations. The concordance between these studies is unclear. In this study, we used a meta-analysis of two prognostic GWAs and a replication cohort to identify the strongest associations and to evaluate the loci suggested in previous studies. We attempt to identify those SNPs which could impact overall survival irrespective of the age of onset.

Methods

To facilitate the meta-analysis and to refine the association signals, SNPs were imputed using data from the 1000 genomes project. Cox-proportional hazard models were used to estimate hazard ratios (HR) in 536 patients from the POSH cohort (Prospective study of Outcomes in Sporadic versus Hereditary breast cancer) and 805 patients from the HEBCS cohort (Helsinki Breast Cancer Study). These hazard ratios were combined using a Mantel-Haenszel fixed effects meta-analysis and a p-value threshold of 5×10⁻⁸ was used to determine significance. Replication was performed in 1523 additional patients from the POSH study.

Results

Although no SNPs achieved genome wide significance, three SNPs have significant association in the replication cohort and combined p-values less than 5.6×10⁻⁶. These SNPs are; rs421379 which is 556 kb upstream of ARRDC3 (HR = 1.49, 95% confidence interval (CI) = 1.27–1.75, P = 1.1×10⁻⁶), rs12358475 which is between ECHDC3 and PROSER2 (HR = 0.75, CI = 0.67–0.85, P = 1.8×10⁻⁶), and rs1728400 which is between LINC00917 and FOXF1.

Conclusions

In a genome wide meta-analysis of two independent cohorts from UK and Finland, we identified potential associations at three distinct loci. Phenotypic heterogeneity and relatively small sample sizes may explain the lack of genome wide significant findings. However, the replication at three SNPs in the validation cohort shows promise for future studies in larger cohorts. We did not find strong evidence for concordance between the few associations highlighted by previous GWAs of breast cancer survival and this study.     

The Effects of Intermittent Fasting during the Month of Ramadan in Chronic Haemodialysis Patients in a Tropical Climate Country

Background

Chronic kidney disease is an emerging problem in the majority Muslim countries. Despite the uncertainties of the risks involved, some Muslim patients undergoing chronic haemodialysis choose to observe intermittent fasting during the month of Ramadan. This study aims to investigate the effect of Ramadan fasting in haemodialysis patients residing in a tropical climate country.

Methods

This prospective cross sectional study recruited Muslim patients on regular haemodialysis from three haemodialysis centres in Kuala Lumpur from 15^th July 2011 to 29^th August 2011. Patients who fasted for any number of days were included (n = 35, 54% female, age 54±11 years). 89% of patients fasted for more than 15 days and 49% were diabetics. Dialysis parameters and blood samples were obtained one week prior to Ramadan and during the last week of Ramadan. The differences in dialysis parameters and biochemical values pre- and end-Ramadan were examined using paired t-test.

Results

Both pre- and post-dialysis weight were significantly decreased during Ramadan fasting compared to the month prior (p = <0.001). There was a significant decrease in the amount of ultrafiltration (p = 0.002). There were no significant differences in dry weight, inter-dialytic weight gain, mean urea reduction ratio or blood pressure measurements comparing pre- and end of Ramadan fasting. There was a significant increase in serum albumin level (p = 0.006) and decrease in serum phosphate level (p = 0.02) at the end of Ramadan.

Conclusion

Ramadan fasting is associated with reduced weight, improved serum albumin and phosphate level in our population of haemodialysis patients. A larger multi-centre study will allow us to understand more about the effects of fasting in this population.     

Cellular Metabolites Enhance the Light Sensitivity of Arabidopsis Cryptochrome through Alternate Electron Transfer Pathways

Cryptochromes are blue light receptors with multiple signaling roles in plants and animals. Plant cryptochrome (cry1 and cry2) biological activity has been linked to flavin photoreduction via an electron transport chain comprising three evolutionarily conserved tryptophan residues known as the Trp triad. Recently, it has been reported that cry2 Trp triad mutants, which fail to undergo photoreduction in vitro, nonetheless show biological activity in vivo, raising the possibility of alternate signaling pathways. Here, we show that Arabidopsis thaliana cry2 proteins containing Trp triad mutations indeed undergo robust photoreduction in living cultured insect cells. UV/Vis and electron paramagnetic resonance spectroscopy resolves the discrepancy between in vivo and in vitro photochemical activity, as small metabolites, including NADPH, NADH, and ATP, were found to promote cry photoreduction even in mutants lacking the classic Trp triad electron transfer chain. These metabolites facilitate alternate electron transfer pathways and increase light-induced radical pair formation. We conclude that cryptochrome activation is consistent with a mechanism of light-induced electron transfer followed by flavin photoreduction in vivo. We further conclude that in vivo modulation by cellular compounds represents a feature of the cryptochrome signaling mechanism that has important consequences for light responsivity and activation.     

Enhanced Phytoremediation of Cadmium-Contaminated Soil by Parthenium hysterophorus Plant: Effect of Gibberellic Acid (GA3) and Synthetic Chelator,Alone and in Combinations

The roles of gibberellic acid (GA₃) and ethylenediaminetetraacetic acid (EDTA) in phytoremediation of cadmium (Cd)-contaminated soil by Parthenium hysterophorus plant was investigated. GA₃ (10^?9, 10^?7, and 10^?5M) was applied as a foliar spray. EDTA was added to soil in a single dose (160 mg/kg soil) and split doses (40 mg/kg soil, four split doses). GA₃ and EDTA were used separately and in various combinations. P. hysterophorus was selected due to its fast growth and unpalatable nature to herbivores to reduce the entrance of metal into the food chain. The Cd phytoextraction potential of the P. hysterophorus plant was evaluated for the first time. Cd significantly reduced plant growth and dry biomass (DBM). GA₃ alone increased the plant growth and biomass in Cd-contaminated soil, whereas EDTA reduced it. GA₃ in combination with EDTA significantly increased the growth and biomass. The highest significant DBM was found in treatment T3 (10^?5M GA₃). All treatments of GA₃ or EDTA significantly enhanced the plant Cd uptake and accumulation compared with control (C1). The highest significant root and stem Cd concentrations were found in the combination treatment T11 (GA₃ 10^?5M + EDTA split doses), whereas in leaves it was found in the EDTA treatments. Cd concentration in plant parts increased in the order of stem < leaves < roots. The combination treatment T9 (GA₃ 10^?7M + EDTA split doses) showed the significantly highest total Cd accumulation (8 times greater than control C1, i.e., only Cd used). The GA₃ treatments accumulated more than 50% of the total Cd in the roots, whereas the EDTA treatments showed more than 50% in the leaves. Root dry biomass showed a positive and significant correlation with Cd accumulation. GA₃ is environment friendly as compared with EDTA. Therefore, further investigation of GA₃ is recommended for phytoremediation research for the remediation of metal-contaminated soil.     

Fish Cholinesterases as Biomarkers of Sublethal Effects of Organophosphorus and Carbamates in Tissues of Labeo Rohita

Organophosphates and carbamates are major agrochemicals that strongly affect different neuroenzymes and the growth of various fish species. Here, we study the effect of sublethal concentrations of profenofos and carbofuran on the activity of acetylcholinesterase (AChE) and butyrylcholinesterase (BuChE) and the associated health risk in fish. Labeo rohita fingerlings were exposed to three sublethal concentrations of profenofos and carbofuran. The minimum cholinesterase activities in the brain, gills, muscle, kidney, liver, and blood were after exposure to profenofos (0.06 mg/L). The minimum AChE and BuChE activities in the brain, gills, muscle, kidney, liver, and blood were after exposure to carbofuran (0.28 and 0.198 mg/L). Exposure to both types of pesticides affected the functions of these organs, including metabolism and neurotransmission, to various extents at different exposure concentrations. These findings suggest that they are required to be properly monitored in the environment, to reduce their toxic effects on nontarget organisms     

Genetic diversity analysis of Zingiber Officinale Roscoe by RAPD collected from subcontinent of India

The present investigation was undertaken for the assessment of 12 accessions of Zingiber officinale Rosc. collected from subcontinent of India by RAPD markers. DNA was isolated using CTAB method. Thirteen out of twenty primers screened were informative and produced 275 amplification products, among which 261 products (94.90%) were found to be polymorphic. The percentage polymorphism of all 12 accessions ranged from 88.23% to 100%. Most of the RAPD markers studied showed different levels of genetic polymorphism. The data of 275 RAPD bands were used to generate Jaccard’s similarity coefficients and to construct a dendrogram by means of UPGMA. Results showed that ginger undergoes genetic variation due to a wide range of ecological conditions. This investigation was an understanding of genetic variation within the accessions. It will also provide an important input into determining resourceful management strategies and help to breeders for ginger improvement program.     

Effect of cadmium on the growth and antioxidant enzymes in two varieties of Brassica juncea

Increasing contamination and higher enrichment ratio of non-essential heavy metal cadmium (Cd) induce various toxic responses in plants when accumulated above the threshold level. These effects and growth responses are genotype and Cd level dependent. An experiment was conducted to analyze the effect of Cd toxicity in Brassica juncea [L] Czern and Coss by selecting its two varieties Varuna and RH-30. Cadmium (0, 25, 50 or 100 mg CdCl₂ kg⁻¹ of soil) fed to soil decreased the values of growth characteristics, activity of nitrate reductase and leaf water potential, whereas activities of antioxidant enzymes and proline content increased with the increasing concentration of Cd, observed at 30 and 60 day stages of growth, in both the varieties. Moreover, Cd uptake by the roots was higher in RH-30 than Varuna. Also the activity of antioxidant enzymes and proline accumulation were higher in Varuna with increasing soil level of Cd. Out of the two varieties, Varuna was more tolerant than RH-30 to Cd stress.     

Missense Mutations in Pyruvate Kinase M2 Promote Cancer Metabolism,Oxidative Endurance,Anchorage Independence,and Tumor Growth in a Dominant Negative Manner

The present study was designed to examine the functional relevance of two heterozygous mutations (H391Y and K422R), observed earlier by us in the Bloom syndrome condition. Cells stably expressing exogenous wild-type or mutant PKM2 (K422R or H391Y) or co-expressing both wild type and mutant (PKM2-K422R or PKM2-H391Y) were assessed for cancer metabolism and tumorigenic potential. Interestingly, cells co-expressing PKM2 and mutant (K422R or H391Y) showed significantly aggressive cancer metabolism as compared with cells expressing either wild-type or mutant PKM2 independently. A similar trend was observed for oxidative endurance, tumorigenic potential, cellular proliferation, and tumor growth. These observations signify the dominant negative nature of mutations. Remarkably, PKM2-H391Y co-expressed cells showed a maximal effect on all the studied parameters. Such a dominant negative impaired function of PKM2 in tumor development is not known; this study demonstrates for the first time the possible predisposition of Bloom syndrome patients with impaired PKM2 activity to cancer and the importance of studying genetic variations in PKM2 in the future to understand their relevance in cancer in general.     

The p38 Pathway Regulates Oxidative Stress Tolerance by Phosphorylation of Mitochondrial Protein IscU

The p38 pathway is an evolutionarily conserved signaling pathway that responds to a variety of stresses. However, the underlying mechanisms are largely unknown. In the present study, we demonstrate that p38b is a major p38 MAPK involved in the regulation of oxidative stress tolerance in addition to p38a and p38c in Drosophila. We further show the importance of MK2 as a p38-activated downstream kinase in resistance to oxidative stresses. Furthermore, we identified the iron-sulfur cluster scaffold protein IscU as a new substrate of MK2 both in Drosophila cells and in mammalian cells. These results imply a new mechanistic connection between the p38 pathway and mitochondria iron-sulfur clusters.