A COMPARISON OF META-ANALYSIS METHODS FOR DETECTING DIFFERENTIALLY EXPRESSED GENES IN MICROARRAY EXPERIMENTS: AN APPLICATION TO MALIGNANT PLEURAL MESOTHELIOMA DATA

The proliferation of microarray experiments and the increasing availability of relevant amount of data in public repositories have created a need for meta-analysis methods to efficiently integrate and validate microarray results from independent but related studies. Despite its increasing popularity, meta-analysis of microarray data is not without problems. In fact, although it shares many features with traditional meta-analysis, most classical meta-analysis methods cannot be directly applied to microarray experiments because of their unique issues. Several meta-analysis techniques have been proposed in the context of microarrays. However, only recently a comprehensive framework to carry out microarray data meta-analysis has been proposed. Moreover very few software packages for microarray meta-analysis implementation exist and most of them either have unclear manuals or are not easy to apply. We applied four meta-analysis methods, the Stouffer’s method, the moderated effect size combination approach, the t-based hierarchical modeling and the rank product method, to a set of three microarray studies on malignant pleural mesothelioma. We focused on differential expression analysis between normal and malignant mesothelioma pleural tissues. Both unfiltered and filtered data were analyzed. The lists of differentially expressed genes provided by each method for either kind of data were compared, also by pathway analysis. These comparisons highlighted a poor overlap between the lists of differentially expressed genes and the related pathways obtained using the unfiltered data. Conversely, a higher concordance of the results, both at the gene and the pathway level, was observed when filtered data were considered. The fact that a significant number of genes were identified by only one of the tested methods shows that the gene ranking is based on different perspectives. In fact, the analyzed methods are based on different assumptions and focus on diverse aspects in selecting significant genes. Since so far there is no consensus on what is (are) the ‘best’ meta-analysis method(s), it may be useful to select candidate genes for further analysis using a combination of different meta-analysis methods. In particular, differentially expressed genes detected by more than one method may be considered as the most reliable ones while genes identified by only a single method may be further explored to expand the knowledge of the biological phenomenon of interest

Heat-shock pretreatment inhibits sorbitol-induced apoptosis in K562, U937 and HeLa cells.

The aim of this study was to determine whether heat-shock pretreatment exerted a protective effect against sorbitol-induced apoptotic cell death in K562, U937 and HeLa cell lines and whether such protection was associated with a decreased cytochrome c release from mithocondria and a decreased activation of caspase-9 and -3. Following heat-shock pretreatment (42 6 0.3C for 1 hr), these cell lines were exposed to sorbitol for 1 hr. Apoptosis was evaluated by DNA fragmentation, whereas caspase-9,-3 activation, cytochrome c release and heat-shock protein70 (HSP70) were assayed by Western Blot. Sorbitol exposure-induced apoptosis in these different cell lines with a marked activation of caspase-9 and caspase- 3, whereas heat-shock pretreatment before sorbitol exposure, induced expression of HSP70 and inhibited sorbitol-mediated cytochrome c release and subsequent activation of caspase-9 and caspase- 3. Similarly, overexpression of HSP70 in the three cell lines studied prevented caspase-9 cleavage and activation as well as cell death. Furthermore, we showed that the mRNA expression of iNOS decreased during both the heat-shock treatment and heat-shock pretreatment before sorbitol exposure. By contrast, the expression of Cu-Zn superoxide dismutase (SOD) and Mn-SOD proteins increased during heat-shock pretreatment before sorbitol exposure. We conclude that, heat-shock pretreatment protects different cell lines against sorbitol-induced apoptosis through a mechanism that is likely to involve SOD family members

The effect of marathon on mRNA expression of anti-apoptotic and pro-apoptotic proteins and sirtuins family in male recreational long-distance runners

<p>Abstract</p> <p>Background</p> <p>A large body of evidence shows that a single bout of strenuous exercise induces oxidative stress in circulating human lymphocytes leading to lipid peroxidation, DNA damage, mitochondrial perturbations, and protein oxidation.</p> <p>In our research, we investigated the effect of physical load on the extent of apoptosis in primary cells derived from blood samples of sixteen healthy amateur runners after marathon (a.m.).</p> <p>Results</p> <p>Blood samples were collected from ten healthy amateur runners peripheral blood mononuclear cells (PBMCs) were isolated from whole blood and bcl-2, bax, heat shock protein (HSP)70, Cu-Zn superoxide dismutase (SOD), Mn-SOD, inducible nitric oxide synthase (i-NOS), SIRT1, SIRT3 and SIRT4 (Sirtuins) RNA levels were determined by Northern Blot analysis. Strenuous physical load significantly increased HSP70, HSP32, Mn-SOD, Cu-Zn SOD, iNOS, GADD45, bcl-2, forkhead box O (FOXO3A) and SIRT1 expression after the marathon, while decreasing bax, SIRT3 and SIRT4 expression (P < 0.0001).</p> <p>Conclusion</p> <p>These data suggest that the physiological load imposed in amateur runners during marathon attenuates the extent of apoptosis and may interfere with sirtuin expression.</p

Capillary barriers during rainfall events in pyroclastic deposits of the Vesuvian area

In the present paper, the capillary barrier formation at the interface between soil layers, which is characterized by textural discontinuities, has been analyzed. This mechanism has been investigated by means of a finite element model of a two-layer soil stratification. The two considered formations, belonging to the pyroclastic succession of the “Pomici di Base” Plinian eruption (22 ka, Santacroce et al., 2008) of the Somma–Vesuvius volcano, are affected by shallow instability phenomena likely caused by progressive saturation during the rainfall events. This mechanism could be compatible with the formation of capillary barriers at the interface between layers of different grain size distributions during infiltration. One-dimensional infiltration into the stratified soil was parametrically simulated considering rainfall events of increasing intensity and duration. The variations in the suction and degree of saturation over time allowed for the evaluation of stability variations in the layers, which were assumed as part of stratified unsaturated infinite slopes