Innovative GenExpA software for selecting suitable reference genes for reliable normalization of gene expression in melanoma.

The algorithms commonly used to select the best stable reference gene in RT-qPCR data analysis have their limitations. We showed that simple selection of the reference gene or pair of genes with the lowest stability value from the pool of potential reference genes-a commonly used approach-is not sufficient to accurately and reliably normalize the target gene transcript and can lead to biologically incorrect conclusions. For reliable assessment of changes in a target gene expression level, we propose our innovative GenExpA software, which works in a manner independent of the experimental model and the normalizer used. GenExpA software selects the best reference by combining the NormFinder algorithm with progressive removal of the least stable gene from the candidate genes in a given experimental model and in the set of daughter models assigned to it. The reliability of references is validated based on the consistency of the statistical analyses of normalized target gene expression levels through all models, described by the coherence score (CS). The use of the CS value imparts a new quality to qPCR analysis because it clarifies how low the stability value of reference must be in order for biologically correct conclusions to be drawn. We tested our method on qPCR data for the B4GALT genes family in melanoma, which is characterized by a high mutation rate, and in melanocytes. GenExpA is available at https://github.com/DorotaHojaLukowicz/GenExpA or https://www.sciencemarket.pl/baza-programow-open-source#oferty .

Upward expansion of distribution ranges of tree species: Contrasting results from two national parks in Western Carpathians.

We analysed the distribution of trees along the elevation gradient in two national parks located in the Western Carpathians (49°30'-49°37' N; 19°28'-20°15' E), dominated by natural forest stands to answer two questions: do immature trees occur at higher elevations compared to mature ones? Has the upper limit of the distribution of the seedlings increased during the period under study, and were the changes proportional to the increase in the mean annual temperature in that period? Data used in our study had been collected in permanent sample plots, distributed regularly over the entire forest area in two national parks. The measurements were taken twice, separated by at least 12 years. We analysed the upper distribution range of the most abundant tree species following tree ontogenic stages for two measurement times. The analysed tree species showed contrasting patterns of the distributions of saplings related to the distributions of mature individuals. In one of the national parks, two species (Silver fir and European beech) showed a significant upward expansion. As three measurements were taken in this park, we found that the expansion has increased over time. In the second national park, located only 45 km to the west from the first one, we found no upward expansion in the distribution of both European beech and Silver fir, while Sycamore maple showed a slight downward trend. We conclude that the dynamics of the tree distributions along the elevation gradient in the mountain areas do not follow a uniform path; the indirect effects of changes in environmental conditions may produce different patterns, reflecting the complex nature of the interactions shaping the distributions of the trees.

XPS, TDS, and AFM studies of surface chemistry and morphology of Ag-covered L-CVD SnO2 nanolayers.

This is well known that the selectivity and sensitivity of tin dioxide (SnO2) thin film sensors for the detection of low concentration of volatile sulfides such as H2S in air can be improved by small amount of Ag additives. In this paper we present the results of comparative X-ray photoelectron spectroscopy (XPS), thermal desorption spectroscopy (TDS), and atomic force microscopy (AFM) studies of the surface chemistry and morphology of SnO2 nanolayers obtained by laser-enhanced chemical vapor deposition (L-CVD) additionally covered with 1 monolayer (ML) of Ag. For as deposited SnO2 nanolayers, a mixture of tin oxide (SnO) and tin dioxide (SnO2) with the [C]/[Sn] ratio of approximately 1.3 was observed. After dry air exposure, the [O]/[Sn] ratio slightly increased to approximately 1.55. Moreover, an evident increasing of C contamination was observed with [C]/[Sn] ratio of approximately 3.5. After TDS experiment, the [O]/[Sn] ratio goes back to 1.3, whereas C contamination evidently decreases (by factor of 3). Simultaneously, the Ag concentration after air exposure and TDS experiment subsequently decreased (finally by factor of approximately 2), which was caused by the diffusion of Ag atoms into the subsurface layers related to the grain-type surface morphology of Ag-covered L-CVD SnO2 nanolayers, as confirmed by XPS ion depth profiling studies. The variation of surface chemistry of the Ag-covered L-CVD SnO2 after air exposure observed by XPS was in a good correlation with the desorption of residual gases from these nanolayers observed in TDS experiments.

Endocannabinoid and cannabinoid-like fatty acid amide levels correlate with pain-related symptoms in patients with IBS-D and IBS-C: a pilot study.

AIMS: Irritable bowel syndrome (IBS) is a functional gastrointestinal (GI) disorder, associated with alterations of bowel function, abdominal pain and other symptoms related to the GI tract. Recently the endogenous cannabinoid system (ECS) was shown to be involved in the physiological and pathophysiological control of the GI function. The aim of this pilot study was to investigate whether IBS defining symptoms correlate with changes in endocannabinoids or cannabinoid like fatty acid levels in IBS patients. METHODS: AEA, 2-AG, OEA and PEA plasma levels were determined in diarrhoea-predominant (IBS-D) and constipation-predominant (IBS-C) patients and were compared to healthy subjects, following the establishment of correlations between biolipid contents and disease symptoms. FAAH mRNA levels were evaluated in colonic biopsies from IBS-D and IBS-C patients and matched controls. RESULTS: Patients with IBS-D had higher levels of 2AG and lower levels of OEA and PEA. In contrast, patients with IBS-C had higher levels of OEA. Multivariate analysis found that lower PEA levels are associated with cramping abdominal pain. FAAH mRNA levels were lower in patients with IBS-C. CONCLUSION: IBS subtypes and their symptoms show distinct alterations of endocannabinoid and endocannabinoid-like fatty acid levels. These changes may partially result from reduced FAAH expression. The here reported changes support the notion that the ECS is involved in the pathophysiology of IBS and the development of IBS symptoms.