High-throughput sequencing technologies, such as the Illumina Hi-seq, are powerful new tools for investigating a wide range of biological and medical problems. Massive and complex data sets produced by the sequencers create a need for development of statistical and computational methods that can tackle the analysis and management of data. The data normalization is one of the most crucial steps of data processing and this process must be carefully considered as it has a profound effect on the results of the analysis. In this work, we focus on a comprehensive comparison of five normalization methods related to sequencing depth, widely used for transcriptome sequencing (RNA-seq) data, and their impact on the results of gene expression analysis. Based on this study, we suggest a universal workflow that can be applied for the selection of the optimal normalization procedure for any particular data set. The described workflow includes calculation of the bias and variance values for the control genes, sensitivity and specificity of the methods, and classification errors as well as generation of the diagnostic plots. Combining the above information facilitates the selection of the most appropriate normalization method for the studied data sets and determines which methods can be used interchangeably.

BackgroundDifferentiated thyroid carcinoma (DTC) originates from thyroid follicular epithelial cells and belongs to a group of slowly progressing tumors with a relatively good prognosis. However, recurrences and metastases are a serious problem in advanced stages. Furthermore, progression from a well differentiated thyroid carcinoma to an aggressive anaplastic one is possible.The majority of differentiated thyroid carcinomas are sporadic but a few alleles increasing the cancer risk are known. One of them is the c.470 T > C (p.I157T, rs17879961) missense substitution in the CHEK2 gene.Aim of the studyThe aim of this study was to investigate whether this specific CHEK2 alteration, c.470 T > C, predisposes the Great Poland (Wielkopolska) population to thyroid cancer.Methods602 differentiated thyroid carcinoma patients and 829 controls randomly selected from population were genotyped for the presence of the c.470C allele using pyrosequencing. Hardy-Weinberg Equilibrium (HWE) was tested for both groups by chi-square distribution and Fisher’s exact test. The odds ratios (ORs), 95% confidence intervals (CIs), and p-values were calculated using the R software.ResultsThe results of genotyping showed the presence of the c.470C allele in 51 patients with a frequency of 4.49%, while in a controls in 42 patients with a frequency of 2.53%. We demonstrated that in the Great Poland population the c.470C CHEK2 variant increases the risk of developing differentiated thyroid cancer almost twice (OR = 1.81, p = 0.004). The risk of papillary thyroid carcinoma in female patients homozygous for the c.470C allele was shown to increase almost 13-fold (OR = 12.81, p = 0.019).ConclusionsIdentification of c.470C CHEK2 gene variant ought to be taken into account by healthcare policymakers. Future well-designed and larger population studies are of great value in confirming these findings. Moreover, a combination of genetic factors together with environmental exposures should also be considered.Electronic supplementary materialThe online version of this article (doi:10.1186/s13053-015-0030-5) contains supplementary material, which is available to authorized users.

The cream with the aqueous extract from leaf of five-leaf serratula proved to be an effective and safe preparation for lightening skin discolorations (66.67 % of the female patients in the study group).

The purpose of this work was to assess the impact of zearalenone (ZEN) and selected hormone regulators on the effectiveness of microspore embryogenesis in anther culture of wheat. The plant material comprised F1 hybrids of winter and spring wheat. Six combinations of media inducing microspore proliferation and formation of embryogenic structures were investigated: two combinations of growth regulators (D - 2,4-D + dicamba, K - 2,4-D + kinetin), each with three ZEN concentrations (0 mL/L, 0.1 mL/L, 0.2 mL/L). A significant increase in microspore embryogenesis effectiveness on media with the addition of ZEN was observed both at the stages of its induction and the formation of green plants in some genotypes. In case of both combinations of growth regulators, an increased concentration of ZEN resulted in more effective induction of microspore embryogenesis. The most effective induction medium was the D medium supplemented with 0.2 mL/L ZEN. As a result of the use of zearalenone together with two combinations of growth regulators, all genotypes tested produced androgenic structures, which indicates the breakdown of genotypic recalcitrant in the analysed hybrids. In addition, green plants were obtained from 18 out of 19 tested hybrids. The addition of ZEN to the medium did not affect the number of regenerated albino plants nor the number of spontaneous genome doublings proportion.

Temperature strongly influences the growth of maize, particularly in the early growth stages. The exogenous application of some amino acids has been proven to have a positive effect on plant growth and development under stressful conditions. The objective of the study was to evaluate the response of maize that was grown under an optimal and stress (fluctuating) temperature to L-Arginine (L-Arg) and Glycine (Gly) application. In the study, it was assumed that the exogenously applied amino acids would alleviate the adverse effects of temperature stress on the maize height, as well as on the biomass of shoots and roots. Ten concentrations of each amino acid from 0.006 mM to 9.0 mM were tested under constant temperature conditions 20–22 °C/23–25 °C (night/day) an fluctuating stress of rising and dropping temperatures between 12–15 °C (night) and 30–38 °C (day). The amino acids were applied to the crop at growth stages V3–V4. In plants that were obtained from seeds pre-treated with L-Arg and Gly, the amino acids increased both the length of radicles and the number of lateral roots. A large discrepancy between the effects of the two amino acids was observed after foliar application. Under optimal thermal conditions, L-Arg increased the mass of shoots and roots by 55–59%. Under stress conditions, root mass was increased even by 100% when compared to the control plants. The best results were recorded at concentrations of 6 mM and 3 mM. Plants that were treated with Gly concentrations generally reached the height of untreated plants or less. It was shown that Gly applied at concentrations of 0.2 mM to 3 mM has a negative effect on the fresh mass of the crop.