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.

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.

Differentiated 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. The 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. 602 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. The 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). Identification 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.

Tenderization based on papain and microwave vacuum drying and puffing (MVDP) as well as adequate processing conditions enabled expansion of slices of the raw meat tissue. The main aim of the study was to use the response surface method and find the conditions of puffing that could maximize the expansion of meat during MVDP. The bound was set on the expansion: the most expanded puffings should be of good quality, including a desirable porous structure. The best combination of values of the MVDP process conditions (e.g., the initial moisture content in meat slices, microwave energy, and the vacuum absolute pressure) was found during experiments using the central composite design. The volume of slices puffed under these conditions was 1.60–1.78 times greater than the volume of slices before MVDP, and the sensory quality index remained acceptable. The research showed that pretreatment reduced the hardness of sample by over 25% and increased its crispiness, which was confirmed in cryo-scanning electron microscopy images.

Androgenesis is potentially the most effective technique for doubled haploid production of wheat. It is not however widely used in breeding programmes due to its main limitation: the genotype dependence. Due to genetic differences between spring and winter wheat, it was assumed that both phenotypes are different in their capacity to conduct androgenesis. And so, the aim of this investigation was to verify the effectiveness of androgenesis induction and plant regeneration of spring and winter wheat genotypes while considering varying amounts of growth hormones in the induction medium. Fifteen genotypes of spring wheat and fifteen of winter wheat were used in the experiment. Six hundred anthers of each of the 30 genotypes were plated and analysed. Previous studies have allowed selection of the best medium for wheat androgenesis and a combination of growth hormones that are the most effective in stimulating microspore proliferation. Therefore, C17 induction media with two combinations of growth hormones were used: I—supplemented only by auxins (2,4-D and dicamba), and II—supplemented by auxin and cytokinin (2,4-D and kinetin). Data was recorded according to the efficiency of androgenic structure formation (ASF), green plant regeneration (GPR), and albino plant regeneration (APR). The results showed that the induction and regeneration of androgenesis in the spring wheat were more efficient than in the winter ones. The spring genotypes formed more androgenic structures and green plants on anthers plated on the medium supplemented only by auxins, in contrast to the winter genotypes which were better induced and regenerated on the medium supplemented by auxin and cytokinin. The study showed that to increase the efficiency of androgenesis, it is necessary to select appropriate factors such as concentration and type of hormones in medium composition, affecting the course of the culturing procedure according to the winter or spring phenotype of donor plants.