IncRna: The R Package for Optimizing lncRNA Identification Processes.

In silico identification of long noncoding RNAs (lncRNAs) is a multistage process including filtering of transcripts according to their physical characteristics (e.g., length, exon-intron structure) and determination of the coding potential of the sequence. A common issue within this process is the choice of the most suitable method of coding potential analysis for the conducted research. Selection of tools on the sole basis of their single performance may not provide the most effective choice for a specific problem. To overcome these limitations, we developed the R library lncRna, which provides functions to easily carry out the entire lncRNA identification process. For example, the package prepares the data files for coding potential analysis to perform error analysis. Moreover, the package gives the opportunity to analyze the effectiveness of various combinations of the lncRNA prediction methods to select the optimal configuration of the entire process.

Soil Contamination with Metals in Mountainous: A Case Study of Jaworzyna Krynicka in the Beskidy Mountains (Poland).

The paper presents the content of six metals (Cd, Cr, Cu, Ni, Pb, and Zn) in the soils of the southern slope of Jaworzyna Krynicka in Poland. Soil samples were collected in polygons, starting from an altitude of 500 m above sea level and ending at an altitude of 1100 m above sea level. Ten soil samples were collected in each polygon. The polygons were set at every 100 m of absolute altitude. The selected research area is an important natural area. The fertile mountain beech forests located there are the most important forest communities in the mountain areas of Poland. They are valuable habitats for plants and animals (especially for large predatory mammals). Every year, numerous tourists and health resort patients visit this place. The results of the research showed that soil contamination in the study area is not high, in particular for altitudes of 500 and 900 m above sea level. At these altitudes, the contents of Cd, Cr, Cu, Ni, Pb, and Zn were similar to the concentrations of these metals in uncontaminated soils. The tests carried out showed very low cadmium content for all absolute altitudes. Zinc, the concentrations of which exceeded natural values, showed the highest content in the tested soils. All the metals tested showed a common tendency of increases in their content in the soils of Jaworzyna Krynicka up to 800 m above sea level. From an altitude of 900 m above sea level, the content of these metals decreased, except for Pb. Only Pb concentrations in Jaworzyna Krynicka soils also increased with the increasing altitude. The research significance of this work is that it is important for assessing the ecological balance in the selected area.

In Silico Identification of lncRNAs Regulating Sperm Motility in the Turkey (Meleagris gallopavo L.).

Long non-coding RNAs (lncRNAs) are transcripts not translated into proteins with a length of more than 200 bp. LncRNAs are considered an important factor in the regulation of countless biological processes, mainly through the regulation of gene expression and interactions with proteins. However, the detailed mechanism of interaction as well as functions of lncRNAs are still unclear and therefore constitute a serious research challenge. In this study, for the first time, potential mechanisms of lncRNA regulation of processes related to sperm motility in turkey were investigated and described. Customized bioinformatics analysis was used to detect and identify lncRNAs, and their correlations with differentially expressed genes and proteins were also investigated. Results revealed the expression of 863 new/unknown lncRNAs in ductus deferens, testes and epididymis of turkeys. Moreover, potential relationships of the lncRNAs with the coding mRNAs and their products were identified in turkey reproductive tissues. The results obtained from the OMICS study may be useful in describing and characterizing the way that lncRNAs regulate genes and proteins as well as signaling pathways related to sperm motility.