A survey of software tools for microRNA discovery and characterization using RNA-seq.

Since the small RNA-sequencing (sRNA-seq) technology became available, it allowed the discovery of thousands new microRNAs (miRNAs) in humans and many other species, providing new data on these small RNAs (sRNAs) of high biological and translational relevance. MiRNA discovery has not yet reached saturation, even in the most studied model organisms, and many researchers are using sRNA-seq in studies with different aims in biomedicine, fundamental research and in applied animal sciences. We review several miRNA discovery and characterization software tools that implement different strategies, providing a useful guide for researchers to select the programs best suiting their study objectives and data. After a brief introduction on miRNA biogenesis, function and characteristics, useful to understand the biological background considered by the algorithms, we survey the current state of miRNA discovery bioinformatics discussing 26 different sRNA-seq-based miRNA prediction software and toolkits released in the past 6 years, including 15 methods specific for miRNA prediction and 11 more general-purpose software suites for sRNA-seq data analysis. We highlight the main features of mature miRNAs and miRNA precursors considered by the methods categorizing them according to prediction strategy and implementation. In addition, we describe a typical miRNA prediction and analysis workflow by delineating the objectives, potentialities and main steps of sRNA-seq data analysis projects, from preparatory data processing to miRNA prediction, quantification and diverse downstream analyses. Finally, we outline the caveats affecting sRNA-seq-based prediction tools, and we indicate the possibilities offered by data set pooling and by integration with other types of high-throughput sequencing data.

Identification of differentially expressed small RNAs and prediction of target genes in Italian Large White pigs with divergent backfat deposition.

The identification of the molecular mechanisms regulating pathways associated with the potential for fat deposition in pigs can lead to the detection of key genes and markers for the genetic improvement of fat traits. Interactions of microRNAs (miRNAs) with target RNAs regulate gene expression and modulate pathway activation in cells and tissues. In pigs, miRNA discovery is far from saturation, and the knowledge of miRNA expression in backfat tissue and particularly of the impact of miRNA variations is still fragmentary. Using RNA-seq, we characterized the small RNA (sRNA) expression profiles in Italian Large White pig backfat tissue. Comparing two groups of pigs divergent for backfat deposition, we detected 31 significant differentially expressed (DE) sRNAs: 14 up-regulated (including ssc-miR-132, ssc-miR-146b, ssc-miR-221-5p, ssc-miR-365-5p and the moRNA ssc-moR-21-5p) and 17 down-regulated (including ssc-miR-136, ssc-miR-195, ssc-miR-199a-5p and ssc-miR-335). To understand the biological impact of the observed miRNA expression variations, we used the expression correlation of DE miRNA target transcripts expressed in the same samples to define a regulatory network of 193 interactions between DE miRNAs and 40 DE target transcripts showing opposite expression profiles and being involved in specific pathways. Several miRNAs and mRNAs in the network were found to be expressed from backfat-related pig QTL. These results are informative for the complex mechanisms influencing fat traits, shed light on a new aspect of the genetic regulation of fat deposition in pigs and facilitate the prospective implementation of innovative strategies of pig genetic improvement based on genomic markers.

Avaliação da descontaminação fúngica de camomila [Chamomilla recutita (L. ) Rauschert] por meio de diferentes métodos caseiros em duas temperaturas / Evaluation of fungal decontamination of chamomile [Chamomilla recutita (L. ) Rauschert] through different home procedures at two temperatures

O aumento no consumo de plantas medicinais vem se transformando em problema de Saúde Pública, devido ao potencial de contaminação microbiana, principalmente por origem natural e condições inadequadas de uso e armazenamento. O presente trabalho teve como objetivo avaliar a descontaminação fúngica de camomila [Chamomilla recutita (L.) Rauschert] através de diferentes processos caseiros (decocção, infusão, água morna). Foram analisadas 10 amostras de camomila, procedentes de diferentes estabelecimentos comerciais. Os resultados das análises microbiológicas indicaram redução da contaminação fúngica na maioria das amostras, porém não atingindo os índices considerados satisfatórios, o que evidencia a necessidade de medidas regulatórias e educacionais que garantam a qualidade destes produtos, desde a produção até a colheita.

The increase in the consumption of medicinal plants has become a Public Health problem due to potential microbiological contamination, especially due to their natural origin and inadequate conditions of use and storage. The present study aimed to evaluate the fungal decontamination of chamomile [Chamomilla recutita (L.) Rauschert] through different home procedures (decoction, infusion, warm water). Ten chamomile samples from different commercial establishments were analyzed. The results of microbiological analyses indicated a reduction in fungal contamination in most samples which, however, did not reach the indexes considered satisfactory, evidencing the need of regulatory and educational measures to guarantee the quality of these products, from production to harvest.