3′UTR-located ALU Elements: Donors of Potetial miRNA Target Sites and Mediators of Network miRNA-based Regulatory Interactions

Recent research data reveal complex, network-based interactions between mobile elements and regulatory systems of eukaryotic cells. In this article, we focus on regulatory interactions between Alu elements and micro RNAs (miRNAs). Our results show that the majority of the Alu sequences inserted in 3′UTRs of analyzed human genes carry strong potential target sites for at least 53 different miRNAs. Thus, 3′UTR-located Alu elements may play the role of mobile regulatory modules that supply binding sites for miRNA regulation. Their abundance and ability to distribute a set of certain miRNA target sites may have an important role in establishment, extension, network organization, and, as we suppose – in the regulation and environment-dependent activation/inactivation of some elements of the miRNA regulatory system, as well as for a larger scale RNA-based regulatory interactions. The Alu-miRNA connection may be crucial especially for the primate/human evolution

MicroInspector: a web tool for detection of miRNA binding sites in an RNA sequence

Regulation of post-transcriptional gene expression by microRNAs (miRNA) has so far been validated for only a few mRNA targets. Based on the large number of miRNA genes and the possibility that one miRNA might influence gene expression of several targets simultaneously, the quantity of ribo-regulated genes is expected to be much higher. Here, we describe the web tool MicroInspector that will analyse a user-defined RNA sequence, which is typically an mRNA or a part of an mRNA, for the occurrence of binding sites for known and registered miRNAs. The program allows variation of temperature, the setting of energy values as well as the selection of different miRNA databases to identify miRNA-binding sites of different strength. MicroInspector could spot the correct sites for miRNA-interaction in known target mRNAs. Using other mRNAs, for which such an interaction has not yet been described, we discovered frequently potential miRNA binding sites of similar quality, which can now be analysed experimentally. The MicroInspector program is easy to use and does not require specific computer skills. The service can be accessed via the MicroInspector web server at

Određivanje mikrobne populacije kiselog tijesta iz Bugarske metagenomskim metodama pomoću triju komercijalnih alata za ekstrakciju DNA

Research background. Sourdough is a spontaneously formed, complex microbial ecosystem of various lactic acid bacteria (LAB) and yeast which, by producing specific metabolites, determines the quality of the baked products. In order to design and control the sourdough with preferred nutritional characteristics, it is crucial that the LAB diversity of the product of interest be elucidated. Experimental approach. Using the opportunities of next-generation sequencing (NGS) of the V1-V3 hypervariable gene region of 16S rRNA, we studied the microbial ecosystem of a whole grain sourdough made of Triticum monococcum, originating from Southwestern Bulgaria. Since the DNA extraction method is considered crucial for the accuracy of the sequencing results, as it can introduce significant differences in the examined microbiota, we used three different commercial kits for DNA isolation and analyzed their impact on the observed bacterial diversity. Results and conclusions. All three DNA extraction kits provided bacterial DNA which passed quality control and was successfully sequenced on Illumina MiSeq platform. The results received from the different DNA protocols showed variations in the microbial profiles. Alpha diversity indices (ACE, Chao1, Shannon, and Simpson) were also different among the three groups of results. Nevertheless, a strong dominance of phylum Firmicutes, class Bacilli, order Lactobacillales, represented mostly by family Lactobacillaceae, genus Lactobacillus (relative abundance of 63.11–82.28%) and family Leuconostocaceae, genus Weissella (relative abundance of 3.67–36.31%) was observed. Lactiplantibacillus plantarum and Levilactobacillus brevis with relative abundance of 16.15–31.24% and 6.21−16.29% respectively, were the two dominant species identified in all three DNA isolates. Novelty and scientific contribution. The presented results give insight into the taxonomic composition of bacterial community of a specific Bulgarian sourdough. Having in mind that the sourdough is a difficult matrix for DNA isolation on the one hand, and that there is no standardized DNA extraction protocol for this matrix on the other hand, this pilot study aims to give a small contribution to the future establishment and validation of such a protocol, which will allow accurate assessment of the specific microbiota of sourdough samples.Pozadina istraživanja. Kiselo tijesto predstavlja spontano oblikovan složeni ekosustav različitih bakterija mliječno-kiselog vrenja i kvasaca koji stvaranjem specifičnih metabolita određuju kakvoću pekarskih proizvoda. Za kreiranje i kontroliranu pripremu kiselog tijesta sa željenim nutritivnim značajkama, neophodno je razumjeti raznolikost mliječno-kiselih bakterija. Eksperimentalni pristup. Sekvenciranjem nove generacije V1-V3 hipervarijabilnih regija 16S rRNA gena ispitali smo mikrobnu zajednicu kiselog tijesta proizvedenog od cjelovitih žitarica vrste Triticum monococcum, porijeklom iz jugozapadne Bugarske. Odabir metode ekstrakcije DNA je ključni korak za dobivanje točnih rezultata sekvenciranja, budući da ona može bitno utjecati na ispitanu mikrobnu zajednicu. Stoga smo odabrali tri komercijalna alata za izolaciju DNA i ispitali njihov učinak na bakterijsku raznolikost. Rezultati i zaključci. Pomoću sva tri alata izdvojen je bakterijski DNA materijal koji je zadovoljio kontrolu kvalitete, te je uspješno sekvenciran na platformi Illumina MiSeq. Rezultati dobiveni različitim DNA protokolima pokazali su razlike u profilima mikrobnih zajednica. Alfa-indeksi raznolikosti (ACE, Chao1, Shannon, i Simpson) također su bili različiti za svaku skupinu. Usprkos tome, opažena je izražena dominacija bakterija koljena Firmicutes, razreda Bacilli, reda Lactobacillales, i to najviše porodice Lactobacillaceae, roda Lactobacillus (relativna zastupljenost od 63,11-82,28 %) i porodice Leuconostocaceae, roda Weissella (relativna zastupljenost od 3,67–36,31 %). Dvije dominantne vrste koje su identificirane u sva tri DNA izolata bile su Lactiplantibacillus plantarum, čija je relativna zastupljenost bila 16,15-31,24 % i Levilactobacillus brevis, čija je relativna zastupljenost bila 6,21-16,29 %. Novina i znanstveni doprinos. Dobiveni rezultati daju uvid u taksonomski sastav bakterijske populacije kiselog tijesta porijeklom iz Bugarske. Imajući na umu da je kiselo tijesto zahtjevna podloga za izolaciju DNA, te da ne postoji standardizirani protokol za njegovu obradu, svrha je ove pilot studije bila dati mali doprinos uspostavljanju i validaciji budućih protokola, koji će omogućiti preciznu evaluaciju specifične mikrobne populacije kiselih tijesta

Combinational effect of mutational bias and translational selection for translation efficiency in tomato (Solanum lycopersicum) cv. Micro-Tom

AbstractWe conducted a comprehensive analysis of codon usage bias (CUB) based on the available non-redundant full-length cDNA (nrFLcDNA) and expressed sequence tags (ESTs) data of cultivar Micro-Tom and evaluated the associations of observed CUB and measurements of transcriptional and translational effectiveness. The analysis presented in our study suggests a correlation, which is negative but highly correlated between Axis 1 and GC3s (r=−0.827, P<0.01), indicating that mutational bias has a significant and dominant repressive role to the choices of GC3. We also observed a strong positive correlation between codon adaptation index (CAI) and translational adaptation index (tAIg) (0.407, P<0.01), which demonstrates the facilitation of efficient translation by the optimal codon usage patterns of the highly expressed genes. We believe that the complete set of optimal codon usage patterns detected in this study will serve as a model to enhance the transgenesis in the studied cultivar of Solanum lycopersicum

Effects of sourdough on rheological properties of dough, quality characteristics and staling time of wholemeal wheat croissants

The present study aimed to obtain good quality croissants from wholegrain wheat flour using baking sourdoughs prepared from single starter cultures of Pediococcus acidilactici 02P108 (PA), Pediococcus pentosaceus SM2D17 (PP) and Enteroccocus durans 09B374 (ED) as an attempt to overcome the usual negative effects of the wholegrain flour on the characteristics of this specific bakery product group. Results showed that the addition of sourdough in the wholegrain wheat dough had similar performance as that of conventional baker’s yeast regarding the rheological characteristics of dough. The dynamic viscosity of all sourdough-leavened samples remained higher than that of the control sample at all tested shear rates. A positive effect of sourdoughs used on the development of baking dough was observed in terms of specific volume improvement, higher degree of softening, and reduced baking loss. However, these positive effects were found as strain-specific. The use of Enteroccocus durans 09B374-made sourdough showed the most distinguished sensory characteristics and the best results regarding croissant staling during storage. The study demonstrated that sourdoughs used in wholemeal wheat croissant dough had positive effect on the quality characteristics and shelf-life of products. However, strain selection proved as of key importance for the successful production of wholemeal wheat croissants.info:eu-repo/semantics/publishedVersio

16S-rRNA-Based metagenomic profiling of the bacterial communities in traditional Bulgarian sourdoughs

Sourdoughs (SDs) are spontaneously formed microbial ecosystems composed of various species of lactic acid bacteria (LAB) and acid-tolerant yeasts in food matrices of cereal flours mixed with water. To date, more than 90 LAB species have been isolated, significantly impacting the organoleptic characteristics, shelf life, and health properties of bakery products. To learn more about the unique bacterial communities involved in creating regional Bulgarian sourdoughs, we examined the metacommunities of five sourdoughs produced by spontaneous fermentation and maintained by backslopping in bakeries from three geographic locations. The 16S rRNA gene amplicon sequencing showed that the former genus Lactobacillus was predominant in the studied sourdoughs (51.0–78.9%). Weissella (0.9–42.8%), Herbaspirillum (1.6–3.8%), Serratia (0.1–11.7%), Pediococcus (0.2–7.5%), Bacteroides (0.1–1.3%), and Sphingomonas (0.1–0.5%) were also found in all 5 samples. Genera Leuconostoc, Enterococcus, Bacillus, and Asaia were sample-specific. It is interesting to note that the genus Weissella was more abundant in wholegrain samples. The greatest diversity at the species level was found in the former genus Lactobacillus, presented in the sourdough samples with 13 species. The UPGMA cluster analysis clearly demonstrated similarity in species’ relative abundance between samples from the same location. In addition, we can conclude that the presence of two main clusters—one including samples from mountainous places (the cities of Smolyan and Bansko) and the other including samples from the city of Ruse (the banks of the Danube River)—may indicate the impact of climate and geographic location (e.g., terrain, elevation, land use, and nearby water bodies and their streams) on the abundance of microbiome taxa. As the bacterial population is crucial for bread standardization, we expect the local bakery sector to be interested in the relationship between process variables and their effect on bacterial dynamics described in this research study.info:eu-repo/semantics/publishedVersio

The Fascinating World of Plant Non-Coding RNAs

Non-coding RNAs (ncRNAs), such as microRNAs (miRNAs), short interfering RNAs (siRNAs), and long non-coding RNAs (lncRNAs), have emerged as pivotal regulators within the plant kingdom [...

Liquid Biopsy: Current Status and Future Perspectives

Since the discovery of the Bence Jones protein in the middle to late 1800s and the subsequent identification of the carcinoembryonic antigen and alpha-fetoprotein in the 1970s, it has been demonstrated that the analysis of biofluids is essential to the diagnostic and follow-up processes of cancer [...