Instalation Package for RNAdigest: A Web-Based Tool for the Analysis and Prediction of Structure - Specific RNAse Digestion Results https://doi.org/10.1371/journal.pone.0096759

<h4>This is installation package containing files to set up the web server "RNAdigest." This software uses mfold RNA structural models in order to predict the results of RNAse digestion experiments. </h4><h4>For more details please see :</h4><p><a href="https://journals.plos.org/plosone/article?id=10.1371/journal.pone.0096759"><strong>RNAdigest: A Web-Based Tool for the Analysis and Prediction of Structure - Specific RNAse Digestion Results</strong> </a><br>Madanecki P, Nozell S, Ochocka R, Collawn JF, Bartoszewski R (2014) RNAdigest: A Web-Based Tool for the Analysis and Prediction of Structure - Specific RNAse Digestion Results. PLOS ONE 9(5): e96759. <a href="https://doi.org/10.1371/journal.pone.0096759">https://doi.org/10.1371/journal.pone.0096759</a></p><p> </p><h4><i><strong>The software was developed for Linux Debian distribution and requires:</strong></i></h4><h4><i><strong> PHP5 environment (the versions of PHP above 5 are not compatible)</strong></i></h4><h4><i><strong>mFold package with sir_graph (the best will be 2014 edition)</strong></i></h4><h4><i><strong>Please also note that you may have to update mFold form address to the current one.</strong></i></h4><h4> </h4><h4>In order to set up the software please unpack the archive to WWW server catalog.</h4><h4> </h4><h3>Please note, that this is the last version of RNAdigest and further development and support is no longer available</h3&gt

16S rRNAgene-based metagenomic analysis of the gut microbial community associated with the DUI species Unio crassus (Bivalvia: Unionidae)

What factors determine biome richness: genetic or environmental? Sex, phylogeny, and tolerance indicated by other symbionts (e.g., endosymbionts) or simply is it related to local habitat, especially if the gut biome is considered? To answer these questions, we investigated the gut microbial profile of both sexes of three Unio crassus populations, species with unique system of mitochondrial DNA inheritance called doubly uniparental inheritance (DUI), living in different ecological conditions. High-throughput sequencing of the V3-V4 hypervariable regions in the bacterial 16S rRNA gene fragment was performed, which resulted in a total of 1,051,647 reads, with 58,424 reads/65 OTUs (operational taxonomic units) per sample on average. We identified a core microbiome, with all individual mussels sharing 69 OTUs (representing 23% of the total number of OTUs). Proteobacteria was the dominant phylum in all samples, followed by Firmicutes, Actinobacteria, and Bacteroidetes. There were no significant differences in gut microbiome compositions between the two sexes of this species; however, we observed different phyla in geographically isolated populations. A non-metric multidimensional scaling plot and dendrogram showed that the bacterial profile complies with the genetic structure of populations. Although we found differences in microbiomes between populations, their genetic structure suggests that the microbiome is weakly related to habitat, and more strongly to phylogeography (on both F and M mitotypes). We found no significant differences in beta diversity between the individuals of the bacterial communities measured using the Bray-Curtis index. Finally, we also examined whether OTUs were represented by symbiotic bacteria that enable cellulose digestion and by endosymbiotic bacteria that play important functions in the biology of their hosts and also affect microevolutionary processes and population phenomena. With regard to the endosymbionts, however, there was no relation to sex of the studied individuals, which suggests that there are no straightforward relations between DUI and microbiome.Funding Agencies|Polish National Science Centre [NCN DEC-2017/01/X/NZ8/01873]; Swedish Research Councils (Vetenskapsradet) [2017-04951]</p

RNAdigest: A Web-Based Tool for the Analysis and Prediction of Structure - Specific RNAse Digestion Results

<div><p>Despite recent developments in analyzing RNA secondary structures, relatively few RNA structures have been determined. To date, many investigators have relied on the traditional method of using structure-specific RNAse enzymes to probe RNA secondary structures. However, if these data were combined with novel computational approaches, investigators would have an informative and valuable tool for RNA structural analysis. To this end, we created the web server “RNAdigest.” RNAdigest uses mfold RNA structural models in order to predict the results of RNAse digestion experiments. Furthermore, RNAdigest also utilizes both RNA sequence and the experimental digestion patterns to formulate the constraints for predicting secondary structures of the RNA. Thus, RNAdigest allows for the structural interpretation of RNAse digestion experiments. Overall, RNAdigest simplifies RNAse digestion result analyses while allowing for the identification of unique fragments. These unique fragments can then be used for testing predicted mfold structures and for designing structural-specific DNA/RNA probes.</p></div

An example of the “digest simulation” mode results screen.

<p><b>A</b>. Simulated digestion results are shown. <b>B</b>. The predicted RNA structure is shown. <b>C</b>. Simulated gel electrophoresis results are shown.</p

Schematic diagram of typical “step by step” workflows for RNAdigest.

<p><b>A</b>. Digest simulation mode is shown. <b>B</b>. Structure prediction mode is shown.</p

Taxonomic classification of the bacterial endosymbiont Wolbachia based on next-generation sequencing: is there molecular evidence for its presence in tardigrades?

We used high-throughput sequencing of 16S rRNA to test whether tardigrade species are infected with Wolbachia parasites. We applied SILVA and Greengenes databases that allowed taxonomic classification of bacterial sequences to OTUs. The results obtained from both databases differed considerably in the number of OTUs, and only the Greengenes database allowed identification of Wolbachia (infection was also supported by comparison of sequences to NCBI database). The putative bacterial endosymbiont Wolbachia was discovered only in adult eutardigrades, while bacteria identified down to the order Rickettsiales were detected in both eutardigrade eggs and adult specimens. Nevertheless, the frequency of Wolbachia in the bacterial communities of the studied eutardigrades was low. Similarly, in our positive control, i.e. a fairy shrimp Streptocephalus cafer, which was found to be infected with Wolbachia in our previous study using Sanger sequencing, only the Rickettsiales were detected. We also carried out phylogenetic reconstruction using Wolbachia sequences from the SILVA and Greengenes databases, Alphaproteobacteria putative endosymbionts and Rickettsiales OTUs obtained in the previous studies on the microbial community of tardigrades as well as Rickettsiales and Wolbachia OTUs obtained in the current study. Our discovery of Wolbachia in tardigrades can fuel new research to uncover the specifics of this interaction.The accepted manuscript in pdf format is listed with the files at the bottom of this page. The presentation of the authors' names and (or) special characters in the title of the manuscript may differ slightly between what is listed on this page and what is listed in the pdf file of the accepted manuscript; that in the pdf file of the accepted manuscript is what was submitted by the author

Analyses of the ΔF508 CFTR fragment with RNAdigest RNAse T1 digestion.

<p><b>A</b>. The simulated digestion analysis of ΔF508 CFTR is shown that includes a 56-base RNAse T1 digestion product along with other digestion products. <b>B</b>. The mfold structure model of the 149-base fragment of ΔF508 CFTR that illustrates the RNAdigest secondary structure constraints.</p

Summary of RNAdigest analysis on published mRNA structures based on RNAse digestion results^*.

<p>*Furthermore, RNAdigest correctly identified the presence and position of the 56-base product of RNAse T1 digestion of deltaF508 CFTR fragment (<a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0096759#pone-0096759-g006" target="_blank"><i>Figure 6</i></a><i>,</i> and <i>Figures S1–S4</i>) <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0096759#pone.0096759-Bartoszewski1" target="_blank">[16]</a>.</p