B\"uchi VASS recognise w-languages that are Sigma^1_1 - complete

This short note exhibits an example of a Sigma^1_1-complete language that can be recognised by a one blind counter B\"uchi automaton (or equivalently a B\"uchi VASS with only one place)

Probing Xist RNA Structure in Cells Using Targeted Structure-Seq

<div><p>The long non-coding RNA (lncRNA) Xist is a master regulator of X-chromosome inactivation in mammalian cells. Models for how Xist and other lncRNAs function depend on thermodynamically stable secondary and higher-order structures that RNAs can form in the context of a cell. Probing accessible RNA bases can provide data to build models of RNA conformation that provide insight into RNA function, molecular evolution, and modularity. To study the structure of Xist in cells, we built upon recent advances in RNA secondary structure mapping and modeling to develop Targeted Structure-Seq, which combines chemical probing of RNA structure in cells with target-specific massively parallel sequencing. By enriching for signals from the RNA of interest, Targeted Structure-Seq achieves high coverage of the target RNA with relatively few sequencing reads, thus providing a targeted and scalable approach to analyze RNA conformation in cells. We use this approach to probe the full-length Xist lncRNA to develop new models for functional elements within Xist, including the repeat A element in the 5’-end of Xist. This analysis also identified new structural elements in Xist that are evolutionarily conserved, including a new element proximal to the C repeats that is important for Xist function.</p></div

Models for RNA conformation in the region containing the Xist C repeats.

<p><b>A.</b> A model for the region of Xist (3101–5090 nt) that overlaps the C repeats. The 14 tandem C repeats alternate in color between green and purple (to facilitate visualization). <b>B.</b> Detailed image depicting the repeated motif found in the C repeats (specifically for 4006-4125 nt) using notation as indicated in Figs <a href="http://www.plosgenetics.org/article/info:doi/10.1371/journal.pgen.1005668#pgen.1005668.g004" target="_blank">4</a> and <a href="http://www.plosgenetics.org/article/info:doi/10.1371/journal.pgen.1005668#pgen.1005668.g005" target="_blank">5</a>. <b>C.</b> Similar detailed image depicting a model of the non-repetitive region 3’ to the last C repeat which shows high evolutionary conservation. The target sequence of LNA-4978, which is predicted to disrupt the structure, and knocks Xist off the chromatin, is shown in yellow. For alignment, see <a href="http://www.plosgenetics.org/article/info:doi/10.1371/journal.pgen.1005668#pgen.1005668.s041" target="_blank">S36 Fig</a>.</p

Xist regions with exceptionally favorable <i>z</i>-scores¹.

<p>Xist regions with exceptionally favorable <i>z</i>-scores¹.</p

Examining the conformations of elements within Xist RNA using a mixture of computational approaches and Targeted Structure-Seq.

<p><b>A.</b> Xist RNA (purple) contains several repetitive elements (indicated as thick regions, labeled A-F), and a conserved stem-loop structure in exon 4 (labeled as e4SL). The predicted <i>z</i>-score for 150 nt windows calculated every 10 nt (negative and positive values in gray and blue, respectively). Boxes indicate overlapping windows with <i>z</i>-score <1<i>σ</i> Xist average, classified as low <i>z</i>-score regions. <b>B.</b> An overview of Targeted Structure-Seq. A target RNA (purple) can be methylated (red circles) with dimethylsulfate (DMS, shown with red methyl group) in cells. After RNA isolation, the sites of methylation are determined using reverse transcription with primers specific for the RNA of interest (purple) but not other RNAs (gray). Sequencing and analysis of these data can be used to determine the DMS reactivity at each base, and can aid in modeling of the cellular conformation of the RNA. <b>C.</b> To determine which termination events were caused by DMS (red) as opposed to spontaneous termination (blue), the termination and read-through events are counted. Using an untreated control to estimate the rate of spontaneous termination, the data is normalized to determine the DMS reactivity at each base (see <a href="http://www.plosgenetics.org/article/info:doi/10.1371/journal.pgen.1005668#sec015" target="_blank">Materials and Methods</a> for details). These data can be used for free energy minimization to model the RNA conformation, which can be further validated by examining the evolutionary conservation of base pairing.</p

DMS reactivity accurately identifies accessible nucleotides in 18S rRNA.

<p><b>A.</b> DMS reactivity profile (red) for A and C bases in the 18S rRNA. Data is shown for treatment with three different DMS conditions (low: 0.4% DMS v/v, 8 min; intermediate: 0.75% v/v DMS, 8 min; high: 2% DMS for 4 min. To emphasize the lower values, some positions (low, n = 17; intermediate, n = 19; high, n = 19) have reactivity above the maximum value shown (<i>P</i>_DMS(<i>i</i>) > 0.1). <b>B.</b> The location of strongly and moderately DMS-reactive nucleotides mapped onto a model of part of the murine 18S rRNA [<a href="http://www.plosgenetics.org/article/info:doi/10.1371/journal.pgen.1005668#pgen.1005668.ref043" target="_blank">43</a>]. The only conflict between the mapping data and the model in this region is indicated with an asterisk (415 nt). The data for the remainder of the structure are shown in <a href="http://www.plosgenetics.org/article/info:doi/10.1371/journal.pgen.1005668#pgen.1005668.s008" target="_blank">S3 Fig</a>.</p

Secondary structure model for Xist Repeat A.

<p>Model based on energy minimization constrained using DMS data from Targeted Structure-Seq results. The predicted free energy () is -103.5 kcal/mol for folding. The structure is annotated to show DMS reactivity, conservation in rodents and mammals, and sites of consistent and compensatory mutations—single and double point-mutations, respectively, which preserve base pairing. Annotations are defined in the key (upper left) and repeats are defined by green shading and labeled accordingly.</p

Comparison of conservation and base-pairing between different models of the repeat A region of Xist.

<p>Comparison of conservation and base-pairing between different models of the repeat A region of Xist.</p

MOESM1 of Collecting near mature and immature orchid seeds for ex situ conservation: ‘in vitro collecting’ as a case study

Additional file 1.  Kruskal-Wallis rank sum test

MOESM1 of Statistical prediction of immunity to placental malaria based on multi-assay antibody data for malarial antigens

Additional file 1. A heatmap that illustrates the observed antibody levels, along with clustering among antibodies (dendrogram in right) and 1377 patients (dendrogram on top). Below the top dendrogram, the panel with red and blue vertical bars represents malaria infected (in red) and none infected (in blue) subjects. Note that log-transformed antibody levels was used for the ease of visualization