Matthews correlation coefficient for predicted binding residues versus the structural similarity SP-score between predicted and known structures of 116 targets.

<p>The correlation coefficient is 0.38.</p

Complete mitochondrial genome of <i>Basilepta melanopus</i> Lefèvre, 1893 (coleoptera: chrysomelidae: eumolpinae), a tea pest from Southern China

The tea pest, Basilepta melanopus Lefèvre 1893 (Chrysomelidae), belongs to the subfamily Eumolpinae. In this study, the complete mitochondrial genome sequence of B. melanopus from southern China was sequenced using the next-generation sequencing technique, assembled, and annotated using bioinformatics tools. The complete mitochondrial genome was 15,905 bp in length. The overall GC content was 22.51%, in which the percentages for the bases A, T, C, and G were 41.23%, 36.26%, 8.92%, and 13.59%, respectively. Thirty-seven genes were predicted, including 13 protein-coding, 22 transfer RNA, and two ribosomal RNA genes. Phylogenetic analysis based on the complete mitochondrial genome sequences of 18 Chrysomelidae taxa revealed that B. melanopus was closely related to Basilepta fulvipes.</p

Hyper-Recombinant Plants: An Emerging Field for Plant Breeding

Novelty is the primary requirement and breeding target for plant breeding, which can make a significant contribution to the new cultivar. The key factor for successful breeding is the genetic variation in the progeny, which depends on the degree of genetic material mixing after meiosis. However, meiotic recombination is tightly astricting in plants, resulting in a limited number of crossovers (COs). Recently, several anti-CO factors have been identified that limiting the meiotic recombination in plants, and the knock-out mutants displayed a significant increase in recombination frequency. This provides a universal tool to manipulate the meiotic recombination in plants by applying anti-CO genes, which will facilitate the breeding procedure. Due to the rapid development of genome sequencing and gene editing technologies, the genomes of more and more plants have been sequenced. In the meanwhile, the efficient CRISPR-Cas9 system has also been established in plants. Thus, it’s time to break the shackles of meiotic recombination to create novel cultivars in the biological era of genomics. Here we summarize the functional studies of the main meiotic recombination suppressors in plants, with the discussion of the possibility to apply the anti-CO genes in plant breeding as an emerging tool, especially for ornamental plant breeding.</p

Binding of metal ions during folding process.

<p>The evolution of the number of bound metal ions (the upper number in the circle) and R_p (the lower number in the circle) during the folding process. The basins are depicted by circles and their positions roughly correspond to the CVs.</p

Performance of various methods for DNA-binding protein prediction (leave-one-out cross validation).

<p>Performance of various methods for DNA-binding protein prediction (leave-one-out cross validation).</p

Detecting DBPs in 18 structural folds shared by DNA-binding and non-binding proteins.

<p>Detecting DBPs in 18 structural folds shared by DNA-binding and non-binding proteins.</p

Free Energy Landscape and Multiple Folding Pathways of an H-Type RNA Pseudoknot

<div><p>How RNA sequences fold to specific tertiary structures is one of the key problems for understanding their dynamics and functions. Here, we study the folding process of an H-type RNA pseudoknot by performing a large-scale all-atom MD simulation and bias-exchange metadynamics. The folding free energy landscapes are obtained and several folding intermediates are identified. It is suggested that the folding occurs via multiple mechanisms, including a step-wise mechanism starting either from the first helix or the second, and a cooperative mechanism with both helices forming simultaneously. Despite of the multiple mechanism nature, the ensemble folding kinetics estimated from a Markov state model is single-exponential. It is also found that the correlation between folding and binding of metal ions is significant, and the bound ions mediate long-range interactions in the intermediate structures. Non-native interactions are found to be dominant in the unfolded state and also present in some intermediates, possibly hinder the folding process of the RNA.</p></div

Comparison of predicted (red) and native structures (green) of target 1yfjD (DAM).

<p>Native structure and DNA are represented by green and orange, respectively. The predicted structure and DNA are denoted by color red and grey. The predicted binding sites and native binding sites are in cyan and yellow colors, respectively.</p

Structures of the unfolded states.

<p>(A) Representative structures of the largest six clusters in the unfolded states. (B) HB map averaged over all the structures in the unfolded states. The formation probabilities are indicated by different colors, as quantified by the color scale beside the figure. The labels inside the figure are also colored, with yellow indicating tertiary interactions between H₁ and L₂ and white non-native HBs. (C) The number of bound metal ions and R_p as a function of Rg plotted for the largest six clusters.</p

Performance of various methods for predicting DNA-binding proteins.

a<p>SN, sensitivity; PR, precision; SP, specificity; ACC, accuracy; MCC, Matthews correlation coefficient.^bMethods based on known protein structures. ^cFrom Ref. <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0096694#pone.0096694-Gao2" target="_blank">[47]</a>^dfrom Ref. <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0096694#pone.0096694-Zhao1" target="_blank">[53]</a>. ^efrom Ref. <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0096694#pone.0096694-Gao3" target="_blank">[48]</a>.</p