Data_Sheet_1_Non-coding RNA expression analysis revealed the molecular mechanism of flag leaf heterosis in inter-subspecific hybrid rice.zip

Heterosis has been used widespread in agriculture, but its molecular mechanism is inadequately understood. Plants have a large number of non-coding RNAs (ncRNAs), among them, functional ncRNAs that have been studied widely containing long non-coding RNA (lncRNA) and circular RNA (circRNA) that play a role in varied biological processes, as well as microRNA (miRNA), which can not only regulate the post-transcriptional expression of target genes, but also target lncRNA and circRNA then participate the competing endogenous RNA (ceRNA) regulatory network. However, the influence of these three ncRNAs and their regulatory relationships on heterosis is unknown in rice. In this study, the expression profile of ncRNAs and the ncRNA regulatory network related to heterosis were comprehensively analyzed in inter-subspecific hybrid rice. A total of 867 miRNAs, 3,278 lncRNAs and 2,521 circRNAs were identified in the hybrid and its parents. Analysis of the global profiles of these three types of ncRNAs indicated that significant differences existed in the distribution and sequence characteristics of the corresponding genes. The numbers of miRNA and lncRNA in hybrid were higher than those in its parents. A total of 784 ncRNAs (169 miRNAs, 573 lncRNAs and 42 circRNAs) showed differentially expressed in the hybrid, and their target/host genes were vital in stress tolerance, growth and development in rice. These discoveries suggested that the expression plasticity of ncRNA has an important role of inter-subspecific hybrid rice heterosis. It is worth mentioning that miRNAs exhibited substantially more variations between hybrid and parents compared with observed variation for lncRNA and circRNA. Non-additive expression ncRNAs and allele-specific expression genes-related ncRNAs in hybrid were provided in this study, and multiple sets of ncRNA regulatory networks closely related to heterosis were obtained. Meanwhile, heterosis-related regulatory networks of ceRNA (lncRNA and circRNA) and miRNA were also demonstrated.</p

Functional analysis of differentially expressed genes (DEGs) based on RNA-Seq data.

<p>GO functional enrichment analysis of differentially expressed genes in R2-v-R1 and R2-v-R3. Based on sequence homology, 1,011 DEGs could be categorized into three main categories (cellular component, molecular function, and biological process), in which there are 14, 17, and 20 functional groups, respectively. Among these groups, the terms cell part (GO: 0044464), binding (GO: 0005488), and metabolic process (GO: 0008152) are dominant in each of the three main categories, respectively.</p

Pyrolysis-Based Technology for Recovering Copper from Transistors on Waste Printed Circuit Boards

Waste electronic components (ECs) recycling is a crucial part of waste printed circuit boards (WPCBs) recycling system. Waste transistors (WTs) are one of the largest obsolete ECs whose recycling technology has been poorly developed. This study presented a pyrolysis-based technology for recovering copper from WTs disassembled from WPCBs, including coarse crushing, pyrolysis, pulverizing, and sieving. First, the WTs were coarsely crushed to reduce the particle size of the epoxy molding compound (EMC). Second, the coarsely crushed WTs were pyrolyzed to damage the cross-linking network structure of EMC and reduce the hardness of EMC. Third, all of the pyrolysis residues were crushed and sieved to separate metals and nonmetals. Finally, an integrated recycling process was proposed based on above studies. In addition, the mechanism of the pyrolysis was analyzed based on bond theory and product analysis to deeply understand the recycling process. Under optimal conditions, 99.16% of copper in WTs were recovered with a purity of 92.75%. This paper provides a method for waste transistors recycling in an efficient and environmentally friendly way

Histogram presentation of gene ontology (GO) classification.

<p>The results are summarized in three main categories: biological process, molecular function and cellular component. The y-axis indicates the number of genes in a category. In three main categories of GO classification, there are 16, 17, and 20 functional groups, respectively. Metabolic process (GO: 0008152), with 851 genes, are dominant in the main category of biological process. Binding (GO: 0005488) and cell part (GO: 0044464) consisted of 6892 and 2688 genes, are dominant in the main categories of molecular function and cellular component, respectively.</p

Distribution of the gene sequences detected in rice developing embryo via RNA-Seq.

<p>Distribution of the gene sequences detected in rice developing embryo via RNA-Seq.</p

Selectfluor-Promoted Sequential Reactions via Allene Intermediates: Metal-Free Construction of Fused Polycyclic Skeletons

Polycyclic skeletons are present in numerous important compounds, such as synthetic intermediates and target molecules of biological interest. In this paper, a Selectfluor-promoted construction of polycyclic skeletons with high synthetic efficiency was developed

Changes in gene expression profile among the different developmental stages.

<p>The number of up-regulated and down-regulated genes between R1 and R2, R2 and R3 are summarized. Between the R1 (3 DAP) and R2 (7 DAP) rice embryo libraries, there are 275 genes up-regulated and 397 genes down-regulated, while there are 128 up-regulated genes and 376 down-regulated genes between the R2 (7 DAP) and R3 (14 DAP) rice embryo libraries.</p

Venn diagram showing the genes expressed in each of the three stages of rice embryo development.

<p>R1, 3–5 DAP; R2, 7 DAP; R3, 14 DAP. Among these genes, 20,856 are expressed at all three developmental stages, 952 are co-expressed in R1 and R2, 792 are co-expressed in R2 and R3, and 793 are co-expressed in R1 and R3. The number of stage-specifically expressed genes is 1,131 (R1), 1,443 (R2), and 1,223 (R3), respectively.</p

Expression patterns in the four expression clusters.

<p>Clusters were obtained by the k-means method on the gene expression profiles of the 1011 modulated genes. R1, 3–5 DAP; R2, 7 DAP; R3, 14 DAP. The most abundant group is Cluster 1, with 543 genes whose expression shows a negative slope during embryogenesis. The second abundant group is Cluster 2, which contained 267 genes whose expression shows a positive slope from 3 to 14 DAP. Cluster 3 is composed of 107 genes that begin to up-regulate at 3–5 DAP, peak at 7 DAP, and decrease thereafter. Cluster 4 consisted of 94 genes that are down-regulated from 3–5 to 7 DAP, then up-regulate to 14 DAP. Their identities and expression clusters are listed in <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0030646#pone.0030646.s004" target="_blank">Table S4</a>.</p

Percent of coverage representing the percentage of genes which expressed in each of the three stages mapped in the rice genome.

<p>R1, 3–5 DAP; R2, 7 DAP; R3, 14 DAP. Gene coverage is the percentage of a gene covered by reads. This value is equal to the ratio of the base number in a gene covered by unique mapping reads to the total bases number of that gene. The distribution of distinct tags over different tag abundance categories show similar patterns for all three RNA-Seq libraries. The similarity distribution has a comparable pattern with more than 20% of the sequences having a similarity >80%, while approximately 80% of the hits has a similar range.</p