A pair of orthologs of a leucine-rich repeat receptor kinase-like disease resistance gene family regulates rice response to raised temperature

<p>Abstract</p> <p>Background</p> <p>Rice <it>Xa3/Xa26 </it>disease-resistance gene encodes a leucine-rich repeat (LRR) receptor kinase-type protein against <it>Xanthomonas oryzae </it>pv. <it>oryzae </it>(<it>Xoo</it>) and belongs to a multigene family. However, the functions of most genes in this family are unknown.</p> <p>Results</p> <p>Here we report that two orthologs of this family, the <it>NRKe </it>from rice variety Nipponbare and <it>9RKe </it>from variety 93-11 at the <it>RKe </it>locus, have similar functions although they encode different proteins. This pair of orthologs could not mediate resistance to <it>Xoo</it>, but they were transcriptionally induced by raised temperature. Transcriptional activation of <it>NRKe </it>or <it>9RKe </it>resulted in the formation of temperature-sensitive lesion mimics, which were spots of dead cells associated with accumulation of superoxides, in different organs of the transgenic plants. These plants were more sensitive to high temperature shock than wild-type controls. Transgenic plants carrying a chimeric protein consisting of the LRR domain of NRKe and the kinase domain of Xa3/Xa26 developed the same lesion mimics as the <it>NRKe</it>-transgenic plants, whereas transgenic plants carrying another chimeric protein consisting of the LRR domain of Xa3/Xa26 and the kinase domain of NRKe were free of lesion mimic. All the transgenic plants carrying a chimeric protein were susceptible to <it>Xoo</it>.</p> <p>Conclusion</p> <p>These results suggest that the <it>RKe </it>locus is involved in rice response to raised temperature. The LRR domain of RKe protein appears to be important to sense increased temperature. The RKe-involved temperature-related pathway and Xa3/Xa26-mediated disease-resistance pathway may partially overlap.</p

Efficient purification and assembly of ribonucleoprotein complex for interaction analysis by MST assay coupled with GaMD simulations

Here, we describe a generic protocol for monitoring protein-RNA interaction using a cleavable GFP fusion of a recombinant RNA-binding protein. We detail each expression and purification step, including high salt and heparin column for contaminant RNA removal. After the assembly of RNA into the ribonucleoprotein complex, the MicroScale Thermophoresis assay enables the binding affinity to be obtained quickly with a small amount of sample. Further Gaussian accelerated molecular dynamics simulations allow us to analyze protein:RNA interactions in detail

Breeding response of transcript profiling in developing seeds of Brassica napus

<p>Abstract</p> <p>Background</p> <p>The upgrading of rapeseed cultivars has resulted in a substantial improvement in yield and quality in China over the past 30 years. With the selective pressure against fatty acid composition and oil content, high erucic acid- and low oil-content cultivars have been replaced by low erucic acid- and high oil-content cultivars. The high erucic acid cultivar Zhongyou 821 and its descendent, low erucic acid cultivar Zhongshuang 9, are representatives of two generations of the most outstanding Chinese rapeseed cultivars (<it>B. napus</it>) developed the past 2 decades. This paper compares the transcriptional profiles of Zhongshuang 9 and Zhongyou 821 for 32 genes that are principally involved in lipid biosynthesis during seed development in order to elucidate how the transcriptional profiles of these genes responded to quality improvement over the past 20 years.</p> <p>Results</p> <p>Comparison of the cultivar Zhongyou 821 with its descendent, Zhongshuang 9, shows that the transcriptional levels of seven of the 32 genes were upregulated by 30% to 109%, including <it>FAD3</it>, <it>ACCase, FAE1</it>, <it>GKTP</it>, <it>Caleosin</it>, <it>GAPDH</it>, and <it>PEPC</it>. Of the 32 genes, 10 (<it>KAS3, β-CT, BcRK6, P450, FatA, Oleosin, FAD6, FatB, α-CT </it>and <it>SUC1</it>) were downregulated by at least 20% and most by 50%. The <it>Napin </it>gene alone accounted for over 75% of total transcription from all 32 genes assessed in both cultivars. Most of the genes showed significant correlation with fatty acid accumulation, but the correlation in ZS9 was significantly different from that in ZY821. Higher <it>KCR2 </it>activity is associated with higher C16:0, C18:0, and C18:2 in both cultivars, lower C22:1 and total fatty acid content in ZY821, and lower 18:1 in ZS9.</p> <p>Conclusion</p> <p>This paper illustrates the response of the transcription levels of 32 genes to breeding in developing rapeseed seeds. Both cultivars showed similar transcription profiles, with the <it>Napin </it>gene predominantly transcribed. Selective pressure for zero erucic acid, low glucosinolate, high oleic acid and high oil content, as well as high yield, resulted in higher <it>FAD3</it>, <it>ACCase, FAE1</it>, <it>GKTP</it>, <it>Caleosin</it>, <it>GAPDH</it>, and <it>PEPC </it>expression levels and lower <it>KAS3, β-CT, BcRK6, P450, FatA, Oleosin, FAD6, FatB, α-CT </it>and <it>SUC1 </it>expression levels. It also resulted in altered relationships between these genes during storage accumulation in seed development.</p

Large expert-curated database for benchmarking document similarity detection in biomedical literature search

Document recommendation systems for locating relevant literature have mostly relied on methods developed a decade ago. This is largely due to the lack of a large offline gold-standard benchmark of relevant documents that cover a variety of research fields such that newly developed literature search techniques can be compared, improved and translated into practice. To overcome this bottleneck, we have established the RElevant LIterature SearcH consortium consisting of more than 1500 scientists from 84 countries, who have collectively annotated the relevance of over 180 000 PubMed-listed articles with regard to their respective seed (input) article/s. The majority of annotations were contributed by highly experienced, original authors of the seed articles. The collected data cover 76% of all unique PubMed Medical Subject Headings descriptors. No systematic biases were observed across different experience levels, research fields or time spent on annotations. More importantly, annotations of the same document pairs contributed by different scientists were highly concordant. We further show that the three representative baseline methods used to generate recommended articles for evaluation (Okapi Best Matching 25, Term Frequency-Inverse Document Frequency and PubMed Related Articles) had similar overall performances. Additionally, we found that these methods each tend to produce distinct collections of recommended articles, suggesting that a hybrid method may be required to completely capture all relevant articles. The established database server located at https://relishdb.ict.griffith.edu.au is freely available for the downloading of annotation data and the blind testing of new methods. We expect that this benchmark will be useful for stimulating the development of new powerful techniques for title and title/abstract-based search engines for relevant articles in biomedical research.Peer reviewe

Point Mutations with Positive Selection Were a Major Force during the Evolution of a Receptor-Kinase Resistance Gene Family of Rice

The rice (Oryza sativa) Xa26 gene, which confers resistance to bacterial blight disease and encodes a leucine-rich repeat (LRR) receptor kinase, resides at a locus clustered with tandem homologous genes. To investigate the evolution of this family, four haplotypes from the two subspecies of rice, indica and japonica, were analyzed. Comparative sequence analysis of 34 genes of 10 types of paralogs of the family revealed haplotype polymorphisms and pronounced paralog diversity. The orthologs in different haplotypes were more similar than the paralogs in the same haplotype. At least five types of paralogs were formed before the separation of indica and japonica subspecies. Only 7% of amino acid sites were detected to be under positive selection, which occurred in the extracytoplasmic domain. Approximately 74% of the positively selected sites were solvent-exposed amino acid residues of the LRR domain that have been proposed to be involved in pathogen recognition, and 73% of the hypervariable sites detected in the LRR domain were subject to positive selection. The family is formed by tandem duplication followed by diversification through recombination, deletion, and point mutation. Most variation among genes in the family is caused by point mutations and positive selection

Correction: Root colonization and growth promotion of soybean, wheat and Chinese cabbage by Bacillus cereus YL6.

[This corrects the article DOI: 10.1371/journal.pone.0200181.]

Design and Control of a Middle Vessel Batch Distillation Process for Separating the Methyl Formate/Methanol/Water Ternary System

The middle vessel batch distillation process for separating the methyl formate/methanol/water ternary system was simulated using Aspen Plus and Aspen Plus Dynamics. The composition control structure (CCS) and temperature control structure (TCS) were studied in a dynamic simulation based on the results of a steady-state simulation. Two temperature control structures, one the traditional TCS and the other TCS with high selectors, show better control performances than CCS. The two control structures can stably control the product purities and liquid holdups in the product vessels at the end of the batch. The results show that TCS with high selectors is better than traditional TCS in terms of the liquid holdups. The performance of the TCS with high selectors is assessed, and controllability is demonstrated

OsWRKY13 Mediates Rice Disease Resistance by Regulating Defense-Related Genes in Salicylate- and Jasmonate-Dependent Signaling

Although 109 WRKY genes have been identified in the rice genome, the functions of most are unknown. Here, we show that OsWRKY13 plays a pivotal role in rice disease resistance. Overexpression of OsWRKY13 can enhance rice resistance to bacterial blight and fungal blast, two of the most devastating diseases of rice worldwide, at both the seedling and adult stages, and shows no influence on the fertility. This overexpression was accompanied by the activation of salicylic acid (SA) synthesis-related genes and SA-responsive genes and the suppression of jasmonic acid (JA) synthesis-related genes and JA-responsive genes. OsWRKY13 bound to the promoters of its own and at least three other genes in SA- and JA-dependent signaling pathways. Its DNA-binding activity was influenced by pathogen infection. These results suggest that OsWRKY13, as an activator of the SA-dependent pathway and a suppressor of JA-dependent pathways, mediates rice resistance by directly or indirectly regulating the expression of a subset of genes acting both upstream and downstream of SA and JA. Furthermore, OsWRKY13 will provide a transgenic tool for engineering wider-spectrum and whole-growth-stage resistance rice in breeding programs