MicroRNAs (miRNAs) are endogenous non-coding small RNAs that play vital regulatory roles in plant growth, development, and environmental stress responses. Cadmium (Cd) is a non-essential heavy metal that is highly toxic to living organisms. To date, a number of conserved and non-conserved miRNAs have been identified to be involved in response to Cd stress in some plant species. However, the miRNA-mediated gene regulatory networks responsive to Cd stress in radish (Raphanus sativus L.) remain largely unexplored. To dissect Cd-responsive miRNAs and their targets systematically at the global level, two small RNA libraries were constructed from Cd-treated and Cd-free roots of radish seedlings. Using Solexa sequencing technology, 93 conserved and 16 non-conserved miRNAs (representing 26 miRNA families) and 28 novel miRNAs (representing 22 miRNA families) were identified. In all, 15 known and eight novel miRNA families were significantly differently regulated under Cd stress. The expression patterns of a set of Cd-responsive miRNAs were validated by quantitative real-time PCR. Based on the radish mRNA transcriptome, 18 and 71 targets for novel and known miRNA families, respectively, were identified by the degradome sequencing approach. Furthermore, a few target transcripts including phytochelatin synthase 1 (PCS1), iron transporter protein, and ABC transporter protein were involved in plant response to Cd stress. This study represents the first transcriptome-based analysis of miRNAs and their targets responsive to Cd stress in radish roots. These findings could provide valuable information for functional characterization of miRNAs and their targets in regulatory networks responsive to Cd stress in radish.

Using 14 months of magnetic field and plasma data observed by the ISEE 1 and 2 spacecraft, ULF waves of period 2–20 min in the outer magnetosphere were studied. Statistical properties of the ULF waves can be summarized as follows: (1) Intense compressional waves are a persistent feature near the two flanks of the magnetosphere. They are mainly polarized in a meridian plane with comparable compressional and transverse amplitudes and have larger amplitude at magnetic latitudes below 20° than at higher latitudes. The magnetic pressure perturbations for the waves are in antiphase with the plasma pressure perturbations; (2) Transverse waves polarized in the azimuthal direction (azimuthal waves) are found to be mainly a nightside phenomenon. Their appearances on the nightside magnetosphere seem to be associated with substorm activity; (3) Compressional wave power and plasma β, the ratio between the plasma pressure and the magnetic field pressure, are correlated, but ULF wave power in the above noted period range is not significantly correlated with AE, plasma pressure or VA; (4) The compressional waves are most likely to be generated internally in the regions where plasma β and field line curvature are large.

In the terrestrial magnetosphere, the inhomogeneous magnetic field and plasma density give rise to a continuous spectrum of field line resonant frequencies. Compressional disturbances with characteristic frequencies lying within the range of the spectrum may couple to transverse oscillations of resonant field lines. The coupling is of particular interest for global compressional modes trapped in the magnetic cavity. These modes decay in time through the coupling, even in the absence of dissipation. The importance of the process is that, through the damping of the global modes, large-scale motion can drive localized field line resonances. In this study, we investigate the mode coupling and examinc the parameter dependence of the damping rate of the global mode. The problem is discussed as an initial value problem in the box model which retains most of the significant physics yet remains mathematically tractable. To treat the coupling, we use the analogy of Landau damping in a homogeneous plasma. From the Laplace transform approach, we obtain the complex frequencies of the compressional wave by finding the singularities of the associated Green's function. Once the complex frequency has been found numerically, we obtain the corresponding waveforms in the box. Many observed wave properties can then be obtained. The calculations agree well with other simulation work and correspond to results obtained for the reflection of radio waves from the ionosphere and for plasma heating by absorption of radiation. ZHU ,•D K•vg•,sor•: COVl,•,gD ULF W,•vgs--ANALYS•S AND SOLUTIONS of electromagnetic waves in overdense plasma, Plasma Ph•ts., 16, 565, 1974.

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For a nonmonotonic Alfvén velocity profile, the global mode of the magnetosphere can be shown to couple to multiple resonant field lines. The mode structure itself is greatly altered by introduction of nonmonotonicity. Because of the rapid decrease of density at the plasmapause, the variation of the Alfvén velocity naturally separates the magnetosphere into inner and outer parts. ULF wave perturbations are found to be trapped in the Alfvén velocity valleys and, under certain circumstances, ULF wave amplitudes in the inner magnetosphere are greatly enhanced. The results obtained may explain some ULF perturbations observed in the low‐latitude regions of the magnetosphere.

BackgroundRadish (Raphanus sativus L.), is an important root vegetable crop worldwide. Glucosinolates in the fleshy taproot significantly affect the flavor and nutritional quality of radish. However, little is known about the molecular mechanisms underlying glucosinolate metabolism in radish taproots. The limited availability of radish genomic information has greatly hindered functional genomic analysis and molecular breeding in radish.ResultsIn this study, a high-throughput, large-scale RNA sequencing technology was employed to characterize the de novo transcriptome of radish roots at different stages of development. Approximately 66.11 million paired-end reads representing 73,084 unigenes with a N50 length of 1,095 bp, and a total length of 55.73 Mb were obtained. Comparison with the publicly available protein database indicates that a total of 67,305 (about 92.09% of the assembled unigenes) unigenes exhibit similarity (e –value ≤ 1.0e-5) to known proteins. The functional annotation and classification including Gene Ontology (GO), Clusters of Orthologous Group (COG) and Kyoto Encyclopedia of Genes and Genomes (KEGG) analysis revealed that the main activated genes in radish taproots are predominately involved in basic physiological and metabolic processes, biosynthesis of secondary metabolite pathways, signal transduction mechanisms and other cellular components and molecular function related terms. The majority of the genes encoding enzymes involved in glucosinolate (GS) metabolism and regulation pathways were identified in the unigene dataset by targeted searches of their annotations. A number of candidate radish genes in the glucosinolate metabolism related pathways were also discovered, from which, eight genes were validated by T-A cloning and sequencing while four were validated by quantitative RT-PCR expression profiling.ConclusionsThe ensuing transcriptome dataset provides a comprehensive sequence resource for molecular genetics research in radish. It will serve as an important public information platform to further understanding of the molecular mechanisms involved in biosynthesis and metabolism of the related nutritional and flavor components during taproot formation in radish.Electronic supplementary materialThe online version of this article (doi:10.1186/1471-2164-14-836) contains supplementary material, which is available to authorized users.

Radish (Raphanus sativus L.) is one of the most important vegetable crops worldwide. Taproot thickening represents a critical developmental period that determines yield and quality in radish life cycle. To isolate differentially expressed genes (DGEs) involved in radish taproot thickening process and explore the molecular mechanism underlying taproot development, three cDNA libraries from radish taproot collected at pre-cortex splitting stage (L1), cortex splitting stage (L2), and expanding stage (L3) were constructed and sequenced by RNA-Seq technology. More than seven million clean reads were obtained from the three libraries, from which 4,717,617 (L1, 65.35%), 4,809,588 (L2, 68.24%) and 4,973,745 (L3, 69.45%) reads were matched to the radish reference genes, respectively. A total of 85,939 transcripts were generated from three libraries, from which 10,450, 12,325, and 7392 differentially expressed transcripts (DETs) were detected in L1 vs. L2, L1 vs. L3, and L2 vs. L3 comparisons, respectively. Gene Ontology and pathway analysis showed that many DEGs, including EXPA9, Cyclin, CaM, Syntaxin, MADS-box, SAUR, and CalS were involved in cell events, cell wall modification, regulation of plant hormone levels, signal transduction and metabolisms, which may relate to taproot thickening. Furthermore, the integrated analysis of mRNA-miRNA revealed that 43 miRNAs and 92 genes formed 114 miRNA-target mRNA pairs were co-expressed, and three miRNA-target regulatory networks of taproot were constructed from different libraries. Finally, the expression patterns of 16 selected genes were confirmed using RT-qPCR analysis. A hypothetical model of genetic regulatory network associated with taproot thickening in radish was put forward. The taproot formation of radish is mainly attributed to cell differentiation, division and expansion, which are regulated and promoted by certain specific signal transduction pathways and metabolism processes. These results could provide new insights into the complex molecular mechanism underlying taproot thickening and facilitate genetic improvement of taproot in radish.

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