Endogenous small-noncoding RNAs and their roles in chilling response and stress acclimation in Cassava

BACKGROUND: Small noncoding RNA (sncRNA), including microRNAs (miRNAs) and endogenous small-interfering RNAs (endo-siRNAs) are key gene regulators in eukaryotes, playing critical roles in plant development and stress tolerance. Trans-acting siRNAs (ta-siRNAs), which are secondary siRNAs triggered by miRNAs, and siRNAs from natural antisense transcripts (nat-siRNAs) are two well-studied classes of endo-siRNAs. RESULTS: In order to understand sncRNAs’ roles in plant chilling response and stress acclimation, we performed a comprehensive study of miRNAs and endo-siRNAs in Cassava (Manihot esculenta), a major source of food for the world populations in tropical regions. Combining Next-Generation sequencing and computational and experimental analyses, we profiled and characterized sncRNA species and mRNA genes from the plants that experienced severe and moderate chilling stresses, that underwent further severe chilling stress after chilling acclimation at moderate stress, and that grew under the normal condition. We also included castor bean (Ricinus communis) in our study to understand conservation of sncRNAs. In addition to known miRNAs, we identified 32 (22 and 10) novel miRNAs as well as 47 (26 and 21) putative secondary siRNA-yielding and 8 (7 and 1) nat-siRNA-yielding candidate loci in Cassava and castor bean, respectively. Among the expressed sncRNAs, 114 miRNAs, 12 ta-siRNAs and 2 nat-siRNAs showed significant expression changes under chilling stresses. CONCLUSION: Systematic and computational analysis of microRNAome and experimental validation collectively showed that miRNAs, ta-siRNAs, and possibly nat-siRNAs play important roles in chilling response and chilling acclimation in Cassava by regulating stress-related pathways, e.g. Auxin signal transduction. The conservation of these sncRNA might shed lights on the role of sncRNA-mediated pathways affected by chilling stress and stress acclimation in Euphorbiaceous plants. ELECTRONIC SUPPLEMENTARY MATERIAL: The online version of this article (doi:10.1186/1471-2164-15-634) contains supplementary material, which is available to authorized users

Proton irradiation effect on SCDs

The Low Energy X-ray Telescope is a main payload on the Hard X-ray Modulation Telescope satellite. The swept charge device is selected for the Low Energy X-ray Telescope. As swept charge devices are sensitive to proton irradiation, irradiation test was carried out on the HI-13 accelerator at the China Institute of Atomic Energy. The beam energy was measured to be 10 MeV at the SCD. The proton fluence delivered to the SCD was $3\times10^{8}\mathrm{protons}/\mathrm{cm}^{2}$ over two hours. It is concluded that the proton irradiation affects both the dark current and the charge transfer inefficiency of the SCD through comparing the performance both before and after the irradiation. The energy resolution of the proton-irradiated SCD is 212 [email protected] keV at $-60\,^{\circ}\mathrm{C}$, while it before irradiated is 134 eV. Moreover, better performance can be reached by lowering the operating temperature of the SCD on orbit

Mutation signatures implicate aristolochic acid in bladder cancer development

10.1186/s13073-015-0161-3Genome Medicine71Article number 3

Characteristics and properties of a polysaccharide isolated from Wolfiporia cocos as potential dietary supplement for IBS

IntroductionAs low FODMAP (Fermentable oligosaccharides, disaccharides, monosaccharides and polyols) diet therapy is recommended for most of Irritable Bowel Syndrome (IBS) patients, the consequent insufficient of dietary fibers (DFs) intake exert an adverse impact on intestinal health. It is necessary to find suitable DFs for IBS patients.MethodsThis study extracted a water-insoluble polysaccharide from Wolfiporia cocos (WIP) by alkali-extraction and acid-precipitation method. Its molecular weight was detected by high performance gel permeation chromatography (HPGPC) analysis. The structure of WIP was analyzed by Fourier transform infrared (FT-IR) spectrum, Nuclear Magnetic Resonance (NMR) spectra and X-ray diffraction (XRD). The properties related to stability, digestion, viscosity, osmotic activity, adsorption and fermentation were investigated, aimed to explore the feasibility of WIP as a new DF supplement for patients with IBS. In addition, 16S rRNA sequencing analysis was conducted to explore its effects on IBS-related gut microbiota.Results and DiscussionThe results showed that WIP had a single homogeneous composition and the molecular weight was 8.1 × 103 Da. WIP was indicated as a kind of pyranose form with β anomeric configuration and the main chain of WIP was 1,3-β-glucan with amorphous structure. In addition to good thermal stability, WIP also has low bioavailability and can reach the colon mostly without being digested. Moreover, the low viscosity and osmotic activity, the high water- swelling and water/oil-holding capacity, fructose adsorption capacity and poor fermentation performance of WIP demonstrated that it is suitable for IBS patients. It is worth noting that WIP regulates IBS associated gut microbiota effectively, such as the abundance of Lachnospiraceae and Prevotella. These findings provide a theoretical basis for the development of WIP as a dietary supplement for IBS patients with low FODMAP diet therapy.GRAPHICAL ABSTRAC

Methyl 4-(4-fluoro­phen­yl)-6-isopropyl-2-(methylsulfonyl)pyrimidine-5-carbox­ylate

The asymmetric unit of the title compound, C16H17FN2O4S, contains three independent mol­ecules, in which the pyrimidine and benzene rings are oriented at dihedral angles of 41.72 (3)°, 26.21 (3)° and 36.49 (3)°. Intra­molecular C—H⋯O hydrogen bonds result in the formation of two six- and one seven-membered non-planar rings, which have have twist conformations. In the crystal structure, inter­molecular C—H⋯O hydrogen bonds link the mol­ecules