Structurexplor : a platform for the exploration of structural features of RNA secondary structures

Abstract : Summary: Discovering function-related structural features, such as the cloverleaf shape of transfer RNA secondary structures, is essential to understand RNA function. With this aim, we have developed a platform, named Structurexplor, to facilitate the exploration of structural features in populations of RNA secondary structures. It has been designed and developed to help biologists interactively search for, evaluate and select interesting structural features that can potentially explain RNA functions

The super-n-motifs model : a novel alignment-free approach for representing and comparing RNA secondary structures

Abstract : Motivation: Comparing ribonucleic acid (RNA) secondary structures of arbitrary size uncovers structural patterns that can provide a better understanding of RNA functions. However, performing fast and accurate secondary structure comparisons is challenging when we take into account the RNA configuration (i.e. linear or circular), the presence of pseudoknot and G-quadruplex (G4) motifs and the increasing number of secondary structures generated by high-throughput probing techniques. To address this challenge, we propose the super-n-motifs model based on a latent analysis of enhanced motifs comprising not only basic motifs but also adjacency relations. The super-n-motifs model computes a vector representation of secondary structures as linear combinations of these motifs. Results: We demonstrate the accuracy of our model for comparison of secondary structures from linear and circular RNA while also considering pseudoknot and G4 motifs. We show that the supern- motifs representation effectively captures the most important structural features of secondary structures, as compared to other representations such as ordered tree, arc-annotated and string representations. Finally, we demonstrate the time efficiency of our model, which is alignment free and capable of performing large-scale comparisons of 10 000 secondary structures with an efficiency up to 4 orders of magnitude faster than existing approaches

Zigbee-Based Positioning System For Coal Miners

AbstractChina's present communication systems in coal mine can not effectively provide the information such as dynamic distribution of coal miners in work and production environment. Hence, rescue efforts are hard to be carried out in case of coal mine accident. To deal with this problem, the paper at first introduces the characteristics, structure and network construction method of ZigBee protocol. Then, by using the ZigBee technology based on IEEE802.15.4 criteria, the wireless communication network and the structure of ZigBee communication module for coal mine are studied and designed. At last, multilateration positioning algorithm is employed to realize the positioning of coal miners. Coal miner positioning system enters into computer management system via network, laying important actual significance to the production safety and emergent resuce of coal mine

Towards Dynamic Structure Changes Detection in Financial Series via Causal Analysis

International audienceThis is a preliminary paper describing the concepts and principles for a sequential approach towards causal detection in a financial system presented by large-scale data. In particular, we focus on both the regime-switching and causal discovery detection models. This is to address the problem of heterogeneous conditions when analysing nonlinear characteristics from the financial markets. Thus handling the dynamics of multiple regimes in a series and new data to obtain valid answers to causal queries of interest. The availability of large-scale time series data presents new opportunities in knowledge discovery because the insight that can be gained from a causal perspective in a nonlinear system would be tremendous for asset allocation. However, largescale series are prone to biases, including sampling selection. For decades, the main ways to study nonlinear time series analysis has been isolated to statistical analysis, largely restricted to parametric models. We here present an approach for handling a nonlinear system, infused with a causal solution in a temporal mining task

Purification and Characterization of a CkTLP Protein from Cynanchum komarovii Seeds that Confers Antifungal Activity

BACKGROUND: Cynanchum komarovii Al Iljinski is a desert plant that has been used as analgesic, anthelminthic and antidiarrheal, but also as a herbal medicine to treat cholecystitis in people. We have found that the protein extractions from C. komarovii seeds have strong antifungal activity. There is strong interest to develop protein medication and antifungal pesticides from C. komarovii for pharmacological or other uses. METHODOLOGY/PRINCIPAL FINDINGS: An antifungal protein with sequence homology to thaumatin-like proteins (TLPs) was isolated from C. komarovii seeds and named CkTLP. The three-dimensional structure prediction of CkTLP indicated the protein has an acid cleft and a hydrophobic patch. The protein showed antifungal activity against fungal growth of Verticillium dahliae, Fusarium oxysporum, Rhizoctonia solani, Botrytis cinerea and Valsa mali. The full-length cDNA was cloned by RT-PCR and RACE-PCR according to the partial protein sequences obtained by nanoESI-MS/MS. The real-time PCR showed the transcription level of CkTLP had a significant increase under the stress of abscisic acid (ABA), salicylic acid (SA), methyl jasmonate (MeJA), NaCl and drought, which indicates that CkTLP may play an important role in response to abiotic stresses. Histochemical staining showed GUS activity in almost the whole plant, especially in cotyledons, trichomes and vascular tissues of primary root and inflorescences. The CkTLP protein was located in the extracellular space/cell wall by CkTLP::GFP fusion protein in transgenic Arabidopsis. Furthermore, over-expression of CkTLP significantly enhanced the resistance of Arabidopsis against V. dahliae. CONCLUSIONS/SIGNIFICANCE: The results suggest that the CkTLP is a good candidate protein or gene for contributing to the development of disease-resistant crops

Response of sediment organic phosphorus composition to lake trophic status in China

Organic phosphorus (Po) constitutes the most important fraction of P in lake sediments, and the compositional properties of Po affect its behavior in lake ecosystems. In this study, 31P NMR, FT-IR spectroscopy, and UV–visible absorbance spectroscopy were combined to identify the dynamic composition of sediment Po across two sets of lakes in China ranging from oligotrophic to eutrophic, and their possible effects on lake eutrophication were evaluated. The results showed that sediment Po content (accounting for 24–75% of TP) was positively correlated with trophic status in both Eastern Plain and Yun-Gui Plateau lakes of China, and the linear relationship was more stable compared to total P (TP), implying that sediment Po may be a superior indicator of trophic status than TP. The Po component, phosphonate accounted for only 0.4% or less of Po, while the monoester P and diester P, accounted for 2–24% and 0.5–5% of Po, respectively, and were the main factors causing Po to increase with the increasing trophic status. The factors were closely related to the enhanced organic sewage load and intensification of contemporary sedimentation of phytoplankton. As trophic status increased, sediment Po might integrate into larger amounts of aromatic substances and functional groups, which could enhance the stability of Po in sediments. Furthermore, sediments from lakes with higher trophic status exhibited a higher degree of humification and molecular weights, which impart resistance to biodegradation, and therefore, reduced the risk of sediment Po release. However, the massive accumulation of bioavailable Po (monoester and diester P) allows possible degradation, supporting algal growth and maintains eutrophic status because there is abundant alkaline phosphatase in eutrophic lakes. Thus, to control lake eutrophication more effectively, targeted actions are urgently required to reduce the accumulation and degradation of Po in lake sediment