PPM1D phosphatase, a target of p53 and RBM38 RNA-binding protein, inhibits p53 mRNA translation via dephosphorylation of RBM38.

PPM1D phosphatase, also called wild-type p53-induced phosphatase 1, promotes tumor development by inactivating the p53 tumor suppressor pathway. RBM38 RNA-binding protein, also called RNPC1 and a target of p53, inhibits p53 messenger RNA (mRNA) translation, which can be reversed by GSK3 protein kinase via phosphorylation of RBM38 at serine 195. Here we showed that ectopic expression of RBM38 increases, whereas knockdown of RBM38 inhibits, PPM1D mRNA translation. Consistent with this, we found that RBM38 directly binds to PPM1D 3'-untranslated region (3'-UTR) and promotes expression of a heterologous reporter gene that carries PPM1D 3'-UTR in a dose-dependent manner. Interestingly, we showed that PPM1D directly interacts with and dephosphorylates RBM38 at serine 195. Furthermore, we showed that PPM1D modulates p53 mRNA translation and p53-dependent growth suppression through dephosphorylation of RBM38. These findings provide evidence that the crosstalk between PPM1D and RBM38, both of which are targets and modulators of p53, has a critical role in p53 expression and activity

Flexible protein folding by ant colony optimization

Protein structure prediction is one of the most challenging topics in bioinformatics. As the protein structure is found to be closely related to its functions, predicting the folding structure of a protein to judge its functions is meaningful to the humanity. This chapter proposes a flexible ant colony (FAC) algorithm for solving protein folding problems (PFPs) based on the hydrophobic-polar (HP) square lattice model. Different from the previous ant algorithms for PFPs, the pheromones in the proposed algorithm are placed on the arcs connecting adjacent squares in the lattice. Such pheromone placement model is similar to the one used in the traveling salesmen problems (TSPs), where pheromones are released on the arcs connecting the cities. Moreover, the collaboration of effective heuristic and pheromone strategies greatly enhances the performance of the algorithm so that the algorithm can achieve good results without local search methods. By testing some benchmark two-dimensional hydrophobic-polar (2D-HP) protein sequences, the performance shows that the proposed algorithm is quite competitive compared with some other well-known methods for solving the same protein folding problems

High-resolution DEM generated from LiDAR data for water resource management

Terrain patterns play an important role in determining the nature of water resources and related hydrological modelling. Digital Elevation Models (DEMs), offering an efficient way to represent ground surface, allow automated direct extraction of hydrological features (Garbrecht and Martz, 1999), thus bringing advantages in terms of processing efficiency, cost effectiveness, and accuracy assessment, compared with traditional methods based on topographic maps, field surveys, or photographic interpretations. However, researchers have found that DEM quality and resolution affect the accuracy of any extracted hydrological features (Kenward et al., 2000). Therefore, DEM quality and resolution must be specified according to the nature and application of the hydrological features. The most commonly used DEM in Victoria, Australia is Vicmap Elevation delivered by the Land Victoria, Department of Sustainability and Environment. It was produced by using elevation data mainly derived from existing contour map at a scale of 1:25,000 and digital stereo capture, providing a state-wide terrain surface representation with a horizontal resolution of 20 metres. The claimed standard deviations, vertical and horizontal, are 5 metres and 10 metres respectively (Land- Victoria, 2002). In worst case, horizontal errors could be up to ±30m. Although high resolution stereo aerial photos provide a potential way to generate high resolution DEMs, under the limitations of currently used technologies by prevalent commercial photogrammetry software, only DSMs (Digital Surface Models) other than DEMs can be directly generated. Manual removal of the nonground data so that the DSM is transformed into a DEM is time consuming. Therefore, using stereo aerial photos to produce DEM with currently available techniques is not an accurate and costeffective method. Light Detection and Ranging (LiDAR) data covering 6900 km² of the Corangamite Catchment area of Victoria were collected over the period 19 July 2003 to 10 August 2003. It will be used to support a series of salinity and water management projects for the Corangamite Catchment Management Authority (CCMA). The DEM derived from the LiDAR data has a vertical accuracy of 0.5m and a horizontal accuracy of 1.5m. The high quality DEM leads to derive much detailed terrain and hydrological attributes with high accuracy. Available data sources of DEMs in a catchment management area were evaluated in this study, including the Vicmap DEM, a DEM generated from stereo aerial photos, and LiDAR-derived DEM. LiDAR technology and LiDAR derived DEM were described. In order to assess the capability of LiDAR-derived DEM for improving the quality of extracted hydrological features, sub-catchment boundaries and drainage networks were generated from the Vicmap DEM and the LiDAR-derived DEM. Results were compared and analysed in terms of accuracy and resolution of DEMs. Elevation differences between Vicmap and LiDAR-derived DEMs are significant, up to 65m in some areas. Subcatchment boundaries derived from these two DEMs are also quite different. In spite of using same resolution for the Vicmap DEM and the LiDARderived DEM, high accuracy LiDAR-derived DEM gave a detailed delineation of sub-catchment. Compared with results derived from LiDAR DEM, the drainage networks derived from Vicmap DEM do not give a detailed description, and even lead to discrepancies in some areas. It is demonstrated that a LiDAR-derived DEM with high accuracy and high resolution offers the capability of improving the quality of hydrological features extracted from DEMs

Modeling the AgInSbTe Memristor

The AgInSbTe memristor shows gradual resistance tuning characteristics, which makes it a potential candidate to emulate biological plastic synapses. The working mechanism of the device is complex, and both intrinsic charge-trapping mechanism and extrinsic electrochemical metallization effect are confirmed in the AgInSbTe memristor. Mathematical model of the AgInSbTe memristor has not been given before. We propose the flux-voltage controlled memristor model. With piecewise linear approximation technique, we deliver the flux-voltage controlled memristor model of the AgInSbTe memristor based on the experiment data. Our model fits the data well. The flux-voltage controlled memristor model and the piecewise linear approximation method are also suitable for modeling other kinds of memristor devices based on experiment data