Insights into the Host Specificity of a New Oomycete Root Pathogen,Pythium brassicum P1: Whole Genome Sequencing and Comparative Analysis Reveals Contracted Regulation of Metabolism,Protein Families,and Distinct Pathogenicity Repertoire

Pythium brassicum P1 Stanghellini, Mohammadi, Förster, and Adaskaveg is an oomycete root pathogen that has recently been characterized. It only attacks plant species belonging to Brassicaceae family, causing root necrosis, stunting, and yield loss. Since P. brassicum P1 is limited in its host range, this prompted us to sequence its whole genome and compare it to those of broad host range Pythium spp. such as P. aphanidermatum and P. ultimum var. ultimum. A genomic DNA library was constructed with a total of 374 million reads. The sequencing data were assembled using SOAPdenovo2, yielding a total genome size of 50.3 Mb contained in 5434 scaffolds, N50 of 30.2 Kb, 61.2% G+C content, and 13,232 putative protein-coding genes. Pythium brassicum P1 had 175 species-specific gene families, which is slightly below the normal average. Like P. ultimum, P. brassicum P1 genome did not encode any classical RxLR effectors or cutinases, suggesting a significant difference in virulence mechanisms compared to other oomycetes. Pythium brassicum P1 had a much smaller proportions of the YxSL sequence motif in both secreted and non-secreted proteins, relative to other Pythium species. Similarly, P. brassicum P1 had the fewest Crinkler (CRN) effectors of all the Pythium species. There were 633 proteins predicted to be secreted in the P. brassicum P1 genome, which is, again, slightly below average among Pythium genomes. Pythium brassicum P1 had only one cadherin gene with calcium ion-binding LDRE and DxND motifs, compared to Pythium ultimum having four copies. Pythium brassicum P1 had a reduced number of proteins falling under carbohydrate binding module and hydrolytic enzymes. Pythium brassicum P1 had a reduced complement of cellulase and pectinase genes in contrast to P. ultimum and was deficient in xylan degrading enzymes. The contraction in ABC transporter families in P. brassicum P1 is suggested to be the result of a lack of diversity in nutrient uptake and therefore host range.     

Structural and Functional Insights into the Transmembrane Domain Association of Eph Receptors

Eph receptors are the largest family of receptor tyrosine kinases and by interactions with ephrin ligands mediate a myriad of processes from embryonic development to adult tissue homeostasis. The interaction of Eph receptors, especially at their transmembrane (TM) domains is key to understanding their mechanism of signal transduction across cellular membranes. We review the structural and functional aspects of EphA1/A2 association and the techniques used to investigate their TM domains: NMR, molecular modelling/dynamics simulations and fluorescence. We also introduce transmembrane peptides, which can be used to alter Eph receptor signaling and we provide a perspective for future studies.     

MR imaging of the prostate in clinical practice

Magnetic resonance imaging (MRI) is the imaging tool of choice in the evaluation of prostate cancer. The main applications of MR imaging in the management of prostate cancer are: (1) to guide targeted biopsy when prostate cancer is clinically suspected and previous ultrasound-guided biopsy results are negative; (2) to localize and stage prostate cancer and provide a roadmap for treatment planning; and (3) to detect residual or locally recurrent cancer after treatment. Other MR techniques such as proton MR spectroscopic imaging (MRSI), diffusion-weighted imaging (DWI), and contrast-enhanced MRI (CE-MRI) complement conventional MR imaging by providing metabolic and functional information that can improve the accuracy of prostate cancer detection and characterization. In everyday clinical practice, and to account for patient comfort, MR imaging studies are limited to 1 h. To obtain consistently high-quality images, a well-designed protocol is necessary. Routine MR imaging can be supplemented by other MR techniques such as MRSI, DWI or CE-MRI depending on the expertise available and the clinical questions that need to be answered. This review summarizes the role of MR imaging in the management of prostate cancer and describes practical approaches to implementing anatomic, metabolic and functional MR imaging techniques in the clinic.     

Role of Process Variables on Solid Particle Erosion of Polymer Composites: A Critical Review

This paper presents a review of the reported research works that are related to the solid particle erosion behavior of polymers and polymeric composites. Attention is paid to the effects of test parameters such as erodent type, size of the erodent, impingement angle, impact velocity and stand of distance. on the erosion wear rate of polymer composites. Various predictions and models proposed by different authors to describe and quantify the erosion rate are mentioned and their suitability is checked. Recent findings on the erosion response of multi-component hybrid composites are also presented. Lastly the implementation of design of experiments and statistical techniques in making the parametric appraisal of the erosion process of composites is discussed.     

Social and spatial order in villages in India

The paper explores the social, ecological, and religious factors which shape the village forms in India. Linear, nucleated and dispersed villages have been identified with different regions. Caste and kinship groups form the basic unit of a neighbourhood. The castes ranked on a hierarchical scale, locate themselves in a centre-periphery distribution in the village. This layout also expresses the duality between ritually pure and polluting space and defines the social interaction patterns between the different castes.     

Some new results in porous silicon

Efforts have been made to see the effect of some standard microelectronic processing steps on porous silicon. Our diffusion experiments for making p-n junctions confirm that this material can withstand high temperatures of the order of 800°C to 1000°C. A new technique for photolithography has been suggested to obtain porous silicon in selected areas. Etch stop method to control the thickness of the porous layer and an organic protective layer for porous silicon have also been suggested. Models proposed by other workers to explain luminescence in porous silicon are not sufficient to explain many experimental observations. A hybrid model is suggested.     

Enhanced indexing for risk averse investors using relaxed second order stochastic dominance

The less efficient markets offer scope for enhanced indexing (EI), an investment strategy of portfolio selection which seeks to earn more return than the benchmark index. In this context, we examine the use of relaxed second order stochastic dominance (RSSD) by introducing underachievement and overachievement variables in the second order stochastic dominance (SSD), for EI. We propose a linear optimization model that maximizes the mean return subject to the constraints formed using RSSD. We impose bounds on the ratio of the total underachievement to the sum of total underachievement and total overachievement variables depicting the risk-return tradeoff in the model. The proposed model for EI is inspired from many applications of SSD and almost SSD (ASSD). We examine the performance of the proposed model with the SSD model, EI model of maximizing mean return and minimizing the underperformance (MM) from the benchmark index, \(\epsilon \)-almost second order stochastic dominance (\(\epsilon \)-ASSD) model, and the naïve 1/N portfolio, on two Indian stock indices, CNX 100 and CNX 200, through a rolling window strategy. To widen the empirical analysis, we also compare all models on the eight publicly available real financial data sets from Beasley OR library through a single window strategy. The portfolios from the proposed model are shown to produce statistically significant mean excess return and excess Sharpe ratio (both from the benchmark indices) more often than the MM and \(\epsilon \)-ASSD models. Also, the portfolios from the proposed model always have smaller violation area in SSD constraints from benchmark indices than the MM and \(\epsilon \)-ASSD models.     

Microstructural, photocatalysis and electrochemical investigations on CeTi2O6 thin films

The properties of sol–gel derived CeTi₂O₆ thin films deposited using a solution of cerium chloride heptahydrate and titanium propoxide in ethanol are discussed. The effect of annealing temperature on structural, optical, photoluminescence, photocatalysis and electrochemical characteristics has been examined. Lowest annealing temperature for the formation of crystalline CeTi₂O₆ phase in these samples is identified as 580 °C. The optical transmittance of the films is observed to be independent of the annealing temperature. The optical energy bandgap of the 600 °C annealed film for indirect transition is influenced by the presence of anatase phase of TiO₂ in its structure. Fourier transform infrared spectroscopy investigations have evidenced increased bond strength of the Ti–O–Ti network in the films as a function of annealing temperature. The photoluminescence intensity of the films has shown dependence on the annealing temperature with the films fired at 450 °C exhibiting the maximum photoluminescence activity. The decomposition of methyl orange and eosin (yellow) under UV–visible light irradiation in the presence of crystalline CeTi₂O₆ films shows the presence of photoactivity in these films. The photocatalytic response of CeTi₂O₆ films is found to be superior to the TiO₂ films. In comparison to crystalline films, the amorphous films have shown superior electrochemical characteristics. The 500 °C annealed amorphous films have exhibited the most appropriate properties for incorporation in electrochromic devices comprising tungsten oxide as the primary electrochromic electrode.