Discerning intersecting fusion‐activation pathways in the Nipah virus using machine learning

The fusion of Nipah with host cells is facilitated by two of their glycoproteins, the G and the F proteins. The binding of cellular ephrins to the G head domain causes the G stalk domain to interact differently with F, which activates F to mediate virus–host fusion. To gain insight into how the ephrin‐binding signal transduces from the head to the stalk domain of G, we examine quantitatively the differences between the conformational ensembles of the G head domain in its ephrin‐bound and unbound states. We consider the human ephrins B2 and B3, and a double mutant of B2, all of which trigger fusion. The ensembles are generated using molecular dynamics, and the differences between them are quantified using a new machine learning method. We find that the portion of the G head domain whose conformational density is altered equivalently by the three ephrins is large, and comprises ～25% of the residues in the G head domain. This subspace also includes the residues that are known to be important to F activation, which suggests that it contains at least one common signaling pathway. The spatial distribution of the residues constituting this subspace supports the model of signal transduction in which the signal transduces via the G head dimer interface. This study also adds to the growing list of examples where signaling does not depend solely on backbone deviations. In general, this study provides an approach to filter out conserved patterns in protein dynamics. Proteins 2014; 82:3241–3254. © 2014 Wiley Periodicals, Inc.     

Bacterial inhibition of Orobanche aegyptiaca and Orobanche cernua radical elongation

The ability of different bacteria to inhibit Orobanche radical elongation was examined. Seeds of Orobanche aegyptiaca Pers. and O. cernua Loefl. were induced to germinate with the Growth Regulator GR24 in the presence or absence of test bacterium. Radical lengths were estimated microscopically on a scale relative to seed length (0–5 seed lengths) after 5 days of incubation at 25°C. The results indicated that Pseudomonas aeruginosa QUBC1, P. fluorescens QUBC3, Bacillus atrophaeus QUBC16, and B. subtilis QUBC18 significantly inhibited radical elongation (P≤0.01) of both O. aegyptiaca and O. cernua relative to control radicals, whereas Microbacterium hydrocarbonoxydans QUBC11 and Ochrobactrum anthropi QUBC13 showed less inhibitory effects. Other bacterial isolates had no inhibitory effects. Bacterial isolates were identified using the universal method in addition to morphological and biochemical features. The establishment of the inhibitory effect of the most promising isolates, B. atrophaeus QUBC16 and P. aeruginosa QUBC1 on radical elongation of both Orobanche spp. is a step towards utilizing such bacteria as biocontrol agents against O. aegyptiaca, O. cernua, and potentially other Orobanche species.     

Non‐edible oil seed producing Calophyllum inophyllum ideal for India's future biofuel development

The impending climate change crisis has stimulated enormous interest in the development of biofuel globally. The supporters of biofuel hail that it is naturally carbon‐neutral whereas the critiques argue that the large‐scale plantations and production of biofuel based on Jatropha can not only strain agricultural resources but also threaten future food security. India's subsistence farmers are often faced with challenges and constraints of poverty. Foremost among the challenges are the marginal environmental conditions for agriculture often influenced by erratic rainfall, drought, poor soil quality, and unreliable irrigation water supply. In this article, we have presented a case study on the potential to use nonedible seeds from naturally occurring tree species, Calophyllum inophyllum to meet the increasing demand for biofuel production in India.     

Disulfiram and Its Copper Chelate Attenuate Cisplatin-Induced Acute Nephrotoxicity in Rats Via Reduction of Oxidative Stress and Inflammation

Biological Trace Element Research - The use of cisplatin (CP) in chemotherapy of resistant cancers is limited due to its dose-dependent nephrotoxicity. Disulfiram (DSF), the aversion therapy for...