Stabilization of the integrase‐DNA complex by Mg2+ ions and prediction of key residues for binding HIV‐1 integrase inhibitors

The HIV‐1 integrase is an attractive target for the therapeutics development against AIDS, as no host homologue of this protein has been identified. The integrase strand transfer inhibitors (INSTIs), including raltegravir, specifically target the second catalytic step of the integration process by binding to the DDE motif of the catalytic site and coordinating Mg²⁺ ions. Recent X‐ray crystallographic structures of the integrase/DNA complex from prototype foamy virus allowed to investigate the role of the different partners (integrase, DNA, Mg²⁺ ions, raltegravir) in the complex stability using molecular dynamics (MD) simulations. The presence of Mg²⁺ ions is found to be essential for the stability, whereas the simultaneous presence of raltegravir and Mg²⁺ ions has a destabilizing influence. A homology model of HIV‐1 integrase was built on the basis of the X‐ray crystallographic information, and protein marker residues for the ligand binding were detected by clustering the docking poses of known HIV‐1 integrase inhibitors on the model. Interestingly, we had already identified some of these residues to be involved in HIV‐1 resistance mutations and in the stabilization of the catalytic site during the MD simulations. Classification of protein conformations along MD simulations, as well as of ligand docking poses, was performed by using an original learning method, based on self‐organizing maps. This allows us to perform a more in‐depth investigation of the free‐energy basins populated by the complex in MD simulations on the one hand, and a straightforward classification of ligands according to their binding residues on the other hand. Proteins 2014; 82:466–478. © 2013 Wiley Periodicals, Inc.     

RppH-dependent pyrophosphohydrolysis of mRNAs is regulated by direct interaction with DapF in Escherichia coli

Similar to decapping of eukaryotic mRNAs, the RppH-catalyzed conversion of 5′-terminal triphosphate to monophosphate has recently been identified as the rate-limiting step for the degradation of a subset of mRNAs in Escherichia coli. However, the regulation of RppH pyrophosphohydrolase activity is not well understood. Because the overexpression of RppH alone does not affect the decay rate of most target mRNAs, the existence of a mechanism regulating its activity has been suggested. In this study, we identified DapF, a diaminopimelate (DAP) epimerase catalyzing the stereoinversion of L,L-DAP to meso-DAP, as a regulator of RppH. DapF showed a high affinity interaction with RppH and increased its RNA pyrophosphohydrolase activity. The simultaneous overexpression of both DapF and RppH increased the decay rates of RppH target RNAs by about a factor of two. Together, our data suggest that the cellular level of DapF is a critical factor regulating the RppH-catalyzed pyrophosphate removal and the subsequent degradation of target mRNAs.     

Reassessment of the Role of TSC,mTORC1 and MicroRNAs in Amino Acids-Meditated Translational Control of TOP mRNAs

TOP mRNAs encode components of the translational apparatus, and repression of their translation comprises one mechanism, by which cells encountering amino acid deprivation downregulate the biosynthesis of the protein synthesis machinery. This mode of regulation involves TSC as knockout of TSC1 or TSC2 rescued TOP mRNAs translation in amino acid-starved cells. The involvement of mTOR in translational control of TOP mRNAs is demonstrated by the ability of constitutively active mTOR to relieve the translational repression of TOP mRNA upon amino acid deprivation. Consistently, knockdown of this kinase as well as its inhibition by pharmacological means blocked amino acid-induced translational activation of these mRNAs. The signaling of amino acids to TOP mRNAs involves RagB, as overexpression of active RagB derepressed the translation of these mRNAs in amino acid-starved cells. Nonetheless, knockdown of raptor or rictor failed to suppress translational activation of TOP mRNAs by amino acids, suggesting that mTORC1 or mTORC2 plays a minor, if any, role in this mode of regulation. Finally, miR10a has previously been suggested to positively regulate the translation of TOP mRNAs. However, we show here that titration of this microRNA failed to downregulate the basal translation efficiency of TOP mRNAs. Moreover, Drosha knockdown or Dicer knockout, which carries out the first and second processing steps in microRNAs biosynthesis, respectively, failed to block the translational activation of TOP mRNAs by amino acid or serum stimulation. Evidently, these results are questioning the positive role of microRNAs in this mode of regulation.     

<Emphasis Type="Italic">Pezothrips brunicornis</Emphasis> Mirab-balou et Tong (Thysanoptera,Thripidae): a Newly Recorded from Iran Species

The third species of the genus Pezothrips Karny, P. brunicornis Mirab-balou et Tong, is recorded for the first time from Iran. It was collected on flowers of Dianthus macranthoides in the Dalab forests in Manesht and Ghelarang protected area, northeastern part of Ilam Province.     

Biological studies of synthesized silver nanoparticles using <Emphasis Type="Italic">Prosopis farcta</Emphasis>

The evaluation of cytotoxic and apoptotic activities of silver nanoparticles (Ag-NPs) synthesized by aqueous extract of Prosopis farcta was investigated against lung (A549) and colon (HT-29) cell lines. The cytotoxic activity of nanoparticles was performed using MTT assay, while their apoptotic activity was tested using TUNEL method. The obtained results of MTT showed that the cell viability of A549 was dependent on the nanoparticles concentration and incubation time. Therefore, although the cytotoxic effect increased as the Ag-NPs concentration and incubation time heightened, yet the viability of HT-29 cells seems to be dependent only on the incubation time. The apoptotic results of the nanoparticles showed more than 50% of apoptosis on A549 and HT-29 cell lines, which in this case, HT-29 demonstrated 100% apoptosis at concentrations of more than 400 µg/ml. It seems that Ag-NPs synthesized using P. farcta extract can serve as anti-cancer agent in the treatment many cancers through creating or discovering new drug forms.     

Intelligent Touchscreen Joystick for Controlling Electric Wheelchair

Background

The objective of this research was to design, implement, use and evaluate a human-machine touch interface for driving an electric wheelchair. This new interface allows control of the electric wheelchair with touch screen smartphone technologies (android, IOS or Windows phone). In addition, an intelligent calibration algorithm, based on the neural network (NN), is implemented in this interface to overcome manoeuvring problems, namely the inability to move correctly in one or more directions.

Incorporating service and user information and latent features to predict QoS for selecting and recommending cloud service compositions

The rapid growth of published cloud services in the Internet makes the service selection and recommendation a challenging task for both users and service providers. In cloud environments, software re services collaborate with other complementary services to provide complete solutions to end users. The service selection is performed based on QoS requirements submitted by end users. Software providers alone cannot guarantee users’ QoS requirements. These requirements must be end-to-end, representing all collaborating services in a cloud solution. In this paper, we propose a prediction model to compute end-to-end QoS values for vertically composed services which are composed of three types of cloud services: software (SaaS), infrastructure (IaaS) and data (DaaS) services. These values can be used during the service selection and recommendation process. Our model exploits historical QoS values and cloud service and user information to predict unknown end-to-end QoS values of composite services. The experiments demonstrate that our proposed model outperforms other prediction models in terms of the prediction accuracy. We also study the impact of different parameters on the prediction results. In the experiments, we used real cloud services’ QoS data collected using our developed QoS monitoring and collecting system.