Novel Relay Selection Rules for Average Interference-Constrained Cognitive AF Relay Networks

Cooperative relaying combined with selection exploits spatial diversity to significantly improve the performance of interference-constrained secondary users in an underlay cognitive radio (CR) network. However, unlike conventional relaying, the state of the links between the relay and the primary receiver affects the choice of the relay. Further, while the optimal amplify-and-forward (AF) relay selection rule for underlay CR is well understood for the peak interference-constraint, this is not so for the less conservative average interference constraint. For the latter, we present three novel AF relay selection (RS) rules, namely, symbol error probability (SEP)-optimal, inverse-of-affine (IOA), and linear rules. We analyze the SEPs of the IOA and linear rules and also develop a novel, accurate approximation technique for analyzing the performance of AF relays. Extensive numerical results show that all the three rules outperform several RS rules proposed in the literature and generalize the conventional AF RS rule.

A galactose-functionalized dendritic siRNA-nanovector to potentiate hepatitis C inhibition in liver cells

A RNAi based antiviral strategy holds the promise to impede hepatitis C viral (HCV) infection overcoming the problem of emergence of drug resistant variants, usually encountered in the interferon free direct-acting antiviral therapy. Targeted delivery of siRNA helps minimize adverse `off-target' effects and maximize the efficacy of therapeutic response. Herein, we report the delivery of siRNA against the conserved 5'-untranslated region (UTR) of HCV RNA using a liver-targeted dendritic nano-vector functionalized with a galactopyranoside ligand (DG). Physico-chemical characterization revealed finer details of complexation of DG with siRNA, whereas molecular dynamic simulations demonstrated sugar moieties projecting ``out'' in the complex. Preferential delivery of siRNA to the liver was achieved through a highly specific ligand-receptor interaction between dendritic galactose and the asialoglycoprotein receptor. The siRNA-DG complex exhibited perinuclear localization in liver cells and co-localization with viral proteins. The histopathological studies showed the systemic tolerance and biocompatibility of DG. Further, whole body imaging and immunohistochemistry studies confirmed the preferential delivery of the nucleic acid to mice liver. Significant decrease in HCV RNA levels (up to 75%) was achieved in HCV subgenomic replicon and full length HCV-JFH1 infectious cell culture systems. The multidisciplinary approach provides the `proof of concept' for restricted delivery of therapeutic siRNAs using a target oriented dendritic nano-vector.

Evidence for N-7 guanine methyl transferase activity encoded within the modular domain of RNA-dependent RNA polymerase L of a Morbillivirus

Post-transcriptional modification of viral mRNA is essential for the translation of viral proteins by cellular translation machinery. Due to the cytoplasmic replication of Paramyxoviruses, the viral-encoded RNA-dependent RNA polymerase (RdRP) is thought to possess all activities required for mRNA capping and methylation. In the present work, using partially purified recombinant RNA polymerase complex of rinderpest virus expressed in insect cells, we demonstrate the in vitro methylation of capped mRNA. Further, we show that a recombinant C-terminal fragment (1717-2183 aa) of L protein is capable of methylating capped mRNA, suggesting that the various post-transcriptional activities of the L protein are located in independently folding domains.

Tailor-Made Distribution of Nanoparticles in Blend Structure toward Outstanding Electromagnetic Interference Shielding

Engineering blend structure with tailor-made distribution of nanoparticles is the prime requisite to obtain materials with extraordinary properties. Herein, a unique strategy of distributing nanoparticles in different phases of a blend structure has resulted in >99% blocking of incoming electromagnetic (EM) radiation. This is accomplished by designing a ternary polymer blend structure using polycarbonate (PC), poly(vinylidene fluoride) (PVDF), and poly(methyl methacrylate) (PMMA) to simultaneously improve the structural, electrical, and electromagnetic interference shielding (EMI). The blend structure was made conducting by preferentially localizing the multi-wall nanotubes (MWNTs) in the PVDF phase. By taking advantage of pp stacking MWNTs was noncovalently modified with an imidazolium based ionic liquid (IL). Interestingly, the enhanced dispersion of IL-MWNTs in PVDF improved the electrical conductivity of the blends significantly. While one key requisite to attenuate EM radiation (i.e., electrical conductivity) was achieved using MWNTs, the magnetic properties of the blend structure was tuned by introducing barium ferrite (BaFe) nanoparticles, which can interact with the incoming EM radiation. By suitably modifying the surface of BaFe nanoparticles, we can tailor their localization under the macroscopic processing condition. The precise localization of BaFe nanoparticles in the PC phase, due to nucleophilic substitution reaction, and the MWNTs in the PVDF phase not only improved the conductivity but also facilitated in absorption of the incoming microwave radiation due to synergetic effect from MWNT and BaFe. The shielding effectiveness (SE) was measured in X and K-u band, and an enhanced SE of -37 dB was noted at 18 GHz frequency. PMMA, which acted as an interfacial modifier in PC/PVDF blends further, resulting in a significant enhancement in the mechanical properties besides retaining high SE. This study opens a new avenue in designing mechanically strong microwave absorbers with a suitable combination of materials.

Epoxy composites containing cobalt(II)-porphine anchored multiwalled carbon nanotubes as thin electromagnetic interference shields, adhesives and coatings

Herein a facile strategy has been adopted to design epoxy based adhesive/coating materials that can shield electromagnetic radiation. Multiwalled carbon nanotubes (MWNTs) were non-covalently modified with an ionic liquid and 5,10,15,20-tetrakis(4-methoxyphenyl)-21H,23H-porphine cobalt(II) (Co-TPP). The dispersion state of modified MWNTs in the composites was assessed using a scanning electron microscope. The electrical conductivity of the composites was improved with the addition of IL and Co-TPP. The shielding effectiveness was studied as a function of thickness and intriguingly, composites with as thin as 0.5 mm thickness were observed to reflect 497% of the incoming radiation. Carbon fibre reinforced polymer substrates were used to demonstrate the adhesive properties of the designed epoxy composites. Although, the shielding effectiveness of epoxy/MWNT composites with or without IL and Co-TPP is nearly the same for 0.5 mm thick samples, the lap shear test under tensile loading revealed an extraordinary adhesive bond strength for the epoxy/IL-MWNT/Co-TPP composites in contrast to neat epoxy. For instance, the lap shear strength of epoxy/IL-MWNT/Co-TPP composites was enhanced by 100% as compared to neat epoxy. Furthermore, the composites were thermally stable for practical utility in electronic applications as inferred from thermogravimetric analysis.

Roles for Transcription Factors Sp1, NF-kappa B, IRF3, and IRF7 in Expression of the Human IFNL4 Gene

The expression of a biologically active human IFN4 depends on the presence of a frameshift deletion polymorphism within the first exon of the interferon lambda 4 (IFNL4) gene. In this report, we use the lung carcinoma-derived cell line, A549, which is genetically viable to express a functional IFN4, to address transcriptional requirements of the IFNL4 gene. We show that the GC-rich DNA-binding transcription factor (TF) specificity protein 1 (Sp1) is recruited to the IFNL4 promoter and has a role in induction of gene expression upon stimulation with viral RNA mimic poly(I:C). By using RNAi and overexpression strategies, we also show key roles in IFNL4 gene expression for the virus-inducible TFs, nuclear factor kappa-light-chain-enhancer of activated B cells (NF-B), IFN regulatory factor 3 (IRF3), and IRF7. Interestingly, we also observe that overexpression of IFN4 influences IFNL4 promoter activity, which may further be dependent on the retinoic acid-inducible gene-I (RIG-I)-like receptor pathway. Together, our work for the first time reports on the functional characterization of the human IFNL4 promoter.

Differential binding of ppGpp and pppGpp to E-coli RNA polymerase: photo-labeling and mass spectral studies

(p) ppGpp, a secondary messenger, is induced under stress and shows pleiotropic response. It binds to RNA polymerase and regulates transcription in Escherichia coli. More than 25 years have passed since the first discovery was made on the direct interaction of ppGpp with E. coli RNA polymerase. Several lines of evidence suggest different modes of ppGpp binding to the enzyme. Earlier cross-linking experiments suggested that the beta-subunit of RNA polymerase is the preferred site for ppGpp, whereas recent crystallographic studies pinpoint the interface of beta'/omega-subunits as the site of action. With an aim to validate the binding domain and to follow whether tetra-and pentaphosphate guanosines have different location on RNA polymerase, this work was initiated. RNA polymerase was photo-labeled with 8-azido-ppGpp/8-azido-pppGpp, and the product was digested with trypsin and subjected to mass spectrometry analysis. We observed three new peptides in the trypsin digest of the RNA polymerase labeled with 8-azido-ppGpp, of which two peptides correspond to the same pocket on beta'-subunit as predicted by X-ray structural analysis, whereas the third peptide was mapped on the beta-subunit. In the case of 8-azido-pppGpp-labeled RNA polymerase, we have found only one cross-linked peptide from the beta'-subunit. However, we were unable to identify any binding site of pppGpp on the beta-subunit. Interestingly, we observed that pppGpp at high concentration competes out ppGpp bound to RNA polymerase more efficiently, whereas ppGpp cannot titrate out pppGpp. The competition between tetraphosphate guanosine and pentaphosphate guanosine for E. coli RNA polymerase was followed by gel-based assay as well as by a new method known as DRaCALA assay.

Elucidating the cancer-specific genetic alteration spectrum of glioblastoma derived cell lines from whole exome and RNA sequencing

Cell lines derived from tumor tissues have been used as a valuable system to study gene regulation and cancer development. Comprehensive characterization of the genetic background of cell lines could provide clues on novel genes responsible for carcinogenesis and help in choosing cell lines for particular studies. Here, we have carried out whole exome and RNA sequencing of commonly used glioblastoma (GBM) cell lines (U87, T98G, LN229, U343, U373 and LN18) to unearth single nucleotide variations (SNVs), indels, differential gene expression, gene fusions and RNA editing events. We obtained an average of 41,071 SNVs out of which 1,594 (3.88%) were potentially cancer-specific. The cell lines showed frequent SNVs and indels in some of the genes that are known to be altered in GBM-EGFR, TP53, PTEN, SPTA1 and NF1. Chromatin modifying genes-ATRX, MLL3, MLL4, SETD2 and SRCAP also showed alterations. While no cell line carried IDH1 mutations, five cell lines showed hTERT promoter activating mutations with a concomitant increase in hTERT transcript levels. Five significant gene fusions were found of which NUP93-CYB5B was validated. An average of 18,949 RNA editing events was also obtained. Thus we have generated a comprehensive catalogue of genetic alterations for six GBM cell lines.

Elucidating the cancer-specific genetic alteration spectrum of glioblastoma derived cell lines from whole exome and RNA sequencing

Cell lines derived from tumor tissues have been used as a valuable system to study gene regulation and cancer development. Comprehensive characterization of the genetic background of cell lines could provide clues on novel genes responsible for carcinogenesis and help in choosing cell lines for particular studies. Here, we have carried out whole exome and RNA sequencing of commonly used glioblastoma (GBM) cell lines (U87, T98G, LN229, U343, U373 and LN18) to unearth single nucleotide variations (SNVs), indels, differential gene expression, gene fusions and RNA editing events. We obtained an average of 41,071 SNVs out of which 1,594 (3.88%) were potentially cancer-specific. The cell lines showed frequent SNVs and indels in some of the genes that are known to be altered in GBM-EGFR, TP53, PTEN, SPTA1 and NF1. Chromatin modifying genes-ATRX, MLL3, MLL4, SETD2 and SRCAP also showed alterations. While no cell line carried IDH1 mutations, five cell lines showed hTERT promoter activating mutations with a concomitant increase in hTERT transcript levels. Five significant gene fusions were found of which NUP93-CYB5B was validated. An average of 18,949 RNA editing events was also obtained. Thus we have generated a comprehensive catalogue of genetic alterations for six GBM cell lines.

A strategy to achieve enhanced electromagnetic interference shielding at ultra-low concentration of multiwall carbon nanotubes in P alpha MSAN/PMMA blends in the presence of a random copolymer PS-r-PMMA

A unique strategy was adopted to achieve an ultra-low electrical percolation threshold of multiwall carbon nanotubes (MWNTs) (0.25 wt%) in a classical partially miscible blend of poly-alpha-methylstyrene-co-acrylonitrile and poly(methyl methacrylate) (P alpha MSAN/PMMA), with a lower critical solution temperature. The polymer blend nanocomposite was prepared by standard melt-mixing followed by annealing above the phase separation temperature. In a two-step mixing protocol, MWNTs were initially melt-mixed with a random PS-r-PMMA copolymer and subsequently diluted with 85/15 P alpha MSAN/PMMA blends in the next mixing step. Mediated by the PS-r-PMMA, the MWNTs were mostly localized at the interface and bridged the PMMA droplets. This strategy led to enhanced electromagnetic interference (EMI) shielding effectiveness at 0.25 wt% MWNTs through multiple scattering from MWNT-covered droplets, as compared to the blends without the copolymer, which were transparent to electromagnetic radiation.

Direct Link-Aware Relay Selection for Average Interference-Constrained Underlay Cognitive Radio

Cooperative relaying combined with selection exploits spatial diversity to significantly improve the performance of interference-constrained secondary users in an underlay cognitive radio network. We present a novel and optimal relay selection (RS) rule that minimizes the symbol error probability (SEP) of an average interference-constrained underlay secondary system that uses amplify-and-forward relays. A key point that the rule highlights for the first time is that, for the average interference constraint, the signal-to-interference-plus-noise-ratio (SINR) of the direct source-to-destination (SI)) link affects the choice of the optimal relay. Furthermore, as the SINR increases, the odds that no relay transmits increase. We also propose a simpler, more practical, and near-optimal variant of the optimal rule that requires just one bit of feedback about the state of the SD link to the relays. Compared to the SD-unaware ad hoc RS rules proposed in the literature, the proposed rules markedly reduce the SEP by up to two orders of magnitude.

Distributed Nonparametric Sequential Spectrum Sensing under Electromagnetic Interference

We propose a distributed sequential algorithm for quick detection of spectral holes in a Cognitive Radio set up. Two or more local nodes make decisions and inform the fusion centre (FC) over a reporting Multiple Access Channel (MAC), which then makes the final decision. The local nodes use energy detection and the FC uses mean detection in the presence of fading, heavy-tailed electromagnetic interference (EMI) and outliers. The statistics of the primary signal, channel gain and the EMI is not known. Different nonparametric sequential algorithms are compared to choose appropriate algorithms to be used at the local nodes and the Fe. Modification of a recently developed random walk test is selected for the local nodes for energy detection as well as at the fusion centre for mean detection. We show via simulations and analysis that the nonparametric distributed algorithm developed performs well in the presence of fading, EMI and outliers. The algorithm is iterative in nature making the computation and storage requirements minimal.