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Viruses that replicate in the cytoplasm cannot access the host nuclear capping machinery. These viruses have evolved viral meth-yltransferase(s) to methylate N-7 and 2'-0 cap of their RNA; alternatively, they "snatch" host mRNA cap to form the 5' end of viral RNA. The function of 2'-0 methylation of viral RNA cap is to mimic cellular mRNA and to evade host innate immune re-striction. A cytoplasmic virus defective in 2'-0 methylation is replicative, but its viral RNA lacks 2'-0 methylation and is recog-nized and eliminated by the host immune response. Such a mutant virus could be rationally designed as a live attenuated vac-cine. Here, we use Japanese encephalitis virus (JEV), an important mosquito-borne flavivirus, to prove this novel vaccine concept. We show that JEV methyltransferase is responsible for both N-7 and 2'-0 cap methylations as well as evasion of host innate immune response. Recombinant virus completely defective in 2'-0 methylation was stable in cell culture after being pas-saged for >30 days. The mutant virus was attenuated in mice, elicited robust humoral and cellular immune responses, and re-tained the engineered mutation iti vivo. A single dose of immunization induced full protection against lethal challenge with JEV strains in mice. Mechanistically, the attenuation phenotype was attributed to the enhanced sensitivity of the mutant virus to the antiviral effects of interferon and IFIT proteins. Collectively, the results demonstrate the feasibility of using 2'-0 methylation-defective virus as a vaccine approach; this vaccine approach should be applicable to other flaviviruses and nonflaviviruses that encode their own viral 2'-0 methyltransferases. [ABSTRACT FROM AUTHOR]

The dengue virus (DENV) is a mosquito-borne pathogen responsible for an estimated 100 million human infections annually. The viral genome encodes a two-component trypsin-like protease that contains the cofactor region from the nonstructural protein NS2B and the protease domain from NS3 (NS3pro). The NS2B-NS3pro complex plays a crucial role in viral maturation and has been identified as a potential drug target. Using a DENV protease construct containing NS2B covalently linked to NS3pro via a Gly4-Ser-Gly4 linker ("linked protease"), previous x-ray crystal structures show that the C-terminal fragment of NS2B is remote from NS3pro and exists in an open state in the absence of an inhibitor; however, in the presence of an inhibitor, NS2B complexes with NS3pro to form a closed state. This linked enzyme produced NMR spectra with severe signal overlap and line broadening. To obtain a protease construct with a resolved NMR spectrum, we expressed and purified an unlinked protease complex containing a 50-residue segment of the NS2B cofactor region and NS3pro without the glycine linker using a coexpression system. This unlinked protease complex was catalytically active at neutral pH in the absence of glycerol and produced dispersed cross-peaks in a 1H-15N heteronuclear single quantum correlation spectrum that enabled us to conduct backbone assignments using conventional techniques. In addition, titration with an active-site peptide aldehyde inhibitor and paramagnetic relaxation enhancement studies demonstrated that the unlinked DENV protease exists predominantly in a closed conformation in solution. This protease complex can serve as a useful tool for drug discovery against DENV. [ABSTRACT FROM AUTHOR]

We report a highly reproducible method to crystallize the RNA-dependent RNA polymerase (RdRp) domain of dengue virus serotype 3 (DENV-3), allowing structure refinement to a 1.79-Å resolution and revealing amino acids not seen previously. We also present a DENV-3 polymerase/inhibitor cocrystal structure at a 2.1-Å resolution. The inhibitor binds to the RdRp as a dimer and causes conformational changes in the protein. The improved crystallization conditions and new structural information should accelerate structure-based drug discovery. [ABSTRACT FROM AUTHOR]

Flavivirus nonstructural protein 2A (NS2A) is a component of the viral replication complex that functions in virion assembly and antagonizes the host immune response. Although flavivirus NS2A is known to associate with the endoplasmic reticulum (ER) membrane, the detailed topology of this protein has not been determined. Here we report the first topology model of flavivirus NS2A on the ER membrane. Using dengue virus (DENV) NS2A as a model, we show that (i) the N-terminal 68 amino acids are located in the ER lumen, with one segment (amino acids 30 to 52) that interacts with ER membrane without traversing the lipid bilayer; (ii) amino acids 69 to 209 form five transmembrane segments, each of which integrally spans the ER membrane; and (iii) the C-terminal tail (amino acids 210 to 218) is located in the cytosol. Nuclear magnetic resonance (NMR) structural analysis showed that the first membrane-spanning segment (amino acids 69 to 93) consists of two helices separated by a "helix breaker." The helix breaker is formed by amino acid P85 and one positively charged residue, R84. Functional analysis using replicon and genome-length RNAs of DENV-2 indicates that P85 is not important for viral replication. However, when R84 was replaced with E, the mutation attenuated both viral RNA synthesis and virus production. Remarkably, an R84A mutation did not affect viral RNA synthesis but blocked intracellular formation of infectious virions. Collectively, the mutagenesis results demonstrate that NS2A functions in both DENV RNA synthesis and virion assembly/maturation. The topology model of DENV NS2A provides a good starting point for studying how flavivirus NS2A modulates viral replication and evasion of host immune response. [ABSTRACT FROM AUTHOR]

By combining exotic band dispersion with nontrivial band topology, an interesting type of band structure, namely, the flat Chern band, has recently been proposed to spawn high-temperature fractional quantum Hall states. Despite the proposal of several theoretical lattice models, however, it remains doubtful whether such a "romance of flatland" could exist in a real material. Here, we present a first-principles design of a two-dimensional indium-phenylene organometallic framework that realizes a nearly flat Chern band right around the Fermi level by combining lattice geometry, spin-orbit coupling, and ferromagnetism. An effective four-band model is constructed to reproduce the first-principles results. Our design, in addition, provides a general strategy to synthesize topologically nontrivial materials by virtue of organic chemistry and nanotechnology. [ABSTRACT FROM AUTHOR]

VPg uridylylation is essential for picornavirus RNA replication. The VPg uridylylation reaction consists of the binding of VPg to 3D polymerase (3DpoL) and the transfer of UMP by 3DpoL to the hydroxyl group of the third amino acid Tyr of VPg. Previous studies suggested that different picornaviruses employ distinct mechanisms during VPg binding and uridylylation. Here, we report a novel site (Site-311, located at the base of the palm domain of EV71 3DpoL) that is essential for EV71 VPg uridylylation as well as viral replication. Ala substitution of amino acids (T313, F314, and 1317) at Site-311 reduced the VPg uridylylation activity of 3DpoL by > 90%. None of the Site-311 mutations affected the RNA elongation activity of 3DpoL, which indicates that Site-311 does not directly participate in RNA polymerization. However, mutations that abrogated VPg uridylylation significantly reduced the VPg binding ability of 3DpoL, which suggests that Site-311 is a potential VPg binding site on enterovirus 71 (EV71) 3DpoL. Mutation of a polymerase active site in 3DpoL and Site-311 in 3DpoL remarkably enables trans complementation to restore VPg uridylylation. In contrast, two distinct Site-311 mutants do not cause trans complementation in vitro. These results indicate that Site-311 is a VPg binding site that stabilizes the VPg molecule during the VPg uridylylation process and suggest a two-molecule model for 3DpoL during EV71 VPg uridylylation, such that one 3DpoL presents the hydroxyl group of Tyr3 of VPg to the polymerase active site of another 3DpoL, which in turn catalyzes VPg→VPg-pU conversion. For genome-length RNA, the Site-311 mutations that reduced VPg uridylylation were lethal for EV71 replication, which indicates that Site-311 is a potential antiviral target. [ABSTRACT FROM AUTHOR]

Newly assembled dengue viruses (DENV) undergo maturation to become infectious particles. The maturation process involves major rearrangement of virus surface premembrane (prM) and envelope (E) proteins. The prM-E complexes on immature viruses are first assembled as trimeric spikes in the neutral pH environment of the endoplasmic reticulum. When the virus is transported to the low pH environment of the exosomes, these spikes rearrange into dimeric structures, which lie parallel to the virus lipid envelope. The proteins involved in driving this process are unknown. Previous cryoelectron microscopy studies of the mature DENV showed that the prM-stem region (residues 111-131) is membrane-associated and may interact with the E proteins. Here we investigated the prM-stem region in modulating the virus maturation process. The binding of the prM-stem region to the E protein was shown to increase significantly at low pH compared with neutral pH in ELISAs and surface plasmon resonance studies. In addition, the affinity of the prM-stem region for the liposome, as measured by fluorescence correlation spectroscopy, was also increased when pH is lowered. These results suggest that the prM-stem region forms a tight association with the virus membrane and attracts the associated E protein in the low pH environment of exosomes. This will lead to the surface protein rearrangement observed during maturation. [ABSTRACT FROM AUTHOR]

The article provides recommendations for the design and conduct of early-phase clinical trials on the safety and antiviral efficacy candidate dengue therapeutic agents. It notes that an effective antiviral therapy could result in fewer patients requiring admission to hospital and could potentially reduce transmission of dengue viruses to mosquitoes. It suggests the need to establish a standardized and consistent framework for dengue therapeutic trials to facilitate better data management.

Opinion dynamics focuses on the opinion evolution in a social community. Recently, some models of continuous opinion dynamics under bounded confidence were proposed by Deffuant and Krause, et al. In the literature, agents were generally assumed to have a homogeneous confidence level. This paper proposes an extended model for a group of agents with heterogeneous confidence levels. First, a social differentiation theory is introduced and a social group is divided into opinion subgroups with distinct confidence levels. Second, a multi-level heterogeneous opinion formation model is formulated under the framework of bounded confidence. Finally, computer simulations are conducted to study the collective opinion evolution, focusing on three key factors: the fractions of heterogeneous agents, the initial opinions, and the group size. The simulation results demonstrate that the number of final opinions depends on the fraction of closeminded agents when the group size and the initial opinions are fixed; the final opinions converge more easily when the initial opinions are closer; and the number of final opinions can be approximately modeled by a linear increasing function of the group size and the increasing rate is the fraction of close-minded agents. [ABSTRACT FROM AUTHOR]

Determining the number of clusters in a data set is an essential yet difficult step in cluster analysis. Since this task involves more than one criterion it can be modeled as a multiple criteria decision making (MCDM) problem. This paper proposes a multiple criteria decision making (MCDM)-based approach to estimate the number of clusters for a given data set. In this approach MCDM methods consider different numbers of clusters as alternatives and the outputs of any clustering algorithm on validity measures as criteria. The proposed method is examined by an experimental study using three MCDM methods the well-known clustering algorithm-k-means ten relative measures and fifteen public-domain UCI machine learning data sets. The results show that MCDM methods work fairly well in estimating the number of clusters in the data and outperform the ten relative measures considered in the study. [ABSTRACT FROM AUTHOR]

RNA modification plays an important role in modulating host-pathogen interaction. Flavivirus NS5 protein encodes N-7 and 2'-O methyltransferase activities that are required for the formation of 5' type I cap (m7 GpppAm) of viral RNA genome. Here we reported, for the first time, that flavivirus NS5 has a novel internal RNA methylation activity. Recombinant NS5 proteins of West Nile virus and Dengue virus (serotype 4; DENV-4) specifically methylates polyA, but not polyG, polyC, or polyU, indicating that the methylation occurs at adenosine residue. RNAs with internal adenosines substituted with 2'-O-methyladenosines are not active substrates for internal methylation, whereas RNAs with adenosines substituted with N6- methyladenosines can be efficiently methylated, suggesting that the internal methylation occurs at the 2'-OH position of adenosine. Mass spectroscopic analysis further demonstrated that the internal methylation product is 2'-O-methyladenosine. Importantly, genomic RNA purified from DENV virion contains 2'-O-methyladenosine. The 2'-O methylation of internal adenosine does not require specific RNA sequence since recombinant methyltransferase of DENV-4 can efficiently methylate RNAs spanning different regions of viral genome, host ribosomal RNAs, and polyA. Structure-based mutagenesis results indicate that K61-D146-K181-E217 tetrad of DENV-4 methyltransferase forms the active site of internal methylation activity; in addition, distinct residues within the methyl donor (S-adenosyl-L-methionine) pocket, GTP pocket, and RNA-binding site are critical for the internal methylation activity. Functional analysis using flavivirus replicon and genome-length RNAs showed that internal methylation attenuated viral RNA translation and replication. Polymerase assay revealed that internal 2'-O-methyladenosine reduces the efficiency of RNA elongation. Collectively, our results demonstrate that flavivirus NS5 performs 2'-O methylation of internal adenosine of viral RNA in vivo and host ribosomal RNAs in vitro. [ABSTRACT FROM AUTHOR]

Dengue is a mosquito-borne viral hemorrhagic disease that is a major threat to human health in tropical and subtropical regions. Here we report crystal structures of a peptide covalently bound to dengue virus serotype 3 (DENV-3) protease as well as the serine-protease inhibitor aprotinin bound to the same enzyme. These structures reveal, for the first time, a catalytically active, closed conformation of the DENV protease. In the presence of the peptide, the DENV-3 protease forms the closed conformation in which the hydrophilic β-hairpin region of NS2B wraps around the NS3 protease core, in a manner analogous to the structure of West Nile virus (WNV) protease. Our results confirm that flavivirus proteases form the closed conformation during proteolysis, as previously proposed for WNV. The current DENV-3 protease structures reveal the detailed interactions at the P4' to P3 sites of the substrate. The new structural information explains the sequence preference, particularly for long basic residues in the nonprime side, as well as the difference in substrate specificity between the WNV and DENV proteases at the prime side. Structural analysis of the DENV-3 protease-peptide complex revealed a pocket that is formed by residues from NS2B and NS3; this pocket also exists in the WNV NS2B/NS3 protease structure and could be targeted for potential antivirus development. The structural information presented in the current study is invaluable for the design of specific inhibitors of DENV protease. [ABSTRACT FROM AUTHOR]

The envelope (E) of dengue virus (DENV) is a determinant of tropism and virulence. At the C terminus of E protein, there is a stem region containing two amphipathic a-helical domains (EH1 and EH2) and a stretch of conserved sequences in between. The crystal structure of E protein at the postfusion state suggested the involvement of the stem during the fusion; however, the critical domains or residues involved remain unknown. Site-directed mutagenesis was carried out to replace each of the stem residues at the hydrophobic face with an alanine or proline in a DENV serotype 4 (DENV4) precursor membrane (prM)/E expression construct. Most of the 15 proline mutations at either EH1 or EH2 severely affected the assembly of virus-like particles (VLPs). Radioimmunoprecipitation and membrane flotation assays revealed that EH1 mutations primarily affect prM-E heterodimerization and EH2 mutations affect the membrane binding of the stem. Introducing four proline mutations at either EH1 or EH2 into a DENV2 replicon packaging system greatly affects assembly and entry. Moreover, introducing these mutations into a DENV2 infectious clone confirmed the impairment in assembly and infectivity. Sequencing analysis of adaptive mutations in passage 5 viruses revealed a change to a leucine or wild-type residue at the original site, suggesting the importance of maintaining the helical structure. Collectively, these findings suggest that the EH1 and EH2 domains are involved in both assembly and entry steps of the DENV replication cycle; this feature, together with the high degree of sequence conservation, suggests that the stem region is a potential target of antiviral strategies. [ABSTRACT FROM AUTHOR]

West Nile virus (WNV) replicates in the skin; however, cell targets in the skin have not been identified. In the current studies, WNV infected the epidermis and adnexal glands of mouse skin, and the epidermal cells were identified as keratinocytes by double labeling for WNV antigen and keratin 10. Inoculation of mice with WNV replicon particles resulted in high levels of replication in the skin, suggesting that keratinocytes are an initial target of WNV. In addition, primary keratinocytes produced infectious virus in vitro. In conclusion, keratinocytes are cell targets of WNV in vivo and may play an important role in pathogenesis. [ABSTRACT FROM AUTHOR]

Flavivirus NS5 protein encodes methyltransferase and RNA-dependent RNA polymerase (RdRp) activities. Structural analysis of flavivirus RdRp domains uncovered two conserved cavities (A and B). Both cavities are located in the thumb subdomains and represent potential targets for development of allosteric inhibitors. In this study, we used dengue virus as a model to analyze the function of the two RdRp cavities. Amino acids from both cavities were subjected to mutagenesis analysis in the context of genome-length RNA and recombinant NS5 protein; residues critical for viral replication were subjected to revertant analysis. For cavity A, we found that only one (Lys-756) of the seven selected amino acids is critical for viral replication. Alanine substitution of Lys-756 did not affect the RdRp activity, suggesting that this residue functions through a nonenzymatic mechanism. For cavity B, all four selected amino acids (Leu-328, Lys-330, Trp-859, and Ile-863) are critical for viral replication. Biochemical and revertant analyses showed that three of the four mutated residues (Leu-328, Trp-859, and Ile-863) function at the step of initiation of RNA synthesis, whereas the fourth residue (Lys-330) functions by interacting with the viral NS3 helicase domain. Collectively, our results have provided direct evidence for the hypothesis that cavity B, but not cavity A, from dengue virus NS5 polymerase could be a target for rational drug design. [ABSTRACT FROM AUTHOR]

Flaviviruses are a group of single-stranded, positive-sense RNA viruses causing ∼100 million infections per year. We have recently shown that flaviviruses produce a unique, small, noncoding RNA (∼0.5 kb) derived from the 3' untranslated region (UTR) of the genomic RNA (gRNA), which is required for flavivirus-induced cytopathicity and pathogenicity (G. P. Pijlman et al., Cell Host Microbe, 4: 579-591, 2008). This RNA (subgenomic flavivirus RNA [sfRNA]) is a product of incomplete degradation of gRNA presumably by the cellular 5'-3' exoribonuclease XRN1, which stalls on the rigid secondary structure stem-loop II (SL-II) located at the beginning of the 3' UTR. Mutations or deletions of various secondary structures in the 3' UTR resulted in the loss of full-length sfRNA (sfRNA1) and production of smaller and less abundant sfRNAs (sfRNA2 and sfRNA3). Here, we investigated in detail the importance of West Nile virus Kunjin (WNVKUN) 3' UTR secondary structures as well as tertiary interactions for sfRNA formation. We show that secondary structures SL-IV and dumbbell 1 (DB1) downstream of SL-II are able to prevent further degradation of gRNA when the SL-II structure is deleted, leading to production of sfRNA2 and sfRNA3, respectively. We also show that a number of pseudoknot (PK) interactions, in particular PK1 stabilizing SL-II and PK3 stabilizing DB1, are required for protection of gRNA from nuclease degradation and production of sfRNA. Our results show that PK interactions play a vital role in the production of nuclease-resistant sfRNA, which is essential for viral cytopathicity in cells and pathogenicity in mice. [ABSTRACT FROM AUTHOR]

The N-terminal domain of the flavivirus NS5 protein functions as a methyltransferase (MTase). It sequentially methylates the N7 and 2'-O positions of the viral RNA cap structure (GpppA→7meGpppA→7meGpppA29-O-me). The same NS5 domain could also have a guanylyltransferase activity (GTP+ppA-RNA→GpppA). The mechanism by which this protein domain catalyzes these three distinct functions is currently unknown. Here we report the crystallographic structure of DENV-3 MTase in complex with a 5'-capped RNA octamer (GpppAGAACCUG) at a resolution of 2.9 Å. Two RNA octamers arranged as kissing loops are encircled by four MTase monomers around a 2-fold non-crystallography symmetry axis. Only two of the four monomers make direct contact with the 5' end of RNA. The RNA structure is stabilised by the formation of several intra and intermolecular base stacking and non-canonical base pairs. The structure may represent the product of guanylylation of the viral genome prior to the subsequent methylation events that require repositioning of the RNA substrate to reach to the methyl-donor sites. The crystal structure provides a structural explanation for the observed trans-complementation of MTases with different methylation defects. [ABSTRACT FROM AUTHOR]

Interferons (IFNs) are key mediators of the host innate antiviral immune response. To identify IFNstimulated genes (ISGs) that instigate an antiviral state against two medically important flaviviruses, West Nile virus (WNV) and dengue virus (DENV), we tested 36 ISGs that are commonly induced by IFN-α for antiviral activity against the two viruses. We discovered that five ISGs efficiently suppressed WNV and/or DENV infection when they were individually expressed in HEK293 cells. Mechanistic analyses revealed that two structurally related cell plasma membrane proteins, IFITM2 and IFITM3, disrupted early steps (entry and/or uncoating) of the viral infection. In contrast, three IFN-induced cellular enzymes, viperin, ISG20, and double-stranded-RNA-activated protein kinase, inhibited steps in viral proteins and/or RNA biosynthesis. Our results thus imply that the antiviral activity of IFN-α is collectively mediated by a panel of ISGs that disrupt multiple steps of the DENV and WNV life cycles. [ABSTRACT FROM AUTHOR]

During apoptosis, dying cells are swiftly removed by phagocytes. It is not fully understood how apoptotic cells are recognized by phagocytes. Here we report the identification and characterization of the Caenorhabditis elegans ttr-52 gene, which encodes a transthyretin-like protein and is required for efficient cell corpse engulfment. The TTR-52 protein is expressed in, and secreted from, C. elegans endoderm and clusters around apoptotic cells. Genetic analysis indicates that TTR-52 acts in the cell corpse engulfment pathway mediated by CED-1, CED-6 and CED-7 and affects clustering of the phagocyte receptor CED-1 around apoptotic cells. TTR-52 recognizes surface-exposed phosphatidylserine (PtdSer) in vivo and binds to both PtdSer and the extracellular domain of CED-1 in vitro. TTR-52 is therefore the first bridging molecule identified in C. elegans that mediates recognition of apoptotic cells by crosslinking the PtdSer 'eat me' signal with the phagocyte receptor CED-1. [ABSTRACT FROM AUTHOR]

Energy harvesting technologies that are engineered to miniature sizes, while still increasing the power delivered to wireless electronics,(1, 2) portable devices, stretchable electronics,(3) and implantable biosensors,(4, 5) are strongly desired. Piezoelectric nanowire- and nanofiber-based generators have potential uses for powering such devices through a conversion of mechanical energy into electrical energy.(6) However, the piezoelectric voltage constant of the semiconductor piezoelectric nanowires in the recently reported piezoelectric nanogenerators(7-12) is lower than that of lead zirconate titanate (PZT) nanomaterials. Here we report a piezoelectric nanogenerator based on PZT nanofibers. The PZT nanofibers, with a diameter and length of approximately 60 nm and 500 μm, were aligned on interdigitated electrodes of platinum fine wires and packaged using a soft polymer on a silicon substrate. The measured output voltage and power under periodic stress application to the soft polymer was 1.63 V and 0.03 μW, respectively. [ABSTRACT FROM AUTHOR]

Excessive lose of customer account is becoming a major headache for VIP E-Mail hosting companies. Analysis of what kind of customer is more prone to lose and finding the appropriate measures to sustain those customers has become urgent needs. Recently, classification models based on mathematical programming have been widely used in business intelligence. The purpose of this paper is to propose several multiple criteria programming methods for classification and apply these methods to VIP E-Mail behavior classification. We first introduce a model for a generalized multiple criteria programming based classification method, specifically four particular forms, and then we use a cross-validation method to test the stability and accuracy of multiple criteria programming methods on VIP E-Mail accounts. Finally, we compare our models with Support Vector Machine (SVM). The results show that the classification models based on mathematical programming are satisfactorily accurate and stable on a VIP E-Mail dataset. Therefore, it can be concluded that applying the proposed method on VIP E-Mail behavior analysis can provide stable and credible results. [ABSTRACT FROM AUTHOR]

Scapuloperoneal spinal muscular atrophy (SPSMA) and hereditary motor and sensory neuropathy type IIC (HMSN IIC, also known as HMSN2C or Charcot-Marie-Tooth disease type 2C (CMT2C)) are phenotypically heterogeneous disorders involving topographically distinct nerves and muscles. We originally described a large New England family of French-Canadian origin with SPSMA and an American family of English and Scottish descent with CMT2C. We mapped SPSMA and CMT2C risk loci to 12q24.1–q24.31 with an overlapping region between the two diseases. Further analysis reduced the CMT2C risk locus to a 4-Mb region. Here we report that SPSMA and CMT2C are allelic disorders caused by mutations in the gene encoding the transient receptor potential cation channel, subfamily V, member 4 (TRPV4). Functional analysis revealed that increased calcium channel activity is a distinct property of both SPSMA- and CMT2C-causing mutant proteins. Our findings link mutations in TRPV4 to altered calcium homeostasis and peripheral neuropathies, implying a pathogenic mechanism and possible options for therapy for these disorders. [ABSTRACT FROM AUTHOR]

Flavivirus methyltransferase catalyzes both guanine N7 and ribose 2′-OH methylations of the viral RNA cap (GpppA-RNA→m7GpppAm-RNA). The methyltransferase is physically linked to an RNA-dependent RNA polymerase (RdRp) in the flaviviral NS5 protein. Here, we report genetic interactions of West Nile virus (WNV) methyltransferase with the RdRp and the 5′-terminal stem-loop of viral genomic RNA. Genome-length RNAs, containing amino acid substitutions of D146 (a residue essential for both cap methylations) in the methyltransferase, were transfected into BHK-21 cells. Among the four mutant RNAs (D146L, D146P, D146R, and D146S), only D146S RNA generated viruses in transfected cells. Sequencing of the recovered viruses revealed that, besides the D146S change in the methyltransferase, two classes of compensatory mutations had reproducibly emerged. Class 1 mutations were located in the 5′-terminal stem-loop of the genomic RNA (a G35U substitution or U38 insertion). Class 2 mutations resided in NS5 (K61Q in methyltransferase and W751R in RdRp). Mutagenesis analysis, using a genome-length RNA and a replicon of WNV, demonstrated that the D146S substitution alone was lethal for viral replication; however, the compensatory mutations rescued replication, with the highest rescuing efficiency occurring when both classes of mutations were present. Biochemical analysis showed that a low level of N7 methylation of the D146S methyltransferase is essential for the recovery of adaptive viruses. The methyltransferase K61Q mutation facilitates viral replication through improved N7 methylation activity. The RdRp W751R mutation improves viral replication through an enhanced polymerase activity. Our results have clearly established genetic interactions among flaviviral methyltransferase, RdRp, and the 5′ stem-loop of the genomic RNA. [ABSTRACT FROM AUTHOR]

We investigated the effects of increasing soil NaCl concentration on intracellular compartmentalization of salt and on the activities of antioxidant enzymes (superoxide dismutase (SOD), ascorbic peroxidase (APX), catalase (CAT) and glutathione reductase (GR)) and their role in the regulation of reactive oxygen species (ROS; O2− and H2O2) in leaves and xylem sap of salt-tolerant Populus euphratica Oliv. and salt-sensitive P. popularis cv. 35-44. Mesophyll cells of P. euphratica exhibited a high capacity for NaCl exclusion and compartmentalization of salt in vacuoles compared with P. popularis. In P. popularis, the salt treatment resulted in large accumulations of Na+ and Cl− in leaves that induced significant increases in O2− and H2O2 production despite marked increases in the activities of antioxidant enzymes in leaves and xylem sap. Separation of the isoforms of leaf SOD, APX and CAT by polyacrylamide gel electrophoresis followed by in-gel activity staining revealed that the salt-induced activities of APX and CAT were the result of increases in activities of all the isoenzymes. Leaf injury and shedding of aged leaves occurred following the oxidative burst in P. popularis, indicating that the increased activities of antioxidant enzymes in P. popularis were insufficient to counter the harmful effects of ROS at high soil NaCl concentrations. Unlike P. popularis plants, P. euphratica plants did not exhibit an oxidative burst in response to the NaCl treatments, because of (1) a high salt exclusion capacity and effective compartmentalization of salt in vacuoles, and (2) up-regulation of antioxidant enzymatic activities after the onset of salt stress. We conclude that P. euphratica plants subjected to saline conditions control ROS homeostasis through two pathways: (1) by maintaining cellular ionic homeostasis and thereby limiting the NaCl-induced enhancement of ROS production under long-term saline conditions; and (2) by rapidly up-regulating antioxidant defenses to prevent oxidative damage. [ABSTRACT FROM PUBLISHER]

The dependence of CS2predissociation upon rotational quantum number Kat vibrational levels below the barrier to linearity of the 1B2(1u) state has been investigated in detail with laser spectroscopy, by using a heated supersonic source to increase the intensities of hot band transitions. Predissociation lifetimes were determined from rotational contour simulations of 13 vibronic bands in the CS photofragment excitation (PHOFEX) spectrum, each terminating at the same upper vibrational level but via transitions with different Knumber (K0, 1, 2, respectively). The rovibrational populations of CS fragment at these excitation bands were derived from the laser-induced fluorescence (LIF) spectrum, and were used further to obtain the dissociation branching ratios S(1D)/S(3P) as well as the excess energy partitionings after dissociation. The lifetimes and the branching ratios were found to be sensitively dependent on quantum number K; the lifetime decreases with the increase of K, and the branching ratio increases with K. Analysis shows that quantum number Kinfluences the S(1D) channel more effectively than the S(3P) channel. About 28 and 15% of the total available energy is taken up by the CS vibrational and rotational degrees of freedom, respectively. Systematic analysis indicates that the two electronic states interacting with 1B2(1u) state should be bent, and the state correlating with S(1D) channel should be more bent. [ABSTRACT FROM AUTHOR]

Externalization of phosphatidylserine, which is normally restricted to the inner leaflet of plasma membrane, is a hallmark of mammalian apoptosis. It is not known what activates and mediates the phosphatidylserine externalization process in apoptotic cells. Here, we report the development of an annexin V-based phosphatidylserine labelling method and show that a majority of apoptotic germ cells in Caenorhabditis elegans have surface-exposed phosphatidylserine, indicating that phosphatidylserine externalization is a conserved apoptotic event in worms. Importantly, inactivation of the gene encoding either the C. elegans apoptosis-inducing factor (AIF) homologue (WAH-1), a mitochondrial apoptogenic factor, or the C. elegans phospholipid scramblase 1 (SCRM-1), a plasma membrane protein, reduces phosphatidylserine exposure on the surface of apoptotic germ cells and compromises cell-corpse engulfment. WAH-1 associates with SCRM-1 and activates its phospholipid scrambling activity in vitro. Thus WAH-1, after its release from mitochondria during apoptosis, promotes plasma membrane phosphatidylserine externalization through its downstream effector, SCRM-1. [ABSTRACT FROM AUTHOR]

In the present study, we investigated the effects of increasing salinity on growth, gas exchange, abscisic acid (ABA), calmodulin (CaM), and the relevance to salt tolerance in seedlings of Populus euphratica Oliv. and cuttings of P. “pupularis 35–44” (P. popularis) and P. x euramericana cv. I-214 (P. cv. Italica). The relative growth rates of shoot height (RGRH) for P. cv. Italica and P. popularis were severely reduced by increasing salt stress, whereas the growth reduction was relatively less in P. euphratica. Similarly, P. euphratica maintained higher net photosynthetic rates (Pn) and unit transpiration rates ( TRN) than P. cv. Italica and P. popularis under conditions of higher salinity. Salinity caused a significant increase in leaf ABA and CaM in the three genotypes after the onset of stress, but NaCl-induced ABA and CaM accumulation was more pronounced in P. euphratica, suggesting that P. euphratica plants are more sensitive in sensing soil salinity than the other two poplars. Furthermore, P. euphratica maintained relatively higher ABA and CaM concentrations under conditions of high salinity. The higher capacity to synthesize stress signals, namely ABA and CaM, in P. euphratica and the contribution of this to the salt resistance of P. euphratica are discussed. (Managing editor: Ping He) [ABSTRACT FROM AUTHOR]

RNA elements within flavivirus genomes are potential targets for antiviral therapy. A panel of phosphorodiamidate morpholino oligomers (PMOs), whose sequences are complementary to RNA elements located in the 5′- and 3′-termini of the West Nile (WN) virus genome, were designed to anneal to important cis-acting elements and potentially to inhibit WN infection. A novel Arg-rich peptide was conjugated to each PMO for efficient cellular delivery. These PMOs exhibited various degrees of antiviral activity upon incubation with a WN virus luciferase-replicon-containing cell line. Among them, PMOs targeting the 5′-terminal 20 nucleotides (5′End) or targeting the 3′-terminal element involved in a potential genome cyclizing interaction (3′CSI) exhibited the greatest potency. When cells infected with an epidemic strain of WN virus were treated with the 5′End or 3′CSI PMO, virus titers were reduced by approximately 5 to 6 logs at a 5 µM concentration without apparent cytotoxicity. The 3′CSI PMO also inhibited mosquito-borne flaviviruses other than WN virus, and the antiviral potency correlated with the conservation of the targeted 3′CSI sequences of specific viruses. Mode-of-action analyses showed that the 5′End and 3′CSI PMOs suppressed viral infection through two distinct mechanisms. The 5′End PMO inhibited viral translation, whereas the 3′CSI PMO did not significantly affect viral translation but suppressed RNA replication. The results suggest that antisense PMO-mediated blocking of cis-acting elements of flavivirus genomes can potentially be developed into an anti-flavivirus therapy. In addition, we report that although a full-length WN virus containing a luciferase reporter (engineered at the 3′ untranslated region of the genome) is not stable, an early passage of this reporting virus can be used to screen for inhibitors against any step of the virus life cycle. [ABSTRACT FROM AUTHOR]

The interferon (IFN) response is the first line of defense against viral infections, and the majority of viruses have developed different strategies to counteract IFN responses in order to ensure their survival in an infected host. In this study, the abilities to inhibit IFN signaling of two closely related West Nile viruses, the New York 99 strain (NY99) and Kunjin virus (KUN), strain MRM61C, were analyzed using reporter plasmid assays, as well as immunofluorescence and Western blot analyses. We have demonstrated that infections with both NY99 and KUN, as well as transient or stable transfections with their replicon RNAs, inhibited the signaling of both alpha/beta IFN (IFN-α/β) and gamma IFN (IFN-γ) by blocking the phosphorylation of STAT1 and its translocation to the nucleus. In addition, the phosphorylation of STAT2 and its translocation to the nucleus were also blocked by KUN, NY99, and their replicons in response to treatment with IFN-α. IFN-α signaling and STAT2 translocation to the nucleus was inhibited when the KUN nonstructural proteins NS2A, NS2B, NS3, NS4A, and NS4B, but not NS1 and NS5, were expressed individually from the pcDNA3 vector. The results clearly demonstrate that both NY99 and KUN inhibit IFN signaling by preventing STAT1 and STAT2 phosphorylation and identify nonstructural proteins responsible for this inhibition. [ABSTRACT FROM AUTHOR]

Recent outbreaks of West Nile Virus (WNV) have been associated with an increase in morbidity and mortality in humans, birds, and many other species. We have initiated studies to define the molecular mechanisms by which a recent pathogenic isolate of WNV evades the host cell innate antiviral response. Biochemical and microarray analyses demonstrated that WNV induced the expression of beta interferon (IFN-β) and several IFN-stimulated genes late in infection of cultured human cells. The late expression of these antiviral genes was due to the delayed activation of the transcription factor IFN regulatory factor 3 (IRF-3). Despite this host response, WNV was still able to replicate efficiently. The effect of the IRF-3 pathway on WNV replication was assessed by examining virus replication and spread in cultures of wild-type or IRF-3-null mouse embryo fibroblasts. The absence of IRF-3 was marked by a significant increase in plaque size and a sustained production of infectious particles. Although the activation of the IRF-3 pathway was not sufficient to block virus replication, our results suggest that IRF-3 target genes function to constrain WNV infection and limit cell-to-cell virus spread. [ABSTRACT FROM AUTHOR]

We have previously developed replicon vectors derived from the Australian flavivirus Kunjin that have a unique noncytopathic nature and have been shown to direct prolonged high-level expression of encoded heterologous genes in vitro and in vivo and to induce strong and long-lasting immune responses to encoded immunogens in mice. To facilitate further applications of these vectors in the form of virus-like particles (VLPs), we have now generated a stable BHK packaging cell line, tetKUNCprME, carrying a Kunjin structural gene cassette under the control of a tetracycline-inducible promoter. Withdrawal of tetracycline from the medium resulted in production of Kunjin structural proteins that were capable of packaging transfected and self-amplified Kunjin replicon RNA into the secreted VLPs at titers of up to 1.6 × 10[sup 9] VLPs per ml. Furthermore, secreted KUN replicon VLPs from tetKUNCprME cells could be harvested continuously for as long as 10 days after RNA transfection, producing a total yield of more than 10[sup 10] VLPs per 10[sup 6] transfected cells. Passaging of VLPs on Vero cells or intracerebral injection into 2- to 4-day-old suckling mice illustrated the complete absence of any infectious Kunjin virus, tetKUNCprME cells were also capable of packaging replicon RNA from closely and distantly related flaviviruses, West Nile virus and dengue virus type 2, respectively. The utility of high-titer KUN replicon VLPs was demonstrated by showing increasing CD8[sup +]-T-cell responses to encoded foreign protein with increasing doses of KUN VLPs. A single dose of 2.5 × 10[sup 7] VLPs carrying the human respiratory syncytial virus M2 gene induced 1,400 CD8 T cells per 10[sup 6] splenocytes in an ex vivo gamma interferon enzyme-linked immunospot assay. The packaging cell line thus represents a significant advance in the development of the noncytopathic Kunjin virus replicon-based gene expression system and may be widely applicable to the basic studies of flavivirus RNA packaging and virus assembly as well as to the development of gene expression systems based on replicons from different flaviviruses. [ABSTRACT FROM AUTHOR]

We have developed a reporting replicon of West Nile virus (WNV) that could be used to quantitatively distinguish viral translation and RNA replication. A Renilla luciferase (Rluc) gene was fused in-frame with the open reading frame of a subgenomic replicon in the position where the viral structural region was deleted, resulting in RlucRep. Transfection of BHK cells with RlucRep RNA yielded two distinctive Rluc signal peaks, one between 2 and 10 h and the other after 26 h posttransfection. By contrast, only the 2- to 10-h Rluc signal peak was observed in cells transfected with a mutant replicon containing an inactivated viral polymerase NS5 (RlucRep-NSSmt). Immunofluorescence and real-time reverse transcriptase PCR assays showed that the levels of viral protein expression and RNA replication increased in cells transfected with the RlucRep but not in those transfected with the RlucRep-NS5mt. These results suggest that the Rluc signal that occurred at 2 to 10 h posttransfection reflects viral translation of the input replicon, while the Rluc activity after 26 h posttransfection represents RNA replication. Using this system, we showed that mutations of conserved sequence (CS) elements within the 3' untranslated region of the mosquito-borne flaviviruses did not significantly affect WNV translation but severely diminished or completely abolished RNA replication. Mutations of CS1 that blocked the potential base pairing with a conserved sequence in the 5' region of the capsid gene (5'CS) abolished RNA replication. Restoration of the 5'CS-CS1 interaction rescued viral replication. Replicons containing individual deletions of CS2, repeated CS2 (RCS2), CS3, or RCS3 were viable, but their RNA replication was dramatically compromised. These results demonstrate that genome cyclization through the 5'CS-CS1 interaction is essential for WNV RNA replication, whereas CS2, RCS2, CS3, and RCS3 facilitate, but are dispensable for, WNV replication. [ABSTRACT FROM AUTHOR]

It is well known that data mining has been implemented by statistical regressions, induction decision tree, neural networks, rough set, fuzzy set and etc. This paper promotes a multiple criteria linear programming (MCLP) approach to data mining based on linear discriminant analysis. This paper first describes the fundamental connections between MCLP and data mining, including several general models of MCLP approaches. Given the general models, it focuses on a designing architecture of MCLP-data mining algorithms in terms of a process of real-life business intelligence. This architecture consists of finding MCLP solutions, preparing mining scores, and interpreting the knowledge patterns. Secondly, this paper elaborates the software development of the MCLP-data mining algorithms. Based on a pseudo coding, two versions of software (SAS- and Linux-platform) will be discussed. Finally, the software performance analysis over business and experimental databases is reported to show its mining and prediction power. As a part of the performance analysis, a series of data testing comparisons between the MCLP and induction decision tree approaches are demonstrated. These findings suggest that the MCLP-data mining techniques have a great potential in discovering knowledge patterns from a large-scale real-life database or data warehouse. [ABSTRACT FROM AUTHOR]

The mammalian interferon (IFN) signaling pathway is a primary component of the innate antiviral response. As such, viral pathogens have devised multiple mechanisms to antagonize this pathway and thus facilitate infection. Dengue virus (DENV) encodes several proteins (NS2a, NS4a, and NS4b) that have been shown individually to inhibit the IFN response. In addition, DENV infection results in reduced levels of expression of STAT2, which is required for IFN signaling (M. Jones, A. Davidson, L. Hibbert, P. Gruenwald, J. Schlaak, S. Ball, G. R. Foster, and M. Jacobs, J. Virol. 79:5414-5420, 2005). Translation of the DENV genome results in a single polypeptide, which is processed by viral and host proteases into at least 10 separate proteins. To date, no single DENV protein has been implicated in the targeting of STAT2 for decreased levels of expression. We demonstrate here that the polymerase of the virus, NS5, binds to STAT2 and is necessary and sufficient for its reduced level of expression. The decrease in protein level observed requires ubiquitination and proteasome activity, strongly suggesting an active degradation process. Furthermore, we show that the degradation of but not binding to STAT2 is dependent on the expression of the polymerase in the context of a polyprotein that undergoes proteolytic processing for NS5 maturation. Thus, the mature form of NS5, when not expressed as a precursor, was able to bind to STAT2 but was unable to target it for degradation, establishing a unique role for viral polyprotein processing in providing an additional function to a viral polypeptide. Therefore, we have identified both a novel mechanism by which DENV evades the innate immune response and a potential target for antiviral therapeutics. [ABSTRACT FROM AUTHOR]

RNase footprinting and nitrocellulose filter binding assays were previously used to map one major and two minor binding sites for the cell protein eEF1A on the 3'(+) stem-loop (SL) RNA of West Nile virus (WNV) (3). Base substitutions in the major eEF1A binding site or adjacent areas of the 3'(+) SL were engineered into a WNV infectious clone. Mutations that decreased, as well as ones that increased, eEF1A binding in in vitro assays had a negative effect on viral growth. None of these mutations affected the efficiency of translation of the viral polyprotein from the genomic RNA, but all of the mutations that decreased in vitro eEF1A binding to the 3' SL RNA also decreased viral minus-strand RNA synthesis in transfected cells. Also, a mutation that increased the efficiency of eEF1A binding to the 3' SL RNA increased minus-strand RNA synthesis in transfected cells, which resulted in decreased synthesis of genomic RNA. These results strongly suggest that the interaction between eEF1A and the WNV 3' SL facilitates viral minus-strand synthesis. eEF1A colocalized with viral replication complexes (RC) in infected cells and antibody to eEF1A coimmunoprecipitated viral RC proteins, suggesting that eEF1A facilitates an interaction between the 3' end of the genome and the RC. eEF1A bound with similar efficiencies to the 3'-terminal SL RNAs of four divergent flaviviruses, including a tick-borne flavivirus, and colocalized with dengue virus RC in infected cells. These results suggest that eEF1A plays a similar role in RNA replication for all flaviviruses. [ABSTRACT FROM AUTHOR]

Viral replication relies on the host to supply nucleosides. Host enzymes involved in nucleoside biosynthesis are potential targets for antiviral development. Ribavirin (a known antiviral drug) is such an inhibitor that suppresses guanine biosynthesis; depletion of the intracellular GTP pool was shown to be the major mechanism to inhibit flavivirus. Along similar lines, inhibitors of the pyrimidine biosynthesis pathway could be targeted for potential antiviral development. Here we report on a novel antiviral compound (NITD-982) that inhibits host dihydroorotate dehydrogenase (DHODH), an enzyme required for pyrimidine biosynthesis. The inhibitor was identified through screening 1.8 million compounds using a dengue virus (DENV) infection assay. The compound contains an isoxazole-pyrazole core structure, and it inhibited DENV with a 50% effective concentration (EC50) of 2.4 nM and a 50% cytotoxic concentration (CC50) of >5 μM. NITD-982 has a broad antiviral spectrum, inhibiting both flaviviruses and nonflaviviruses with nanomolar EC90s. We also show that (i) the compound inhibited the enzymatic activity of recombinant DHODH, (ii) an NITD-982 analogue directly bound to the DHODH protein, (iii) supplementing the culture medium with uridine reversed the compound-mediated antiviral activity, and (iv) DENV type 2 (DENV-2) variants resistant to brequinar (a known DHODH inhibitor) were cross resistant to NITD-982. Collectively, the results demonstrate that the compound inhibits DENV through depleting the intracellular pyrimidine pool. In contrast to the in vitro potency, the compound did not show any efficacy in the DENV-AG129 mouse model. The lack of in vivo efficacy is likely due to the exogenous uptake of pyrimidine from the diet or to a high plasma protein-binding activity of the current compound. [ABSTRACT FROM AUTHOR]

Direct piezoelectric potential measurement of single lead ziroconate titanate (PZT) nanofiber under bending using a nanomanipulator inside a scanning electron microscope chamber was presented. The PZT nanofibers, with the diameter and length around 100 nm and 70–100 μm, respectively, were aligned across trenches on a silicon substrate with a thermally grown oxide diffusion barrier and evaporated gold electrodes. A potential of ∼0.4 mV was generated when a bending moment was applied to a PZT nanofiber with an effective length of 4 μm by a tungsten tip of the nanomanipulator. The experiment demonstrated the feasibility of using these PZT nanofibers for nanoscale sensing, actuation, and energy harvesting. [ABSTRACT FROM AUTHOR]

Polyimide/TiO2 nanohybrid films with good corona resistance were prepared by using in situ dispersive polymerization. Effects of the concentration of nano-TiO2 fillers and the corona aging time on the dielectric properties of the films were explored. Results showed that the corona resistance of the hybrid films could be improved with increasing the concentration of TiO2 fillers, and the corona resistance was dependent on the dielectric permittivity of the hybrid films. The mechanism of the corona resistance was also discussed by analyzing the change in electric field and the electron action of TiO2 fillers based on the Fermi–Dirac statistic. [ABSTRACT FROM AUTHOR]

We report the detection of an emission feature at the 12σ level with FWHM line width of about 450 km s−1 toward the nearest quasi-stellar object, QSO Mrk 231. Based on observations with the IRAM 30 m telescope and the Northern Extended Millimeter Array Interferometer, the 11–10 transition of molecular oxygen is the likely origin of the line with rest frequency close to 118.75 GHz. The velocity of the O2 emission in Mrk 231 coincides with the red wing seen in CO emission, suggesting that it is associated with the outflowing molecular gas, located mainly at about 10 kpc away from the central active galactic nucleus (AGN). This first detection of extragalactic molecular oxygen provides an ideal tool to study AGN-driven molecular outflows on dynamic timescales of tens of megayears. O2 may be a significant coolant for molecular gas in such regions affected by AGN-driven outflows. New astrochemical models are needed to explain the implied high molecular oxygen abundance in such regions several kiloparsecs away from the center of galaxies. [ABSTRACT FROM AUTHOR]

We present ALMA observations of the CO(1−0) line and 3 mm continuum emission in eight ultraluminous infrared (IR) quasi-stellar objects (QSOs) at z = 0.06–0.19. All eight IR QSO hosts are clearly resolved in their CO molecular gas emission with a median source size of 3.2 kpc, and seven out of eight sources are detected in 3 mm continuum, which is found to be more centrally concentrated with respect to molecular gas with sizes of 0.4−1.0 kpc. Our observations reveal a diversity of CO morphology and kinematics for the IR QSO systems, which can be roughly classified into three categories: rotating gas disk with ordered velocity gradient, compact CO peak with disturbed velocity, and multiple CO distinct sources undergoing a merger between a luminous QSO and a companion galaxy separated by a few kpc. The molecular gas in three of the IR QSO hosts is found to be rotation-dominated with a ratio of the maximum rotation velocity to the local velocity dispersion of Vrot/σ = 4–6. Basic estimates of the dynamical masses within the CO-emitting regions give masses between 7.4 × 109 and 6.9 × 1010M⊙. We find an increasing trend between black hole mass accretion rate and star formation rate (SFR) over 3 orders of magnitude in far-IR luminosity/SFR, in line with the correlation between QSO bolometric luminosity and star formation activity, indicative of a likely direct connection between active galactic nuclei and star formation activity over galaxy evolution timescales. [ABSTRACT FROM AUTHOR]

We present and maps of six nearby star-forming galaxies, NGC 253, NGC 1068, IC 342, M82, M83, and NGC 6946, obtained with the James Clerk Maxwell Telescope as part of the MALATANG survey. All galaxies were mapped in the central 2′ × 2′ region at 14″ (FWHM) resolution (corresponding to linear scales of ∼0.2–1.0 kpc). The LIR–L′dense relation, where the dense gas is traced by the and the emission, measured in our sample of spatially resolved galaxies is found to follow the linear correlation established globally in galaxies within the scatter. We find that the luminosity ratio, LIR/L′dense, shows systematic variations with LIR within individual spatially resolved galaxies, whereas the galaxy-integrated ratios vary little. A rising trend is also found between LIR/L′dense ratio and the warm-dust temperature gauged by the 70 μm/100 μm flux ratio. We find that the luminosity ratios of IR/HCN (4–3) and IR/HCO+ (4–3), which can be taken as a proxy for the star formation efficiency (SFE) in the dense molecular gas (SFEdense), appear to be nearly independent of the dense gas fraction (fdense) for our sample of galaxies. The SFE of the total molecular gas (SFEmol) is found to increase substantially with fdense when combining our data with those on local (ultra)luminous infrared galaxies and high-z quasars. The mean line ratio measured for the six targeted galaxies is 0.9 ± 0.6. No significant correlation is found for the ratio with the star formation rate as traced by LIR, nor with the warm-dust temperature, for the different populations of galaxies. [ABSTRACT FROM AUTHOR]

We present the analysis of the physical properties of the interstellar medium in the nearby early-type galaxy NGC 3665, based on the far-infrared photometric and spectroscopic data as observed by the Herschel Space Observatory. The fit to the spectral energy distribution reveals a high dust content in the galaxy, with a dust-to-stellar mass ratio of /M* ∼ 1.1 × 10−4 that is nearly three times larger than the mean value of local S0+S0a galaxies. For the ionized regions (H ii regions), the electron density (ne) is around 49.5 ± 11.9 cm−3 based on the [N ii] 122 μm/[N ii] 205 μm ratio. For the photodissociation regions, the heating efficiency ranges from 1.26 × 10−3 to 1.37 × 10−3 based on the ([C ii]+[O i] 63 μm)/, which is slightly lower than other local galaxies; the hydrogen nucleus density and the strength of the far-UV radiation field are n ∼ 104 cm−3 and G0 ∼ 10−0.25, respectively. The above results are consistent with the presence of weak active galactic nuclei and a low level of star-forming activity in NGC 3665. Our results give strong support to the “morphological quenching” scenario, where a compact, massive bulge can stabilize the amount of cool gas against star formation. [ABSTRACT FROM AUTHOR]

At , the formation of new stars is dominated by dusty galaxies whose far-IR emission indicates they contain colder dust than local galaxies of a similar luminosity. We explore the reasons for the evolving IR emission of similar galaxies over cosmic time using (1) local galaxies from GOALS (), (2) galaxies at from 5MUSES (), and (3) IR luminous galaxies spanning from GOODS and Spitzer xFLS (). All samples have Spitzer mid-IR spectra, and Herschel and ground-based submillimeter imaging covering the full IR spectral energy distribution, allowing us to robustly measure , , and for every galaxy. Despite similar infrared luminosities, dusty star-forming galaxies (DSFG) have a factor of 5 higher dust masses and 5 K colder temperatures. The increase in dust mass is linked to an increase in the gas fractions with redshift, and we do not observe a similar increase in stellar mass or star formation efficiency. , a proxy for , is strongly correlated with independently of redshift. We measure merger classification and galaxy size for a subsample, and there is no obvious correlation between these parameters and or . In DSFG, the change in can fully account for the observed colder dust temperatures, suggesting that any change in the spatial extent of the interstellar medium is a second-order effect. [ABSTRACT FROM AUTHOR]

With the aim of exploring the fast evolutionary path from the blue cloud of star-forming galaxies to the red sequence of quiescent galaxies in the local universe, we select a local advanced merging infrared luminous and ultraluminous galaxy (adv-merger (U)LIRGs) sample and perform careful dust extinction corrections to investigate their positions in the star formation rate–M*, u − r, and NUV − r color–mass diagrams. The sample consists of 89 (U)LIRGs at the late merger stage, obtained from cross-correlating the Infrared Astronomical Satellite Point Source Catalog Redshift Survey and 1 Jy ULIRGs samples with the Sloan Digital Sky Survey DR7 database. Our results show that of adv-merger (U)LIRGs are localized above the 1σ line of the local star-forming galaxy main sequence. We also find that all adv-merger (U)LIRGs are more massive than and as blue as the blue cloud galaxies after corrections for Galactic and internal dust extinctions, with and of them outside the blue cloud on the u − r and NUV − r color–mass diagrams, respectively. These results, combined with the short timescale for exhausting the molecular gas reservoir in adv-merger (U)LIRGs ( to years), imply that the adv-merger (U)LIRGs are likely at the starting point of the fast evolutionary track previously proposed by several groups. While the number density of adv-merger (U)LIRGs is only of the blue cloud star-forming galaxies in the local universe, this evolutionary track may play a more important role at high redshift. [ABSTRACT FROM AUTHOR]

West Nile virus (WNV) is similar to other RNA viruses in that it forms genetically complex populations within hosts. The virus is maintained in nature in mosquitoes and birds, with each host type exerting distinct influences on virus populations. We previously observed that prolonged replication in mosquitoes led to increases in WNV genetic diversity and diminished pathogenesis in mice without remarkable changes to the consensus genome sequence. We therefore sought to evaluate the relationships between individual and group phenotypes in WNV and to discover novel viral determinants of pathogenesis in mice and fitness in mosquitoes and birds. Individual plaque size variants were isolated from a genetically complex population, and mutations conferring a small-plaque and mouse-attenuated phenotype were localized to the RNA helicase domain of the NS3 protein by reverse genetics. The mutation, an Asp deletion, did not alter type I interferon production in the host but rendered mutant viruses more susceptible to interferon compared to wild type (WT) WNV. Finally, we used an in vivo fitness assay in Culex quinquefasciatus mosquitoes and chickens to determine whether the mutation in NS3 influenced fitness. The fitness of the NS3 mutant was dramatically lower in chickens and moderately lower in mosquitoes, indicating that RNA helicase is a major fitness determinant of WNV and that the effect on fitness is host specific. Overall, this work highlights the complex relationships that exist between individual and group phenotypes in RNA viruses and identifies RNA helicase as an attenuation and fitness determinant in WNV. [ABSTRACT FROM AUTHOR]

An abstract of the article "The Helical Domains of the Stem Region of Dengue Virus Envelope Protein Are Involved in both Virus Assembly and Entry," by Su-Ru Lin and colleagues is presented.

An abstract of the article "Keratinocytes Are Cell Targets of West Nile Virus In Vivo," by Pei-Yin Lim and colleagues.

Dengue virus (DENV) is the most prevalent mosquito-borne viral pathogen in humans. Neither vaccine nor antiviral therapy is currently available for DENV. We report here that N-sulfonylanthranilic acid derivatives are allosteric inhibitors of DENV RNA-dependent RNA polymerase (RdRp). The inhibitor was identified through high-throughput screening of one million compounds using a primer extension-based RdRp assay [substrate poly(C)/oligo(G)20]. Chemical modification of the initial "hit" improved the compound potency to an IC50 (that is, a concentration that inhibits 50% RdRp activity) of 0.7 µM. In addition to suppressing the primer extension-based RNA elongation, the compound also inhibited de novo RNA synthesis using a DENV subgenomic RNA, but at a lower potency (IC50 of 5 µM). Remarkably, the observed anti-polymerase activity is specific to DENV RdRp; the compound did not inhibit WNV RdRp and exhibited IC50s of >100 µM against hepatitis C virus RdRp and human DNA polymerase α and β. UV cross-linking and mass spectrometric analysis showed that a photoreactive inhibitor could be cross-linked to Met343 within the RdRp domain of DENV NS5. On the crystal structure of DENV RdRp, Met343 is located at the entrance of RNA template tunnel. Biochemical experiments showed that the order of addition of RNA template and inhibitor during the assembly of RdRp reaction affected compound potency. Collectively, the results indicate that the compound inhibits RdRp through blocking the RNA tunnel. This study has provided direct evidence to support the hypothesis that allosteric pockets from flavivirus RdRp could be targeted for antiviral development. [ABSTRACT FROM AUTHOR]

Superinfection exclusion is the ability of an established viral infection to interfere with a second viral infection. Using West Nile virus (WNV) as a model, we show that replicating replicons in BHK-21 cells suppress subsequent WNV infection. The WNV replicon also suppresses superinfections of other flaviviruses but not nonflaviviruses. Mode-of-action analysis indicates that the exclusion of WNV superinfection occurs at the step of RNA synthesis. The continuous culturing of WNV in the replicon-containing cells generated variants that could overcome the superinfection exclusion. The sequencing of the selected viruses revealed mutations in structural (prM S90R or envelope E138K) and nonstructural genes (NS4a K124R and peptide 2K V9M). Mutagenesis analysis showed that the mutations in structural genes nonselectively enhance viral infection in both naïve and replicon-containing BHK-21 cells; in contrast, the mutations in nonstructural genes more selectively enhance viral replication in the replicon-containing cells than in the naïve cells. Mechanistic analysis showed that the envelope mutation functions through the enhancement of virion attachment to BHK-21 cells, whereas the 2K mutation (and, to a lesser extent, the NS4a mutation) functions through the enhancement of viral RNA synthesis. Furthermore, we show that WNV superinfection exclusion is reversible by the treatment of the replicon cells with a flavivirus inhibitor. The preestablished replication of the replicon could be suppressed by infecting the cells with the 2K mutant WNV but not with the wild-type virus. These results suggest that WNV superinfection exclusion is a result of competition for intracellular host factors that are required for viral RNA synthesis. [ABSTRACT FROM AUTHOR]

A correction to the article "Potential measurement from a single lead zirconate titanate nanofiber using a nanomanipulator," that was published in the August 10, 2009 issue.