Near identity of 3′ RNA secondary structure in bromoviruses and cucumber mosaic virus

The 3′ terminal sequences of RNAs 1, 2, 3 and 4 from each of the three bromoviruses (brome mosaic, cowpea chlorotic mottle and broad bean mottle viruses) and also from cucumber mosaic virus display interviral sequence similarity in addition to strong intraviral homology. Interviral similarity is much more evident when RNA secondary, rather than primary, structures are compared. The last 190 bases of the various RNAs can fold into strikingly similar, extensively base-paired secondary structures whose common features are supported by RNA structure mapping. The extreme 3′ end of each viral RNA can base-pair in two distinct configurations. Bromovirus RNA 3s each contain an unusually accessible internal oligo(A) sequence which, in brome mosaic virus at least, is located in the intercistronic noncoding region. Functional implications of these structural features are discussed.     

N-Methyl-d-Aspartate- or Glutamate-Mediated Toxicity in Cultured Rat Cortical Neurons Is Antagonized by FPL 15896AR

Abstract: The neuroprotective action of ( S )-α-phenyl-2-pyridineethanamine dihydrochloride (FPL 15896AR), a novel noncompetitive N -methyl- d -aspartate (NMDA) receptor antagonist, was examined in primary rat cortical neuronal cultures. Exposure of cortical cultures to NMDA (50 µ M ) or glutamate (50 µ M ) for 15 min resulted in the death of 85–95% of the neurons during the next 24 h. This neurotoxicity was completely eliminated by adding FPL 15896AR (50 µ M ) to the cultures during the time of NMDA or glutamate exposure. Neuroprotective concentrations of FPL 15896AR also inhibited other acute effects of NMDA. FPL 15896AR (50 µ M ) prevented the loss of membrane-associated protein kinase C activity that developed by 4 h after transient exposure to 50 µ M NMDA or 50 µ M glutamate. FPL 15896AR also reduced by ∼35% the magnitude of NMDA-triggered increases in intracellular free Ca²⁺ concentration in the cortical cultures. These data indicate that NMDA-mediated toxicity in cultured cortical neurons can be blocked by the NMDA antagonist FPL 15896AR.     

Hepatitis C virus genotype 1a growth and induction of autophagy

We have previously reported that immortalized human hepatocytes (IHH) support the generation of infectious hepatitis C virus (HCV) genotype 1a (clone H77). In the present study, we have investigated the growth of HCV genotype 1a (clone H77) through serial passages and accompanying changes in IHH in response to infection. Eleven serial passages of HCV genotype 1a (clone H77) in IHH were completed. Virus replication was ascertained from the presence of HCV-specific sequences, the detection of core antigen, the virus genome copy number, and the virus titer in IHH culture fluid. Electron microscopy suggested that HCV infection induces autophagic vacuole formation in IHH. Fluorescence microscopy displayed localization of autophagic markers, microtubule-associated protein-1 light chain-3 and Apg5, on the vacuoles of HCV-infected hepatocytes. Taken together, our results suggested that HCV genotype 1a (clone H77) can be serially passaged in IHH and that HCV infection induces an autophagic response in hepatocytes.     

Hepatitis C virus inhibits cell surface expression of HLA-DR, prevents dendritic cell maturation, and induces interleukin-10 production

Hepatitis C virus (HCV) chronic infection is characterized by low-level or undetectable cellular immune responses against HCV antigens. HCV proteins have been shown to affect various intracellular events and modulate immune responses, although the precise mechanisms used to mediate these effects are not fully understood. In this study, we have examined the effect of HCV proteins on the modulation of major histocompatibility complex (MHC) class II expression and other functions important for antigen presentation in humans. Expression of an HCV(1-2962) genomic clone (HCV-FL) in human fibrosarcoma cells (HT1080) inhibited gamma interferon (IFN-gamma)-induced upregulation of human leukocyte antigen-DR (HLA-DR) cell surface expression. Furthermore, inhibition of promoter activities of MHC class II transactivator (CIITA), IFN-gamma-activated site (GAS), and HLA-DR was observed in IFN-gamma-inducible HT1080 cells expressing HCV-FL by in vitro reporter assays. Exposure of human monocyte-derived dendritic cells (DCs) to cell culture-grown HCV (HCVcc) genotype 1a (clone H77) or 2a (clone JFH1) significantly inhibited DC maturation and was associated with the production of IL-10. Furthermore, DCs exposed to HCVcc were impaired in their functional ability to stimulate antigen-specific CD4-positive (CD4(+)) and CD8(+) T-cell responses. Taken together, our results indicated that HCV can have direct and/or indirect inhibitory effects on antigen-presenting cells, resulting in reduction of antigen-specific T-cell activation. These effects may account for or contribute to the low overall level of immunogenicity of HCV observed in chronically infected patients.     

A Steroid in a Lipid Bilayer: Localization, Orientation, and Energetics

Steroid hormones are known to freely partition into lipid bilayers. As a case study, we investigated the behavior of the steroid hormone cortisone in a model lipid bilayer. First, we looked at energy barriers involved in the partitioning of a single molecule into a bilayer using umbrella sampling molecular dynamics simulations. A rather wide well of −4.5 kcal/mol was observed in the interfacial region between the lipid headgroup and tailgroup. Next, using two unconstrained molecular dynamics simulations with cortisone initially positioned at distinct locations within a bilayer, we studied the preferred location and orientation of the molecule. Finally, we observed how cortisone molecules could spontaneously insert and localize in a bilayer from bulk solution. The three independent approaches produced a converged picture of how cortisone behaves in a model lipid bilayer.     

Dissecting protein-RNA recognition sites

We analyze the protein–RNA interfaces in 81 transient binary complexes taken from the Protein Data Bank. Those with tRNA or duplex RNA are larger than with single-stranded RNA, and comparable in size to protein–DNA interfaces. The protein side bears a strong positive electrostatic potential and resembles protein–DNA interfaces in its amino acid composition. On the RNA side, the phosphate contributes less, and the sugar much more, to the interaction than in protein–DNA complexes. On average, protein–RNA interfaces contain 20 hydrogen bonds, 7 that involve the phosphates, 5 the sugar 2′OH, and 6 the bases, and 32 water molecules. The average H-bond density per unit buried surface area is less with tRNA or single-stranded RNA than with duplex RNA. The atomic packing is also less compact in interfaces with tRNA. On the protein side, the main chain NH and Arg/Lys side chains account for nearly half of all H-bonds to RNA; the main chain CO and side chain acceptor groups, for a quarter. The 2′OH is a major player in protein–RNA recognition, and shape complementarity an important determinant, whereas electrostatics and direct base–protein interactions play a lesser part than in protein–DNA recognition.     

Heat shock proteins in toxicology: How close and how far?

The response to stress triggers activation of the genes involved in cell survival and/or cell death. Stress response is a ubiquitous feature of cells that is induced under stress conditions. As a part of this response a set of genes called stress genes are induced to synthesize a group of proteins called heat shock proteins (Hsps). The Hsps play an essential role as molecular chaperones by assisting the correct folding of nascent and stress-accumulated misfolded proteins, and by preventing their aggregation. Because of their sensitivity to even minor assaults, Hsps are suitable as an early warning bio-indicator of cellular hazard. Despite having enormous use in toxicology, the current state of knowledge in defining a mechanism of action or accurately predicting toxicity based on stress gene expression warrants further investigation. The goal of this review is to summarize current developments in the application of stress genes and their products ‘Hsps’ in toxicology with a brief discussion of the caveats. While focusing on hsp70 because of its higher conservation across the taxa and since it is one of the first to be induced under stress conditions, we will also discuss other members of the stress gene family.     

IL-13Rα2 has a protective role in a mouse model of cutaneous inflammation

IL-13 is expressed in lesions of atopic dermatitis (AD) and has been associated with increased disease severity. IL-13 has two cognate receptors: IL-13Rα1 and IL-13Rα2. Although IL-13Rα2 expression is known to be induced in response to IL-13 in keratinocytes, its function in AD has never been evaluated. We characterized the loss of skin barrier function and the development of cutaneous inflammation in IL-13Rα2-null versus wild-type BALB/c mice following an epicutaneous allergen-sensitization/challenge model that shares similarities with human AD. Mice lacking IL-13Rα2 had significantly increased transepidermal water loss, cutaneous inflammation, peripheral eosinophilia, and IgG1 and IgE levels compared with wild-type mice. The rate of resolution of the cutaneous inflammation was not significantly altered in the IL-13Rα2-null mice. IL-13 induced expression of IL-13Rα2 in keratinocyte cell lines and primary human keratinocytes. Depletion of IL-13Rα2 in a keratinocyte cell line resulted in increased STAT6 signaling in response to IL-13. In conclusion, IL-13Rα2 serves a protective role in the pathogenesis of allergic inflammation and loss of skin barrier function in a mouse model of AD, suggesting that it may be an important endogenous regulator of IL-13-induced cutaneous inflammation in humans.