Identifying potential survival strategies of HIV-1 through virus-host protein interaction networks

Background  

The National Institute of Allergy and Infectious Diseases has launched the HIV-1 Human Protein Interaction Database in an effort to catalogue all published interactions between HIV-1 and human proteins. In order to systematically investigate these interactions functionally and dynamically, we have constructed an HIV-1 human protein interaction network. This network was analyzed for important proteins and processes that are specific for the HIV life-cycle. In order to expose viral strategies, network motif analysis was carried out showing reoccurring patterns in virus-host dynamics.     

Structural characterisation of the photoisomers of reactive sulfonated azo dyes by NMR spectroscopy and DFT calculations.

1H NMR spectroscopy coupled with in situ laser irradiation has been used together with density functional theory (DFT) computation to examine the structures of the photoisomers of a series of sulfonated reactive azo dyes. Assignment of 1H NMR spectra acquired at the photostationary state has allowed, for the first time, NMR characterisation of unstable cis isomers of commercially relevant water-soluble azo dyes. Structural features of the two isomeric forms predicted by DFT calculations are clearly reflected in the experimental NMR data. The trans-cis photoisomerisation process could be unambiguously identified in each case, based on the large chemical shift change observed for resonances associated with aromatic protons adjacent to the azo linkage.     

Linking the T cell surface protein CD2 to the actin-capping protein CAPZ via CMS and CIN85

Recruitment of CD2 to the immunological synapse in response to antigen is dependent on its proline-rich cytoplasmic tail. A peptide from this region (CD2:322-339) isolated CMS (human CD2AP); a related protein, CIN85; and the actin capping protein, CAPZ from a T cell line. In BIAcore analyses, the N-terminal SH3 domains of CMS and CIN85 bound CD2:322-339 with similar dissociation constants (KD = approximately 100 microm). CAPZ bound the C-terminal half of CMS and CIN85. Direct binding between CMS/CIN85 and CAPZ provides a link with the actin cytoskeleton. Overexpression of a fragment from the C-terminal half or the N-terminal SH3 domain of CD2AP in a mouse T cell hybridoma resulted in enhanced interleukin-2 production and reduced T cell receptor down-modulation in response to antigen. These adaptor proteins are important in T cell signaling consistent with a role for CD2 in regulating pathways initiated by CMS/CIN85 and CAPZ.     

The viral sigma1 protein and glycoconjugates containing alpha2-3-linked sialic acid are involved in type 1 reovirus adherence to M cell apical surfaces

Type 1 reoviruses invade the intestinal mucosa of mice by adhering selectively to M cells in the follicle-associated epithelium and then exploiting M cell transport activity. The purpose of this study was to identify the apical cell membrane component and viral protein that mediate the M cell adherence of these viruses. Virions and infectious subviral particles of reovirus type 1 Lang (T1L) adhered to rabbit M cells in Peyer's patch mucosal explants and to tissue sections in an overlay assay. Viral adherence was abolished by pretreatment of sections with periodate and in the presence of excess sialic acid or lectins MAL-I and MAL-II (which recognize complex oligosaccharides containing sialic acid linked alpha2-3 to galactose). The binding of T1L particles to polarized human intestinal (Caco-2(BBe)) cell monolayers was correlated with the presence of MAL-I and MAL-II binding sites, blocked by excess MAL-I and -II, and abolished by neuraminidase treatment. Other type 1 reovirus isolates exhibited MAL-II-sensitive binding to rabbit M cells and polarized Caco-2(BBe) cells, but type 2 or type 3 isolates including type 3 Dearing (T3D) did not. In assays using T1L-T3D reassortants and recoated viral cores containing T1L, T3D, or no sigma1 protein, MAL-II-sensitive binding to rabbit M cells and polarized Caco-2(BBe) cells was consistently associated with the T1L sigma1. MAL-II-recognized oligosaccharide epitopes are not restricted to M cells in vivo, but MAL-II immobilized on virus-sized microparticles bound only to the follicle-associated epithelium and M cells. The results suggest that selective binding of type 1 reoviruses to M cells in vivo involves interaction of the type 1 sigma1 protein with glycoconjugates containing alpha2-3-linked sialic acid that are accessible to viral particles only on M cell apical surfaces.     

Microgeographic population structure of brook charr: a comparison of microsatellite and mark-recapture data

Polymorphism at five microsatellite genetic markers (genotyped n  = 496) and mark-recapture tagging data (tagged n  = 9813) were used to define the population structure of brook charr, Salvelinus fontinalis from the Indian Bay watershed, Newfoundland, Canada. Despite the absence of physical barriers to migration among lakes, both genetic and tagging data suggest that brook charr in each lake represent reproductively isolated populations. Exact tests comparing allele frequencies, θ (global value = 0·063), R st (global value = 0·052), individual assignment tests, and Nei's genetic distance provided congruent estimates of population subdivision in agreement with the tagging data (only 2·2% of recaptures were lake-to-lake). The genetic structure of the brook charr populations corresponded with the geographic structure of the drainage basin on a qualitative level, although linear distance over water was not significantly correlated with the tagging data or the genetic distance measures. The agreement between the tagging and the genetic data suggest that microsatellite markers can be useful tools for defining real biological units. The results also suggest that brook charr exhibit microgeographic population structure at the watershed scale, and that this is the scale at which conservation and management of this salmonid might best be implemented.     

Environmental heterogeneity and clonal growth: a study of the capacity for reciprocal translocation in Glechoma hederacea L.

Clonal fragments of Glechoma hederacea L. (Lamiaceae) were subjected to environments in which light and nutrients were supplied with a strictly negative association in space, i.e. when one of these resources was in ample supply the other was scarce. Treatments were chosen to simulate environments in which clones grew either within homogeneous conditions or across patch types (heterogeneous conditions). The hypothesis was tested that reciprocal translocation (i.e. exchange of both nutrients and assimilates) between connected groups of ramets would increase biomass production of clones growing under heterogeneous conditions compared to that of clones growing in homogeneous conditions. A cost-benefit analysis was carried out to test this hypothesis. Results suggested that reciprocal translocation did not occur at the structural scale considered in this experiment; no evidence was found for a significant effect on whole clone biomass of assimilate and/or nutrient translocation between clone parts experiencing contrasting levels of resource supply. It is suggested that predominantly acropetal movement of resources and the pattern of integrated physiological unit formation in G. hederacea are the main properties responsible for the lack of mutual physiological support between connected clonal fragments growing in differing habitat conditions. These properties are expected to promote clonal expansion and the exploitation of new territory, rather than sustaining clone parts in sub-optimal patches of habitat for prolonged periods of time.     

Uptake and metabolism of adenosine by pig aortic endothelial and smooth-muscle cells in culture.

1. Adenosine, a potent vasodilator, is transported very efficiently by pig aortic endothelium in monolayer culture (approx. 50pmol/min per 10(6) cells at 2 micrometer). Uptake proceeds by diffusion at high (millimolar) substrate concentrations, and by two discrete transport processes (Km approx. 3 micrometer and 250 micrometer) at lower concentrations. Over 90% of the adenosine taken up at 10 micrometer or 100 micrometer is rapidly converted into adenine nucleotides (mainly ATP). 2. The high-affinity process is selectively inhibited by dipyridamole and by nitrobenzylthioinosine. Adenine preferentially inhibits the lower-affinity process, papapaverine inhibits both transport processes, and inosine has no significant effect. 3. Pig aortic smooth-muscle cells in culture show no high-affinity transport system for adenosine; uptake is much slower at low concentrations than that by endothelium (approx. 5pmol/min per 10(6) cells at 2 micrometer). Over 80% of the incorporated adenosine at 10 micrometer or 100 micrometer is rapidly converted into adenine nucleotides. 4. The uptake of adenosine by smooth-muscle cells is powerfully inhibited by adenine, but dipyridamole is much less potent than in endothelium. 5. We conclude that endothelial cells are mainly responsible for the removal of circulating adenosine.     

Different incorporation of glucocorticoid hormone into diploid and tetraploid liver nuclei

Tetraploid parenchymal rat liver nuclei incorporate about twice as much (³H)dexamethasone as diploid parenchymal nuclei both in vivo and in vitro. This suggests that the ability of hepatic nuclei to incorporate glucocorticoid hormone is influenced by the number of copies of the genome in these nuclei.