Metric characterization of cluster dynamics on the Sierpinski gasket

We develop and implement an algorithm for the quantitative characterization of cluster dynamics occurring on cellular automata defined on an arbitrary structure. As a prototype for such systems we focus on the Ising model on a finite Sierpsinski Gasket, which is known to possess a complex thermodynamic behavior. Our algorithm requires the projection of evolving configurations into an appropriate partition space, where an information-based metrics (Rohlin distance) can be naturally defined and worked out in order to detect the changing and the stable components of clusters. The analysis highlights the existence of different temperature regimes according to the size and the rate of change of clusters. Such regimes are, in turn, related to the correlation length and the emerging "critical" fluctuations, in agreement with previous thermodynamic analysis, hence providing a non-trivial geometric description of the peculiar critical-like behavior exhibited by the system. Moreover, at high temperatures, we highlight the existence of different time scales controlling the evolution towards chaos.Comment: 20 pages, 8 figure

Metric Features of a Dipolar Model

The lattice spin model, with nearest neighbor ferromagnetic exchange and long range dipolar interaction, is studied by the method of time series for observables based on cluster configurations and associated partitions, such as Shannon entropy, Hamming and Rohlin distances. Previous results based on the two peaks shape of the specific heat, suggested the existence of two possible transitions. By the analysis of the Shannon entropy we are able to prove that the first one is a true phase transition corresponding to a particular melting process of oriented domains, where colored noise is present almost independently of true fractality. The second one is not a real transition and it may be ascribed to a smooth balancing between two geometrical effects: a progressive fragmentation of the big clusters (possibly creating fractals), and the slow onset of a small clusters chaotic phase. Comparison with the nearest neighbor Ising ferromagnetic system points out a substantial difference in the cluster geometrical properties of the two models and in their critical behavior.Comment: 20 pages, 15 figures, submitted to JPhys

Rohlin Distance and the Evolution of Influenza A virus: Weak Attractors and Precursors

The evolution of the hemagglutinin amino acids sequences of Influenza A virus is studied by a method based on an informational metrics, originally introduced by Rohlin for partitions in abstract probability spaces. This metrics does not require any previous functional or syntactic knowledge about the sequences and it is sensitive to the correlated variations in the characters disposition. Its efficiency is improved by algorithmic tools, designed to enhance the detection of the novelty and to reduce the noise of useless mutations. We focus on the USA data from 1993/94 to 2010/2011 for A/H3N2 and on USA data from 2006/07 to 2010/2011 for A/H1N1 . We show that the clusterization of the distance matrix gives strong evidence to a structure of domains in the sequence space, acting as weak attractors for the evolution, in very good agreement with the epidemiological history of the virus. The structure proves very robust with respect to the variations of the clusterization parameters, and extremely coherent when restricting the observation window. The results suggest an efficient strategy in the vaccine forecast, based on the presence of "precursors" (or "buds") populating the most recent attractor.Comment: 13 pages, 5+4 figure

HIV-infected T cells are migratory vehicles for viral dissemination

After host entry through mucosal surfaces, HIV-1 disseminates to lymphoid tissues to establish a generalized infection of the immune system. The mechanisms by which this virus spreads among permissive target cells locally during early stages of transmission, and systemically during subsequent dissemination are not known1. In vitro studies suggest that formation of virological synapses (VSs) during stable contacts between infected and uninfected T cells greatly increases the efficiency of viral transfer2. It is unclear, however, if T cell contacts are sufficiently stable in vivo to allow for functional synapse formation under the conditions of perpetual cell motility in epithelial3 and lymphoid tissues4. Here, using multiphoton intravital microscopy (MP-IVM), we examined the dynamic behavior of HIV-infected T cells in lymph nodes (LNs) of humanized mice. We found that most productively infected T cells migrated robustly, resulting in their even distribution throughout the LN cortex. A subset of infected cells formed multinucleated syncytia through HIV envelope (Env)-dependent cell fusion. Both uncoordinated motility of syncytia as well as adhesion to CD4+ LN cells led to the formation of long membrane tethers, increasing cell lengths to up to 10 times that of migrating uninfected T cells. Blocking the egress of migratory T cells from LNs into efferent lymph, and thus interrupting T cell recirculation, limited HIV dissemination and strongly reduced plasma viremia. Thus, we have found that HIV-infected T cells are motile, form syncytia, and establish tethering interactions that may facilitate cell-to-cell transmission through VSs. While their migration in LNs spreads infection locally, T cell recirculation through tissues is important for efficient systemic viral spread, suggesting new molecular targets to antagonize HIV infection

Viral Evolution and Cytotoxic T Cell Restricted Selection in Acute Infant HIV-1 Infection

Antiretroviral therapy-naive HIV-1 infected infants experience poor viral containment and rapid disease progression compared to adults. Viral factors (e.g. transmitted cytotoxic T- lymphocyte (CTL) escape mutations) or infant factors (e.g. reduced CTL functional capacity) may explain this observation. We assessed CTL functionality by analysing selection in CTL-targeted HIV-1 epitopes following perinatal infection. HIV-1 gag, pol and nef sequences were generated from a historical repository of longitudinal specimens from 19 vertically infected infants. Evolutionary rate and selection were estimated for each gene and in CTL-restricted and non-restricted epitopes. Evolutionary rate was higher in nef and gag vs. pol, and lower in infants with non-severe immunosuppression vs. severe immunosuppression across gag and nef. Selection pressure was stronger in infants with non-severe immunosuppression vs. severe immunosuppression across gag. The analysis also showed that infants with non-severe immunosuppression had stronger selection in CTL-restricted vs. non-restricted epitopes in gag and nef. Evidence of stronger CTL selection was absent in infants with severe immunosuppression. These data indicate that infant CTLs can exert selection pressure on gag and nef epitopes in early infection and that stronger selection across CTL epitopes is associated with favourable clinical outcomes. These results have implications for the development of paediatric HIV-1 vaccines

HSV-2 glycoprotein gD targets the CC domain of tetherin and promotes tetherin degradation via lysosomal pathway.

BACKGROUND: HSV-2 is the major cause of genital herpes. We previously demonstrated that the host viral restriction factor tetherin restricts HSV-2 release and is antagonized by several HSV-2 glycoproteins. However, the mechanisms underlying HSV-2 glycoproteins mediated counteraction of tetherin remain unclear. In this study, we investigated whether tetherin restricts the cell-to-cell spread of HSV-2 and the mechanisms underlying HSV-2 gD mediated antagonism of tetherin. METHODS: Infectious center assays were used to test whether tetherin could affect cell-to-cell spread of HSV-2. Coimmunoprecipitation assays were performed to map the tetherin domains required for HSV-2 gD-mediated downregulation. Immunoflurence assays were performed to detect the accumulation of tetherin in lysosomes or proteasomes. All experiments were repeated for at least three times and the data were performed statistical analysis. RESULTS: 1) Tetherin restricts cell-to-cell spread of HSV-2; 2) HSV-2 gD specifically interacts with the CC domain of tetherin; 3) HSV-2 gD promotes tetherin to the lysosomal degradation pathway. CONCLUSIONS: Tetherin not only restricts HSV-2 release but also its cell-to-cell spread. In turn, HSV-2 gD targets the CC domain of tetherin and promotes its degradation in the lysosome. Findings in this study have increased our understanding of tetherin restriction and viral countermeasures

HIV-1 Nef Employs Two Distinct Mechanisms to Modulate Lck Subcellular Localization and TCR Induced Actin Remodeling

The Nef protein acts as critical factor during HIV pathogenesis by increasing HIV replication in vivo via the modulation of host cell vesicle transport and signal transduction processes. Recent studies suggested that Nef alters formation and function of immunological synapses (IS), thereby modulating exogenous T-cell receptor (TCR) stimulation to balance between partial T cell activation required for HIV-1 spread and prevention of activation induced cell death. Alterations of IS function by Nef include interference with cell spreading and actin polymerization upon TCR engagement, a pronounced intracellular accumulation of the Src kinase Lck and its reduced IS recruitment. Here we use a combination of Nef mutagenesis and pharmacological inhibition to analyze the relative contribution of these effects to Nef mediated alterations of IS organization and function on TCR stimulatory surfaces. Inhibition of actin polymerization and IS recruitment of Lck were governed by identical Nef determinants and correlated well with Nef's association with Pak2 kinase activity. In contrast, Nef mediated Lck endosomal accumulation was separable from these effects, occurred independently of Pak2, required integrity of the microtubule rather than the actin filament system and thus represents a distinct Nef activity. Finally, reduction of TCR signal transmission by Nef was linked to altered actin remodeling and Lck IS recruitment but did not require endosomal Lck rerouting. Thus, Nef affects IS function via multiple independent mechanisms to optimize virus replication in the infected host