Intrahost evolution of HIV-1 phenotypes

HIV-1 evolves constantly within an infected individual, due to its mutation-prone viral enzyme, high viral turnover and pressure from the host immune system. Therefore, viruses isolated at different time points from the same individual are never exactly the same and, accordingly, rarely function the same way. However, if we can understand how HIV-1 phenotypically evolves in the newly infected host and during disease progression, we may develop better therapeutics and perhaps halt the spread of the virus. This thesis is based on studies in which we have investigated how HIV-1 phenotypically evolves within infected individuals. We studied viruses emerging in infected adults, during late stage disease, and in vertically infected children, from shortly after birth until immunodeficiency. Some patients maintained viruses that exclusively used CC chemokine receptor 5 (CCR5) as coreceptor, R5 HIV-1, throughout the infection. Others had viruses whose coreceptor use was altered to include CXC chemokine receptor 4 (CXCR4). We analyzed sequentially obtained viruses from both groups of patients and studied phenotypic features in relation to molecular alterations in the viral envelope glycoproteins (Env). We found that the virus evolution at late stage disease toward increased infectivity and replicative capacity was fairly similar within patients harboring R5 or CXCR4-using HIV-1. The R5 HIV-1 also showed a decrease in trans-infection ability, mediated by the C-type lectin DC-SIGN, at end-stage disease. In addition, end-stage R5 HIV-1 were more sensitivity to certain broadly neutralizing antibodies. Furthermore, phenotypic alterations correlated with the decline in CD4+ T cell count during development of immunodeficiency. The observed evolution in phenotypic features also correlated with molecular alterations of the viral envelope glycoprotein gp120, with an increase in net positive charge and a loss of potential N-linked glycosylation sites (PNGS) at the end-stage of the disease. In addition, the efficiency of HIV-1 DC-SIGN use correlated with the presence of a specific glycan site in gp120. Studies on R5 HIV-1 from vertically infected children and their mothers demonstrated that efficient use of DC-SIGN for trans-infection do not appear to be a benefit for newly transmitted virus variants. Instead, the efficiency of virus DC-SIGN use increased during disease progression, from early after birth until immunodeficiency. These studies reveal that the phenotypes of R5 and CXCR4-using HIV-1 may evolve in an adaptive manner during disease progression and transmission

Carbide precipitation in a low alloyed steel during aging studied by atom probe tomography and thermodynamic modeling

Carbide precipitation in martensitic low alloyed steels contributes to the mechanical properties through precipitation hardening. A high number density of carbides is desired to maximize the hardening effect, which is achieved through the precipitation of carbides on the dislocations in the martensitic structure. In this study, the nucleation, growth, and coarsening of vanadium and molybdenum carbides during aging at 600◦C for periods up to four weeks were investigated. The work covers characterization with atom probe tomography, which showed that the nucleation of V and Mo rich MC/M2C carbides takes place on dislocations. The growth of these carbides proceeds by the diffusion of elements to the dislocations, which has been modeled using Dictra software, confirming the rate of the reaction as well as the depletion of carbide formers in the matrix. For longer aging times, particle coarsening will decrease the number density of particles with a transition from dislocation-based carbides to separate rounded carbides

Geometric Cross-Modal Comparison of Heterogeneous Sensor Data

In this work, we address the problem of cross-modal comparison of aerial data streams. A variety of simulated automobile trajectories are sensed using two different modalities: full-motion video, and radio-frequency (RF) signals received by detectors at various locations. The information represented by the two modalities is compared using self-similarity matrices (SSMs) corresponding to time-ordered point clouds in feature spaces of each of these data sources; we note that these feature spaces can be of entirely different scale and dimensionality. Several metrics for comparing SSMs are explored, including a cutting-edge time-warping technique that can simultaneously handle local time warping and partial matches, while also controlling for the change in geometry between feature spaces of the two modalities. We note that this technique is quite general, and does not depend on the choice of modalities. In this particular setting, we demonstrate that the cross-modal distance between SSMs corresponding to the same trajectory type is smaller than the cross-modal distance between SSMs corresponding to distinct trajectory types, and we formalize this observation via precision-recall metrics in experiments. Finally, we comment on promising implications of these ideas for future integration into multiple-hypothesis tracking systems.Comment: 10 pages, 13 figures, Proceedings of IEEE Aeroconf 201

Investigation of photochemical effects in flame diagnostics with picosecond photofragmentation laser-induced fluorescence

Photofragmentation laser-induced fluorescence (PFLIF) is for the first time performed based on picosecond laser pulses for detection of hydroperoxyl radicals (HO2) in a stoichiometric laminar methane/air flame. Photofragmentation is performed with a pump laser pulse of 80 ps duration and a wavelength of 266 nm, whereupon the produced OH photofragments are detected by a second picosecond probe laser pulse, inducing fluorescence via excitation in the A2Σ+(v = 1) ← X2Π(v = 0) band of OH near 283 nm. Excitation spectra of the OH photofragments formed in the reaction zone were recorded for pump-probe delays ranging from 0 to 5 ns. The spectra suggest that the population distribution of the nascent OH fragments is rotationally cold and that it takes on the order of 5 ns for the nascent non-equilibrium rotational distribution to relax into a thermal distribution. The radial OH-fragment distribution was extracted from spectral images (radial position versus emission wavelength) recorded at six different pump-probe delays. Photochemical OH production was observed both in the reaction zone and the product zone. Comparison with a kinetic model for OH production suggests that more than 20% of the oxygen fragments produced by photolysis in the reaction zone are formed in the excited 1D state, explaining a very rapid initial signal growth. The OH-production model was also compared with previous reaction-zone data, acquired with nanosecond laser pulses in the same flame, indicating that no O(1D), but only O(3P), is formed. A plausible explanation of the discrepancy between the two results is that the picosecond pulses, having more than two-orders of magnitude higher irradiance than the nanosecond pulses used in the previous study, might cause 2-photon photodissociation, allowing production of O(1D). In terms of flame diagnostics with PFLIF, it is concluded that a setup based on nanosecond laser pulses, rather than picosecond pulses, appears preferable since photochemical OH production in the reaction zone can be avoided while for short delay times the ratio between the photofragment signal and the photochemical interference in the product zone, stemming from CO2 photolysis, is sufficiently large to clearly visualize the photofragments

Temperature imaging in low pressure flames using diode laser two-line atomic fluorescence employing a novel indium seeding technique

The use of diode lasers for spatially resolved temperature imaging is demonstrated in low pressure premixed methane-air flames using two-line atomic fluorescence of seeded indium atoms. This work features the advantages of using compact diode lasers as the excitation sources with the benefits of two-dimensional planar imaging, which is normally only performed with high-power pulsed lasers. A versatile and reliable seeding technique with minimal impact on flame properties is used to introduce indium atoms into the combustion environment for a wide range of flame equivalence ratios. A spatial resolution of around 210 µm for this calibration free thermometry technique is achieved for three equivalence ratios at a pressure of 50 mbar in a laminar flat flame

Evolution of DC-SIGN use revealed by fitness studies of R5 HIV-1 variants emerging during AIDS progression

<p>Abstract</p> <p>Background</p> <p>At early stages of infection CCR5 is the predominant HIV-1 coreceptor, but in approximately 50% of those infected CXCR4-using viruses emerge with disease progression. This coreceptor switch is correlated with an accelerated progression. However, those that maintain virus exclusively restricted to CCR5 (R5) also develop AIDS. We have previously reported that R5 variants in these "non-switch virus" patients evolve during disease progression towards a more replicative phenotype exhibiting altered CCR5 coreceptor interactions. DC-SIGN is a C-type lectin expressed by dendritic cells that HIV-1 may bind and utilize for enhanced infection of T cells in <it>trans</it>. To further explore the evolution of the R5 phenotype we analyzed sequential R5 isolates obtained before and after AIDS onset, i.e. at the chronic stage and during end-stage disease, with regard to efficiency of DC-SIGN use in <it>trans</it>-infections.</p> <p>Results</p> <p>Results from binding and <it>trans</it>-infection assays showed that R5 viruses emerging during end-stage AIDS disease displayed reduced ability to use DC-SIGN. To better understand viral determinants underlying altered DC-SIGN usage by R5 viruses, we cloned and sequenced the HIV-1 <it>env </it>gene. We found that end-stage R5 viruses lacked potential N-linked glycosylation sites (PNGS) in the gp120 V2 and V4 regions, which were present in the majority of the chronic stage R5 variants. One of these sites, amino acid position 160 (aa160) in the V2 region, also correlated with efficient use of DC-SIGN for binding and <it>trans</it>-infections. In fitness assays, where head-to-head competitions between chronic stage and AIDS R5 viruses were setup in parallel direct and DC-SIGN-mediated infections, results were further supported. Competitions revealed that R5 viruses obtained before AIDS onset, containing the V2 PNGS at aa160, were selected for in the <it>trans</it>-infection. Whereas, in agreement with our previous studies, the opposite was seen in direct target cell infections where end-stage viruses out-competed the chronic stage viruses.</p> <p>Conclusion</p> <p>Results of our study suggest R5 virus variants with diverse fitness for direct and DC-SIGN-mediated <it>trans</it>-infections evolve within infected individuals at end-stage disease. In addition, our results point to the importance of a glycosylation site within the gp120 V2 region for efficient DC-SIGN use of HIV-1 R5 viruses.</p

Rational design of HIV vaccine and microbicides: report of the EUROPRISE annual conference

EUROPRISE is a Network of Excellence sponsored from 2007 to 2011 by the European Commission within the 6th Framework Program. The Network encompasses a wide portfolio of activities ranging from an integrated research program in the field of HIV vaccines and microbicides to training, dissemination and advocacy. The research program covers the whole pipeline of vaccine and microbicide development from discovery to early clinical trials. The Network is composed of 58 partners representing more than 65 institutions from 13 European countries; it also includes three major pharmaceutical companies (GlaxoSmithKline, Novartis and Sanofi-Pasteur) involved in HIV microbicide and vaccine research. The Network displays a dedicated and informative web page: http://www.europrise.org. Finally, a distinguishing trait of EUROPRISE is its PhD School of students from across Europe, a unique example in the world of science aimed at spreading excellence through training