SGR 1806−20 distance and dust properties in molecular clouds by analysis of flare X-ray echoes

The soft gamma repeater SGR 1806−20 is most famous for its giant flare from 2004, which yielded the highest gamma-ray flux ever observed on Earth. The flare emphasized the importance of determining the distance to the SGR, thus revealing the flare’s energy output, with implications on SGRs energy budget and giant flare rates. We analyse X-ray scattering echoes observed by Swift/X-Ray Telescope (XRT) following the 2006 August 6 intermediate burst of SGR 1806−20. Assuming positions and opacities of the molecular clouds along the line of sight from previous works, we derive direct constraints on the distance to SGR 1806−20, setting a lower limit of 9.4 kpc and an upper limit of 18.6 kpc (90 per cent confidence), compared with a 6–15 kpc distance range by previous works. This distance range matches an energy output of ≈10^(46) erg for the 2004 giant flare. We further use, for the first time, the X-ray echoes in order to study the dust properties in molecular clouds. Analysing the temporal evolution of the observed flux using a dust-scattering model, which assumes a power-law size distribution of the dust grains, we obtain a power-law index of −3.3^(+0.6)_(−0.7) (1σ) and a lower limit of 0.1. µm (2σ) on the dust maximal grain size, both conforming to measured dust properties in the diffused interstellar medium (ISM). We advocate future burst follow-up observations with Swift, Chandra and the planned NuSTAR telescopes, as means of obtaining much superior results from such an analysis

Using Wikipedia to boost collaborative filtering techniques

One important challenge in the field of recommender systems is the sparsity of available data. This problem limits the ability of recommender systems to provide accurate predictions of user ratings. We overcome this problem by using the publicly available user generated information contained in Wikipedia. We identify similarities between items by mapping them to Wikipedia pages and finding similarities in the text and commonalities in the links and categories of each page. These similarities can be used in the recommendation process and improve ranking predictions. We find that this method is most effective in cases where ratings are extremely sparse or nonexistent. Preliminary experimental results on the MovieLens dataset are encouraging

Stapled HIV-1 Peptides Recapitulate Antigenic Structures and Engage Broadly Neutralizing Antibodies

Hydrocarbon stapling can restore bioactive, α-helical structure to natural peptides, yielding research tools and prototype therapeutics to dissect and target protein interactions. Here, we explore the capacity of peptide stapling to generate high fidelity, protease-resistant mimics of antigenic structures for vaccine development. HIV-1 has been refractory to vaccine technologies thus far, although select human antibodies can broadly neutralize HIV-1 by targeting sequences of the gp41 juxtamembrane fusion apparatus. To develop candidate HIV-1 immunogens, we generated and characterized stabilized α-helices of the membrane proximal external region (SAH-MPER) of gp41. SAH-MPER peptides were remarkably protease-resistant and bound to the broadly neutralizing 4E10 and 10E8 antibodies with high affinity, recapitulating the structure of the MPER epitope when differentially engaged by the two anti-HIV Fabs. Thus, stapled peptides may provide a new opportunity to develop chemically-stabilized antigens for vaccination

SGR 1806-20 distance and dust properties in molecular clouds by analysis of a flare x-ray echoes

The soft gamma repeater SGR 1806-20 is most famous for its giant flare from 2004, which yielded the highest gamma-ray flux ever observed on Earth. The flare emphasized the importance of determining the distance to the SGR, thus revealing the flare's energy output, with implications on SGRs energy budget and giant flare rates. We analyze x-ray scattering echoes observed by Swift/XRT following the 2006 August 6 intermediate burst of SGR 1806-20. Assuming positions and opacities of the molecular clouds along the line-of-sight from previous works, we derive direct constrains on the distance to SGR 1806-20, setting a lower limit of 9.4 kpc and an upper limit of 18.6 kpc (90% confidence), compared with a 6-15 kpc distance range by previous works. This distance range matches an energy output of ~10^46 erg/s for the 2004 giant flare. We further use, for the first time, the x-ray echoes in order to study the dust properties in molecular clouds. Analyzing the temporal evolution of the observed flux using a dust scattering model, which assumes a power-law size distribution of the dust grains, we find a power-law index of -3.3_{-0.7}^{+0.6} (1 sigma) and a lower limit of 0.1 micron (2 sigma) on the dust maximal grain size, both conforming to measured dust properties in the diffused interstellar medium (ISM). We advocate future burst follow-up observations with Swift, Chandra and the planned NuSTAR telescopes, as means of obtaining much superior results from such an analysis.Comment: 12 pages, 7 figures, 3 tables, submitted to MNRA

Developmental Pathway of the MPER-Directed HIV-1-Neutralizing Antibody 10E8

Antibody 10E8 targets the membrane-proximal external region (MPER) of HIV-1 gp41, neutralizes >97% of HIV-1 isolates, and lacks the auto-reactivity often associated with MPER-directed antibodies. The developmental pathway of 10E8 might therefore serve as a promising template for vaccine design, but samples from time-of-infection—often used to infer the B cell record—are unavailable. In this study, we used crystallography, next-generation sequencing (NGS), and functional assessments to infer the 10E8 developmental pathway from a single time point. Mutational analysis indicated somatic hypermutation of the 2nd-heavy chain-complementarity determining region (CDR H2) to be critical for neutralization, and structures of 10E8 variants with V-gene regions reverted to genomic origin for heavy-and-light chains or heavy chain-only showed structural differences >2 Å relative to mature 10E8 in the CDR H2 and H3. To understand these developmental changes, we used bioinformatic sieving, maximum likelihood, and parsimony analyses of immunoglobulin transcripts to identify 10E8-lineage members, to infer the 10E8-unmutated common ancestor (UCA), and to calculate 10E8-developmental intermediates. We were assisted in this analysis by the preservation of a critical D-gene segment, which was unmutated in most 10E8-lineage sequences. UCA and early intermediates weakly bound a 26-residue-MPER peptide, whereas HIV-1 neutralization and epitope recognition in liposomes were only observed with late intermediates. Antibody 10E8 thus develops from a UCA with weak MPER affinity and substantial differences in CDR H2 and H3 from the mature 10E8; only after extensive somatic hypermutation do 10E8-lineage members gain recognition in the context of membrane and HIV-1 neutralization

Heterologous Epitope-Scaffold Prime∶Boosting Immuno-Focuses B Cell Responses to the HIV-1 gp41 2F5 Neutralization Determinant

The HIV-1 envelope glycoproteins (Env) gp120 and gp41 mediate entry and are the targets for neutralizing antibodies. Within gp41, a continuous epitope defined by the broadly neutralizing antibody 2F5, is one of the few conserved sites accessible to antibodies on the functional HIV Env spike. Recently, as an initial attempt at structure-guided design, we transplanted the 2F5 epitope onto several non-HIV acceptor scaffold proteins that we termed epitope scaffolds (ES). As immunogens, these ES proteins elicited antibodies with exquisite binding specificity matching that of the 2F5 antibody. These novel 2F5 epitope scaffolds presented us with the opportunity to test heterologous prime∶boost immunization strategies to selectively boost antibody responses against the engrafted gp41 2F5 epitope. Such strategies might be employed to target conserved but poorly immunogenic sites on the HIV-1 Env, and, more generally, other structurally defined pathogen targets. Here, we assessed ES prime∶boosting by measuring epitope specific serum antibody titers by ELISA and B cell responses by ELISpot analysis using both free 2F5 peptide and an unrelated ES protein as probes. We found that the heterologous ES prime∶boosting immunization regimen elicits cross-reactive humoral responses to the structurally constrained 2F5 epitope target, and that incorporating a promiscuous T cell helper epitope in the immunogens resulted in higher antibody titers against the 2F5 graft, but did not result in virus neutralization. Interestingly, two epitope scaffolds (ES1 and ES2), which did not elicit a detectable 2F5 epitope-specific response on their own, boosted such responses when primed with the ES5. Together, these results indicate that heterologous ES prime∶boost immunization regimens effectively focus the humoral immune response on the structurally defined and immunogen-conserved HIV-1 2F5 epitope

Induction of Antibodies in Rhesus Macaques That Recognize a Fusion-Intermediate Conformation of HIV-1 gp41

A component to the problem of inducing broad neutralizing HIV-1 gp41 membrane proximal external region (MPER) antibodies is the need to focus the antibody response to the transiently exposed MPER pre-hairpin intermediate neutralization epitope. Here we describe a HIV-1 envelope (Env) gp140 oligomer prime followed by MPER peptide-liposomes boost strategy for eliciting serum antibody responses in rhesus macaques that bind to a gp41 fusion intermediate protein. This Env-liposome immunization strategy induced antibodies to the 2F5 neutralizing epitope 664DKW residues, and these antibodies preferentially bound to a gp41 fusion intermediate construct as well as to MPER scaffolds stabilized in the 2F5-bound conformation. However, no serum lipid binding activity was observed nor was serum neutralizing activity for HIV-1 pseudoviruses present. Nonetheless, the Env-liposome prime-boost immunization strategy induced antibodies that recognized a gp41 fusion intermediate protein and was successful in focusing the antibody response to the desired epitope

Delineating antibody recognition in polyclonal sera from patterns of HIV-1 isolate neutralization.

Serum characterization and antibody isolation are transforming our understanding of the humoral immune response to viral infection. Here, we show that epitope specificities of HIV-1–neutralizing antibodies in serum can be elucidated from the serum pattern of neutralization against a diverse panel of HIV-1 isolates. We determined “neutralization fingerprints” for 30 neutralizing antibodies on a panel of 34 diverse HIV-1 strains and showed that similarity in neutralization fingerprint correlated with similarity in epitope. We used these fingerprints to delineate specificities of polyclonal sera from 24 HIV-1–infected donors and a chimeric siman-human immunodeficiency virus–infected macaque. Delineated specificities matched published specificities and were further confirmed by antibody isolation for two sera. Patterns of virus-isolate neutralization can thus afford a detailed epitope-specific understanding of neutralizing-antibody responses to viral infection

Structure and immune recognition of trimeric pre-fusion HIV-1 Env.

CAPRISA, 2014.The human immunodeficiency virus type 1 (HIV-1) envelope (Env) spike, comprising three gp120 and three gp41 subunits, is a conformational machine that facilitates HIV-1 entry by rearranging from a mature unliganded state, through receptor-bound intermediates, to a post-fusion state. As the sole viral antigen on the HIV-1 virion surface, Env is both the target of neutralizing antibodies and a focus of vaccine efforts. Here we report the structure at 3.5 Å resolution for an HIV-1 Env trimer captured in a mature closed state by antibodies PGT122 and 35O22. This structure reveals the pre-fusion conformation of gp41, indicates rearrangements needed for fusion activation, and defines parameters of immune evasion and immune recognition. Pre-fusion gp41 encircles amino- and carboxy-terminal strands of gp120 with four helices that form a membrane-proximal collar, fastened by insertion of a fusion peptide-proximal methionine into a gp41-tryptophan clasp. Spike rearrangements required for entry involve opening the clasp and expelling the termini. N-linked glycosylation and sequence-variable regions cover the pre-fusion closed spike; we used chronic cohorts to map the prevalence and location of effective HIV-1-neutralizing responses, which were distinguished by their recognition of N-linked glycan and tolerance for epitope-sequence variation