HIV-1 tropism determination using a phenotypic Env recombinant viral assay highlights overestimation of CXCR4-usage by genotypic prediction algorithms for CRRF01_AE and CRF02_AG

Background: Human Immunodeficiency virus type-1 (HIV) entry into target cells involves binding of the viral envelope (Env) to CD4 and a coreceptor, mainly CCR5 or CXCR4. The only currently licensed HIV entry inhibitor, maraviroc, targets CCR5, and the presence of CXCX4-using strains must be excluded prior to treatment. Co-receptor usage can be assessed by phenotypic assays or through genotypic prediction. Here we compared the performance of a phenotypic Env-Recombinant Viral Assay (RVA) to the two most widely used genotypic prediction algorithms, Geno2Pheno([coreceptor]) and webPSSM. Methods: Co-receptor tropism of samples from 73 subtype B and 219 non-B infections was measured phenotypically using a luciferase-tagged, NL4-3-based, RVA targeting Env. In parallel, tropism was inferred genotypically from the corresponding V3-loop sequences using Geno2Pheno([coreceptor]) (5-20% FPR) and webPSSM-R5X4. For discordant samples, phenotypic outcome was retested using co-receptor antagonists or the validated Trofile (R) Enhanced-Sensitivity-Tropism-Assay. Results: The lower detection limit of the RVA was 2.5% and 5% for X4 and R5 minority variants respectively. A phenotype/genotype result was obtained for 210 samples. Overall, concordance of phenotypic results with Geno2Pheno([coreceptor]) was 85.2% and concordance with webPSSM was 79.5%. For subtype B, concordance with Geno2pheno([coreceptor]) was 94.4% and concordance with webPSSM was 79.6%. High concordance of genotypic tools with phenotypic outcome was seen for subtype C (90% for both tools). Main discordances involved CRF01_AE and CRF02_AG for both algorithms (CRF01_AE: 35.9% discordances with Geno2Pheno([coreceptor]) and 28.2% with webPSSM; CRF02_AG: 20.7% for both algorithms). Genotypic prediction overestimated CXCR4-usage for both CRFs. For webPSSM, 40% discordance was observed for subtype A. Conclusions: Phenotypic assays remain the most accurate for most non-B subtypes and new subtype-specific rules should be developed for non-B subtypes, as research studies more and more draw conclusions from genotypically-inferred tropism, and to avoid unnecessarily precluding patients with limited treatment options from receiving maraviroc or other entry inhibitors

Mexico-UK Sub-millimeter Camera for AsTronomy

MUSCAT is a large format mm-wave camera scheduled for installation on the Large Millimeter Telescope Alfonso Serrano (LMT) in 2018. The MUSCAT focal plane is based on an array of horn coupled lumped-element kinetic inductance detectors optimised for coupling to the 1.1mm atmospheric window. The detectors are fed with fully baffled reflective optics to minimize stray-light contamination. This combination will enable background-limited performance at 1.1 mm across the full 4 arcminute field-of-view of the LMT. The easily accessible focal plane will be cooled to 100 mK with a new closed cycle miniature dilution refrigerator that permits fully continuous operation. The MUSCAT instrument will demonstrate the science capabilities of the LMT through two relatively short science programmes to provide high resolution follow-up surveys of Galactic and extra-galactic sources previously observed with the Herschel space observatory, after the initial observing campaigns. In this paper, we will provide an overview of the overall instrument design as well as an update on progress and scheduled installation on the LMT.Comment: Accepted for publication in the Journal of Low Temperature Detector

Chætognath transcriptome reveals ancestral and unique features among bilaterians

The chætognath transcriptome reveals unusual genomic features in the evolution of this protostome and suggests that it could be used as a model organism for bilaterians

Characteristics and spread to the native population of HIV-1 non-B subtypes in two European countries with high migration rate

Background: Non-B subtypes account for at least 50 % of HIV-1 infections diagnosed in Belgium and Luxembourg. They are considered to be acquired through heterosexual contacts and infect primarily individuals of foreign origin. Information on the extent to which non-B subtypes spread to the local population is incomplete. Methods: Pol and env gene sequences were collected from 410 non-subtype B infections. Profound subtyping was performed using 5 subtyping tools and sequences of both pol and env. Demographic information, disease markers (viral load, CD4 count) and viral characteristics (co-receptor tropism) were compared between subtypes. Maximum likelihood phylogenetic trees were constructed and examined for clustering. Results: The majority of non-B infections were diagnosed in patients originating from Africa (55.8 %), individuals born in Western Europe represented 30.5 %. Heterosexual transmission was the most frequently reported transmission route (79.9 %), MSM transmission accounted for 12.2 % and was significantly more frequently reported for Western Europeans (25.7 % versus 4.3 % for individuals originating from other regions; p < 0.001). Subtypes A and C and the circulating recombinant forms CRF01_AE and CRF02_AG were the most represented and were included in the comparative analysis. Native Western Europeans were underrepresented for subtype A (14.5 %) and overrepresented for CRF01_AE (38.6 %). The frequency of MSM transmission was the highest for CRF01_AE (18.2 %) and the lowest for subtype A (0 %). No differences in age, gender, viral load or CD4 count were observed. Prevalence of CXCR4-use differed between subtypes but largely depended on the tropism prediction algorithm applied. Indications for novel intersubtype recombinants were found in 20 patients (6.3 %). Phylogenetic analysis revealed only few and small clusters of local transmission but could document one cluster of CRF02_AG transmission among Belgian MSM. Conclusions: The extent to which non-B subtypes spread in the native Belgian-Luxembourg population is higher than expected, with 30.5 % of the non-B infections diagnosed in native Western Europeans. These infections resulted from hetero-as well as homosexual transmission. Introduction of non-B variants in the local high at risk population of MSM may lead to new sub-epidemics and/or increased genetic variability and is an evolution that needs to be closely monitored

Preparation of hexagonal GeO2 particles with particle size and crystallinity controlled by peptides, silk and silk-peptide chimeras

We demonstrate the use of silk based proteins to control the particle/crystallite size during GeO2 formation, using a bio-mimetic approach at circumneutral pH and ambient temperature. Multicrystalline GeO2 was prepared from germanium tetraethoxide (TEOG) in the presence of different silk-based proteins: Bombyx mori silk (native silk) and two chimeric proteins prepared by linking a germania binding peptide (Ge28: HATGTHGLSLSH) with Bombyx mori silk via chemical coupling at different peptide loadings (silk-Ge28 10% and silk-Ge28 50%). The mineralisation activity of the silk-based proteins was compared with that of peptide Ge28 as a control system. GeO2 mineralisation was investigated in water and in citric acid/bis-tris propane buffer at pH 6. Morphology, particle size, crystallinity, water and organic content of the materials obtained were analysed to study the effect of added biomolecules and mineralisation environment on material properties. In the presence of silk additives well-defined cube-shape hybrid materials composed of hexagonal germania and up to ca. 5 wt% organic content were obtained. The cubic particles ranged from 0.4 to 1.4m in size and were composed of crystalline domains in the range 35-106 nm depending on the additive used and synthesis conditions

A Deep Chandra ACIS Study of NGC 4151. III. the Line Emission and Spectral Analysis of the Ionization Cone

This paper is the third in a series in which we present deep Chandra ACIS-S imaging spectroscopy of the Seyfert 1 galaxy NGC 4151, devoted to study its complex circum-nuclear X-ray emission. Emission features in the soft X-ray spectrum of the bright extended emission (L[0.3-2keV]~10^40 erg/s) at r>130 pc (2") are consistent with the brighter OVII, OVIII, and NeIX lines seen in the Chandra HETGS and XMM-Newton RGS spectra below 2 keV. We construct emission line images of these features and find good morphological correlations with the narrow line region clouds mapped in [OIII]5007A. Self-consistent photoionization models provide good descriptions of the spectra of the large scale emission, as well as resolved structures, supporting the dominant role of nuclear photoionization, although displacement of optical and X-ray features implies a more complex medium. Collisionally ionized emission is estimated to be <12% of the extended emission. Presence of both low and high ionization spectral components and extended emission in the X-ray image perpendicular to the bicone indicates leakage of nuclear ionization, likely filtered through warm absorbers, instead of being blocked by a continuous obscuring torus. The ratios of [OIII]/soft X-ray flux are approximately constant (~15) for the 1.5 kpc radius spanned by these measurements, indicating a relatively constant ionization parameter, consistent with the photoionized outflow of a wind-like density profile. Using spatially resolved features, we estimate that the mass outflow rate in NGC 4151 is ~2Msun/yr at 130 pc and the kinematic power of the ionized outflow is 1.7x10^41 erg/s, approximately 0.3% of the bolometric luminosity of NGC 4151.Comment: 45 pages. 18 figures. Accepted to Ap

A Deep Chandra ACIS Study of NGC 4151. I. the X-ray Morphology of the 3 kpc-diameter Circum-nuclear Region and Relation to the Cold Interstellar Medium

We report on the imaging analysis of 200 ks sub-arcsecond resolution Chandra ACIS-S observations of the nearby Seyfert 1 galaxy NGC 4151. Bright, structured soft X-ray emission is observed to extend from 30 pc to 1.3 kpc in the south-west from the nucleus, much farther than seen in earlier X-ray studies. The terminus of the north-eastern X-ray emission is spatially coincident with a CO gas lane, where the outflow likely encounters dense gas in the host galactic disk. X-ray emission is also detected outside the boundaries of the ionization cone, which indicates that the gas there is not completely shielded from the nuclear continuum, as would be the case for a molecular torus collimating the bicone. In the central r<200 pc region, the subpixel processing of the ACIS data recovers the morphological details on scales of <30~pc (<0.5") first discovered in Chandra HRC images. The X-ray emission is more absorbed towards the boundaries of the ionization cone, as well as perpendicular to the bicone along the direction of a putative torus in NGC 4151. The innermost region where X-ray emission shows the highest hardness ratio, is spatially coincident with the near-infrared resolved H_2 emission and dusty spirals we find in an HST V-H color image. The agreement between the observed H_2 line flux and the value predicted from X-ray-irradiated molecular cloud models supports photo-excitation by X-rays from the active nucleus as the origin of the H_2 line, although contribution from UV fluorescence or collisional excitation cannot be fully ruled out with current data. The discrepancy between the mass of cold molecular gas inferred from recent CO and near-infrared H_2 observations may be explained by the anomalous CO abundance in this X-ray dominated region. The total H_2 mass derived from the X-ray observation agrees with measurement in Storchi-Bergmann et al.Comment: 33 pages, 9 figures and 2 table

Predominance of the heterozygous CCR5 delta‐24 deletion in African individuals resistant to HIV infection might be related to a defect in CCR5 addressing at the cell surface

Introduction The chemokine receptor CCR5 is the main co-receptor for R5-tropic HIV-1 variants. We have previously described a novel 24-base pair deletion in the coding region of CCR5 among individuals from Rwanda. Here, we investigated the prevalence of hCCR5 Delta 24 in different cohorts and its impact on CCR5 expression and HIV-1 infection in vitro. Methods We screened hCCR5 Delta 24 in a total of 3232 individuals which were either HIV-1 uninfected, high-risk HIV-1 seronegative and seropositive partners from serodiscordant couples, Long-Term Survivors, or HIV-1 infected volunteers from Africa (Rwanda, Kenya, Guinea-Conakry) and Luxembourg, using a real-time PCR assay. The role of the 24-base pair deletion on CCR5 expression and HIV infection was assessed in cell lines and PBMC using mRNA quantification, confocal analysis, flow and imaging cytometry. Results and Discussion Among the 1661 patients from Rwanda, 12 individuals were heterozygous for hCCR5 Delta 24 but none were homozygous. Although heterozygosity for this allele may not confer complete resistance to HIV-1 infection, the prevalence of the mutation was 2.41% (95%CI: 0.43; 8.37) in 83 Long-Term Survivors (LTS) and 0.99% (95%CI: 0.45; 2.14) in 613 HIV-1 exposed seronegative members as compared with 0.35% (95% Cl: 0.06; 1.25) in 579 HIV-1 seropositive members. The prevalence of hCCR5 Delta 24 was 0.55% (95%CI: 0.15; 1.69) in 547 infants from Kenya but the mutation was not detected in 224 infants from Guinea-Conakry nor in 800 Caucasian individuals from Luxembourg. Expression of hCCR5 Delta 24 in cell lines and PBMC showed that the hCCR5 Delta 24 protein is stably expressed but is not transported to the plasma membrane due to a conformational change. Instead, the mutant receptor was retained intracellularly, colocalized with an endoplasmic reticulum marker and did not mediate HIV-1 infection. Co-transfection of hCCR5 Delta 24 and wtCCR5 did not indicate a transdominant negative effect of CCR5 Delta 24 on wtCCR5. Conclusions Our findings indicate that hCCR5 Delta 24 is not expressed at the cell surface. This could explain the higher prevalence of the heterozygous hCCR5 Delta 24 in LTS and HIV-1 exposed seronegative members from serodiscordant couples. Our data suggest an East-African localization of this deletion, which needs to be confirmed in larger cohorts from African and non-African countries