Exploitation of Ebola Virus VP35 Protein to identify new drugs counteracting its type I IFN antagonism

Ebolaviruses (EBOVs) are among the most virulent and deadly pathogens ever known, causing fulminant haemorrhagic fevers in humans and non-human primates. The 2014 outbreak of Ebola virus disease (EVD) in West Africa has claimed more lives than all previous EVD outbreaks combined. The EBOV high mortality rates have been related to the virus-induced impairment of the host innate immunity reaction due to two virus-coded proteins, VP24 and VP35. EBOV VP35 is a multifunctional protein, it is essential for viral replication as a component of the viral RNA polymerase and it also participates in nucleocapsid assembly. Early during EBOV infection, alpha-beta interferon (IFN-α/β) production would be triggered upon recognition of viral dsRNA products by cytoplasmic retinoic acid-inducible gene I (RIG-I)-like receptors (RLRs). However, this recognition is efficiently prevented by the double-stranded RNA (dsRNA) binding activity of the EBOV VP35 protein, which hides RLRs binding sites on the dsRNA phosphate backbone as well the 5’-triphosphate (5’-ppp) dsRNA ends to RIG-I recognition. In addition to dsRNA binding and sequestration, EBOV VP35 inhibits IFN-α/β production preventing the activation of the IFN regulatory factor 3 (IRF-3) by direct interaction with cellular proteins. Previous studies demonstrated that single amino acid changes in the VP35 dsRNA binding domain reduce EBOV virulence, indicating that VP35 is an attractive target for antiviral drugs development. Within this context, here we report the establishment of a novel method to characterize the EBOV VP35 inhibitory function of the dsRNA-dependent RIG-I-mediated IFN-β signaling pathway in a BLS2 cell culture setting. In such system, a plasmid containing the promoter region of IFN-β gene linked with a luciferase reporter gene was transfected, together with a EBOV VP35 mammalian expression plasmid, into the IFN-sensitive A549 cell line, and the IFN-induction was stimulated through dsRNA transfection. Through alanine scanning mutational studies with biochemical, cellular and computational methods we highlighted the importance of some VP35 residues involved in dsRNA end-capping binding, such as R312, K282 and R322, that may serve as target for the development of small-molecule inhibitors against EBOV. Furthermore, we identified a synthetic compound that increased IFN-induction only under antiviral response stimulation and subverted VP35 inhibition, proving to be very attractive for the development of an antiviral drug. In conclusion, our results provide the establishment of a new assay as a straightforward tool for the screening of antiviral compounds that target i) dsRNA-VP35 or cellular protein-VP35 interaction and ii) dsRNA-dependent RIG-I-mediated IFN signaling pathway, in order to potentiate the IFN response against VP35 inhibition, setting the bases for further drug development.

The Physarum polycephalum Genome Reveals Extensive Use of Prokaryotic Two-Component and Metazoan-Type Tyrosine Kinase Signaling.

Physarum polycephalum is a well-studied microbial eukaryote with unique experimental attributes relative to other experimental model organisms. It has a sophisticated life cycle with several distinct stages including amoebal, flagellated, and plasmodial cells. It is unusual in switching between open and closed mitosis according to specific life-cycle stages. Here we present the analysis of the genome of this enigmatic and important model organism and compare it with closely related species. The genome is littered with simple and complex repeats and the coding regions are frequently interrupted by introns with a mean size of 100 bases. Complemented with extensive transcriptome data, we define approximately 31,000 gene loci, providing unexpected insights into early eukaryote evolution. We describe extensive use of histidine kinase-based two-component systems and tyrosine kinase signaling, the presence of bacterial and plant type photoreceptors (phytochromes, cryptochrome, and phototropin) and of plant-type pentatricopeptide repeat proteins, as well as metabolic pathways, and a cell cycle control system typically found in more complex eukaryotes. Our analysis characterizes P. polycephalum as a prototypical eukaryote with features attributed to the last common ancestor of Amorphea, that is, the Amoebozoa and Opisthokonts. Specifically, the presence of tyrosine kinases in Acanthamoeba and Physarum as representatives of two distantly related subdivisions of Amoebozoa argues against the later emergence of tyrosine kinase signaling in the opisthokont lineage and also against the acquisition by horizontal gene transfer.

Age-related immune reconstitution during highly active antiretroviral therapy in human immunodeficiency virus type 1-infected children.

OBJECTIVES: To evaluate the immune reconstitution in HIV-1-infected children in whom highly active antiretroviral therapy (HAART) controlled viral replication and to assess the existence of a relation between the magnitude of this restoration and age. METHODS: All HIV-1-infected children in whom a new HAART decreased plasma viral load below 400 copies/ml after 3 months of therapy were prospectively enrolled in a study of their immune reconstitution. Viral load, lymphocyte phenotyping, determination of CD4+ and CD8+ T cell receptor repertoires and proliferative responses to mitogens and recall antigens were assessed every 3 months during 1 year. RESULTS: Nineteen children were evaluated. Naive and memory CD4+ percentages were already significantly increased after 3 months of HAART. In contrast to memory CD4+ percentages, naive CD4+ percentages continued to rise until 12 months. Age at baseline was inversely correlated with the magnitude of the rise in naive CD4+ cells after 3, 6 and 9 months of therapy but not after 12 months. Although memory and activated CD8+ cells were already decreasing after 3 months, abnormalities of the CD8 T cell receptor repertoire and activation of CD8+ cells persisted at 1 year. HAART increased the response to mitogens as early as 3 months after starting therapy. CONCLUSIONS: In children the recovery of naive CD4+ cells occurs more rapidly if treatment is started at a younger age, but after 1 year of viral replication control, patients of all ages have achieved the same level of restoration. Markers of chronic activation in CD8+ cells persist after 1 year of HAART.

Ambitious mothers – successful daughters: Mothers’ early expectations for children’s education and children’s earnings and sense of control in adult life

Background. Mothers' expectations for their children's educational attainment are related to children's educational and occupational attainment. Studies have yet to establish, however, the long-term links between maternal expectations and offspring earnings, which are not always related to occupational attainment especially in women, or between maternal expectations and offspring sense of control and self-efficacy, which are pivotal factors in career choice and development. Aims. To explore the role of mothers' expectations for their children's educational attainment in children's earnings attainment and sense of control later in life. Method. Data from sweeps of the 1970 British Cohort Study (BCS70) were used. The study sample was those cohort members with complete information on all the variables of interest. The study sample (N = 3,285) was more educated and less disadvantaged than the whole sample. If cohort members of this type are more likely to have a mother who has high expectations, then our results are biased downwards, which suggests that we underestimate the effect of expectations on our two outcome variables. Results. Mothers' expectations at the age of 10 were positively related to daughters' sense of control at the age of 30 even after controlling for ethnicity, educational attainment, and concurrent partner, parent, and labour market participation status, as well as the following confounding variables (measured at the ages of 0–10): general ability and general ability squared, locus of control, emotional and behavioural problems and emotional and behavioural problems squared, socio-economic disadvantage, parental social class, parental family structure, and mothers' education, child-rearing attitudes, and mental health. Mothers' expectations had no effect on sons' adult outcomes. Conclusions. Given that women are particularly at risk for poor psychological and economic outcomes in adulthood, and that this study likely underestimated the effect of expectations on these two outcomes, this is an important conclusion.

Spatial variability of the plankton trophic interaction in the North Sea: a new feature after the early 1970s

Traditionally, marine ecosystem structure was thought to be bottom-up controlled. In recent years, a number of studies have highlighted the importance of top-down regulation. Evidence is accumulating that the type of trophic forcing varies temporally and spatially, and an integrated view – considering the interplay of both types of control – is emerging. Correlations between time series spanning several decades of the abundances of adjacent trophic levels are conventionally used to assess the type of control: bottom-up if positive or top-down if this is negative. This approach implies averaging periods which might show time-varying dynamics and therefore can hide part of this temporal variability. Using spatially referenced plankton information extracted from the Continuous Plankton Recorder, this study addresses the potential dynamic character of the trophic structure at the planktonic level in the North Sea by assessing its variation over both temporal and spatial scales. Our results show that until the early-1970s a bottom-up control characterized the base of the food web across the whole North Sea, with diatoms having a positive and homogeneous effect on zooplankton filter-feeders. Afterwards, different regional trophic dynamics were observed, in particular a negative relationship between total phytoplankton and zooplankton was detected off the west coast of Norway and the Skagerrak as opposed to a positive one in the southern reaches. Our results suggest that after the early 1970s diatoms remained the main food source for zooplankton filter-feeders east of Orkney–Shetland and off Scotland, while in the east, from the Norwegian Trench to the German Bight, filter-feeders were mainly sustained by dinoflagellates.

Factors That Can Undermine the Psychological Benefits of Coastal Environments: Exploring the Effect of Tidal State, Presence, and Type of Litter

The beneficial effects of blue environments have been well documented; however, we do not know how marine litter might modify these effects. Three studies adopted a picture-rating task to examine the influence of litter on preference, perceived restorative quality, and psychological impacts. Photographs varied the presence of marine litter (Study 1) and the type of litter (Studies 2 and 3). The influence of tide and the role of connectedness were also explored. Using both quantitative and qualitative methods, it was shown that litter can undermine the psychological benefits that the coast ordinarily provides, thus demonstrating that, in addition to environmental costs of marine litter, there are also costs to people. Litter stemming from the public had the most negative impact. This research extends our understanding of the psychological benefits from natural coastal environments and the threats to these benefits from abundant and increasing marine litter

Higher incidence of childhood-onset type 1 diabetes mellitus in remote areas: a UK regional small-area analysis

Aims/hypothesis: We investigated the association between the incidence of type 1 diabetes mellitus and remoteness (a proxy measure for exposure to infections) using recently developed techniques for statistical analysis of small-area data.

Subjects, materials and methods: New cases in children aged 0 to 14 years in Northern Ireland were prospectively registered from 1989 to 2003. Ecological analysis was conducted using small geographical units (582 electoral wards) and area characteristics including remoteness, deprivation and child population density. Analysis was conducted using Poisson regression models and Bayesian
hierarchical models to allow for spatially correlated risks that were potentially caused by unmeasured explanatory variables.

Results: In Northern Ireland between 1989 and 2003, there were 1,433 new cases of type 1 diabetes, giving a directly standardised incidence rate of 24.7 per 100,000 personyears. Areas in the most remote fifth of all areas had a significantly (p=0.0006) higher incidence of type 1 diabetes mellitus (incidence rate ratio=1.27 [95% CI 1.07, 1.50]) than those in the most accessible fifth of all areas. There was also a higher incidence rate in areas that were less deprived (p<0.0001) and less densely populated (p=0.002). After adjustment for deprivation and additional adjustment for child population density the association between diabetes and remoteness remained significant (p=0.01 and p=0.03, respectively).

Conclusions/interpretation: In Northern Ireland, there is evidence that remote areas experience higher rates of type 1 diabetes mellitus. This could reflect a reduced or delayed exposure to infections, particularly early in life, in these areas.

Rethinking the early medieval settlement of woodlands: evidence from the western Sussex Weald

The assumptions underlying the interpretation of the early medieval settlement of woodland are challenged through a detailed study of the Weald in western Sussex. The patterns of usage of woodland in England were very varied, and each area needs to be looked at individually. Systems of woodland exploitation did not simply develop from extensive to intensive, but may have taken a number of different forms during the early medieval period. In one area of the Weald, near to Horsham, the woodland appears to have been systematically divided up between different estates. This implies that woodland settlement may not always have developed organically, but this type of landscape could have been planned. It is argued that the historical complexity of woodland landscapes has not been recognised because the evidence has been aggregated. Instead, each strand of evidence needs to be evaluated separately.

Macroturbulent and rotational broadening in the spectra of B-type supergiants.

The absorption-line spectra of early B-type supergiants show significant broadening that implies that an additional broadening mechanism (characterized here as `macroturbulence') is present in addition to rotational broadening. Using high-resolution spectra with signal-to-noise ratios of typically 500, we have attempted to quantify the relative contributions of rotation and macroturbulence, but even with data of this quality significant problems were encountered. However, for all our targets, a model where macroturbulence dominates and rotation is negligible is acceptable; the reverse scenario leads to poor agreement between theory and observation. Additionally, there is marginal evidence for the degree of broadening increasing with line strength, possibly a result of the stronger lines being formed higher in the atmosphere. Acceptable values of the projected rotational velocity are normally less than or equal to 50 km s-1, which may also be a typical upper limit for the rotational velocity. Our best estimates for the projected rotational velocity are typically 10-20 km s-1 and hence compatible with this limit. These values are compared with those predicted by single star evolutionary models, which are initially rapidly rotating. It is concluded that either these models underestimate the rate of rotational breaking or some of the targets may be evolving through a blue loop or are binaries.

B-type supergiants in the SMC: Chemical compositions and comparison of static and unified models

High-resolution UCLES/AAT spectra are presented for nine B-type supergiants in the SMC, chosen on the basis that they may show varying amounts of nuclear-synthetically processed material mixed to their surface. These spectra have been analysed using a new grid of approximately 12 000 non-LTE line blanketed tlusty model atmospheres to estimate atmospheric parameters and chemical composition. The abundance estimates for O, Mg and Si are in excellent agreement with those deduced from other studies, whilst the low estimate for C may reflect the use of the C II doublet at 4267 Å. The N estimates are approximately an order of magnitude greater than those found in unevolved B-type stars or H II regions but are consistent with the other estimates in AB-type supergiants. These results have been combined with results from a unified model atmosphere analysis of UVES/VLT spectra of B-type supergiants (Trundle et al. 2004, A&A, 417, 217) to discuss the evolutionary status of these objects. For two stars that are in common with those discussed by Trundle et al., we have undertaken a careful comparison in order to try to understand the relative importance of the different uncertainties present in such analyses, including observational errors and the use of static or unified models. We find that even for these relatively luminous supergiants, tlusty models yield atmospheric parameters and chemical compositions similar to those deduced from the unified code fastwind.

A non-LTE analysis of the spectra of two narrow lined main sequence stars in the SMC

An analysis of high-resolution VLT/UVES spectra of two B-type main sequence stars, NGC 346-11 and AV 304, in the Small Magellanic Cloud (SMC), has been undertaken, using the non-LTE tlusty model atmospheres to derive the stellar parameters and chemical compositions of each star. The chemical compositions of the two stars are in reasonable agreement. Moreover, our stellar analysis agrees well with earlier analyses of H II regions. The results derived here should be representative of the current base-line chemical composition of the SMC interstellar medium as derived from B-type stars.

A search for star formation around the Galactic halo B-type star PHL 346 with the 2dF spectrograph

A preliminary search for stars that may have formed coevally with the apparently young halo B-type star PHL 346 has been performed with the 2dF multifibre spectrograph on the Anglo- Australian Telescope (AAT). Candidates were selected for spectroscopy from APM scans of B and R Schmidt plates centred on PHL 346. A total of 476 stars of spectral type A or F were found; radial velocity estimates and more accurate spectral type assignments narrowed the number of possible coeval candidates to 6 A-type and 14 F-type stars. A statistical analysis of these results using a comparison with a control field suggests that the number of A-type or F-type candidate stars around PHL 346 is not unexpected, and that they need not be associated with PHL 346. A number of ways to improve the project are suggested.

Opacity in the upper atmospheres of active stars - II. AD Leonis

We present FUV and UV spectroscopic observations of AD Leonis, with the aim of investigating opacity effects in the transition regions of late-type stars. The C III lines in FUSE spectra show significant opacity during both the quiescent and flaring states of AD Leonis, with up to 30% of the expected flux being lost during the latter. Other FUSE emission lines tested for opacity include those of O VI, while C IV, Si IV and N V transitions observed with STIS are also investigated. These lines only reveal modest amounts of opacity with losses during flaring of up to 20%. Optical depths have been calculated for homogeneous and inhomogeneous geometries, giving path lengths of approximate to 20 - 60 km and approximate to 10 - 30 km, respectively, under quiescent conditions. However path lengths derived during flaring are approximate to 2 - 3 times larger. These values are in excellent agreement with both estimates of the small-scale structure observed in the solar transition region, and path lengths derived previously for several other active late-type stars.

The Galactic metallicity gradient

We have previously published intermediate to hi,oh resolution spectroscopic observations of approximately 80 early B-type main-sequence stars situated in 19 Galactic open clusters/associations with Galactocentric distances distributed over 6 less than or equal to R-g less than or equal to 18 kpc. This current study collates and re-analyses these equivalent- width datasets using LTE and non-LTE model atmosphere techniques, in order to determine the stellar atmospheric parameters and abundance estimates for C, N, O, Mg, Al and Si. The latter should be representative of the present-day Galactic interstellar medium. Our extensive observational dataset permits the identification of sub-samples of stars with similar atmospheric parameters and of homogeneous subsets of lines. As such, this investigation represents the most extensive and systematic study of its kind to date. We conclude that the distribution of light elements (CI O, Mg & Si) in the Galactic disk can be represented by a linear, radial gradient of -0.07 +/- 0.01 dex kpc(-1) Our results for nitrogen and oxygen viz. (-0.09 +/- 0.01 dex kpc(-1) and -0.067 +/- 0.008 dex kpc(-1)) are in excellent agreement with that found from the study of HII regions. We have also examined our datasets for evidence of an abrupt discontinuity in the metallicity of the Galactic disk near a Galactocentric distance of 10 kpc (see Twarog et al. 1997). However, there is no evidence to suggest that our data would be better fitted with a two-zone model. Moreover, we observe a N/O gradient of -0.04 +/- 0.02 dex kpc(-1) which is consistent with that found for other spiral galaxies (Vila- Costas gr Edmunds 1993).

Chemical composition of B-type supergiants in the OB 8, OB 10, OB 48, OB 78 associations of M 31

Absolute and differential chemical abundances are presented for the largest group of massive stars in M31 studied to date. These results were derived from intermediate resolution spectra of seven B-type supergiants, lying within four OB associations covering a galactocentric distance of 5-12 kpc. The results are mainly based on an LTE analysis, and we additionally present a full non-LTE, unified model atmosphere analysis of one star (OB 78-277) to demonstrate the reliability of the differential LTE technique. A comparison of the stellar oxygen abundance with that of previous nebular results shows that there is an off set of between similar to0.15-0.4 dex between the two methods which is critically dependent on the empirical calibration adopted for the R 23 parameter with [O/H]. However within the typical errors of the stellar and nebular analyses (and given the strength of dependence of the nebular results on the calibration used) the oxygen abundances determined in each method are fairly consistent. We determine the radial oxygen abundance gradient from these stars, and do not detect any systematic gradient across this galactocentric range. We find that the inner regions of M31 are not, as previously thought, very "metal rich". Our abundances of C, N, O, Mg, Si, Al, S and Fe in the M31 supergiants are very similar to those of massive stars in the solar neighbourhood.