The hypervariable HIV-1 capsid protein residues comprise HLA-driven CD8+ T-cell escape mutations and covarying HLA-independent polymorphisms

One proposed HIV vaccine strategy is to induce Gag-specific CD8(+) T-cell responses that can corner the virus, through fitness cost of viral escape and unavailability of compensatory mutations. We show here that the most variable capsid residues principally comprise escape mutants driven by protective alleles HLA-B*57, -5801, and -8101 and covarying HLA-independent polymorphisms that arise in conjunction with these escape mutations. These covarying polymorphisms are potentially compensatory and are concentrated around three tropism-determining loops of p24, suggesting structural interdependencies. Our results demonstrate complex patterns of adaptation of HIV under immune selection pressure, the understanding of which should aid vaccine design.     

Limited genetic divergence among Australian alpine Poa tussock grasses coupled with regional structuring points to ongoing gene flow and taxonomic challenges

Background and Aims

While molecular approaches can often accurately reconstruct species relationships, taxa that are incompletely differentiated pose a challenge even with extensive data. Such taxa are functionally differentiated, but may be genetically differentiated only at small and/or patchy regions of the genome. This issue is considered here in Poa tussock grass species that dominate grassland and herbfields in the Australian alpine zone.

Methods

Previously reported tetraploidy was confirmed in all species by sequencing seven nuclear regions and five microsatellite markers. A Bayesian approach was used to co-estimate nuclear and chloroplast gene trees with an overall dated species tree. The resulting species tree was used to examine species structure and recent hybridization, and intertaxon fertility was tested by experimental crosses.

Key Results

Species tree estimation revealed Poa gunnii, a Tasmanian endemic species, as sister to the rest of the Australian alpine Poa. The taxa have radiated in the last 0·5–1·2 million years and the non-gunnii taxa are not supported as genetically distinct. Recent hybridization following past species divergence was also not supported. Ongoing gene flow is suggested, with some broad-scale geographic structure within the group.

Conclusions

The Australian alpine Poa species are not genetically distinct despite being distinguishable phenotypically, suggesting recent adaptive divergence with ongoing intertaxon gene flow. This highlights challenges in using conventional molecular taxonomy to infer species relationships in recent, rapid radiations.     

Indoor Residual Spraying in Combination with Insecticide-Treated Nets Compared to Insecticide-Treated Nets Alone for Protection against Malaria: A Cluster Randomised Trial in Tanzania

Background

Insecticide-treated nets (ITNs) and indoor residual spraying (IRS) of houses provide effective malaria transmission control. There is conflicting evidence about whether it is more beneficial to provide both interventions in combination. A cluster randomised controlled trial was conducted to investigate whether the combination provides added protection compared to ITNs alone.

Methods and Findings

In northwest Tanzania, 50 clusters (village areas) were randomly allocated to ITNs only or ITNs and IRS. Dwellings in the ITN+IRS arm were sprayed with two rounds of bendiocarb in 2012. Plasmodium falciparum prevalence rate (PfPR) in children 0.5–14 y old (primary outcome) and anaemia in children <5 y old (secondary outcome) were compared between study arms using three cross-sectional household surveys in 2012. Entomological inoculation rate (secondary outcome) was compared between study arms.IRS coverage was approximately 90%. ITN use ranged from 36% to 50%. In intention-to-treat analysis, mean PfPR was 13% in the ITN+IRS arm and 26% in the ITN only arm, odds ratio = 0.43 (95% CI 0.19–0.97, n = 13,146). The strongest effect was observed in the peak transmission season, 6 mo after the first IRS. Subgroup analysis showed that ITN users were additionally protected if their houses were sprayed. Mean monthly entomological inoculation rate was non-significantly lower in the ITN+IRS arm than in the ITN only arm, rate ratio = 0.17 (95% CI 0.03–1.08).

Conclusions

This is the first randomised trial to our knowledge that reports significant added protection from combining IRS and ITNs compared to ITNs alone. The effect is likely to be attributable to IRS providing added protection to ITN users as well as compensating for inadequate ITN use. Policy makers should consider deploying IRS in combination with ITNs to control transmission if local ITN strategies on their own are insufficiently effective. Given the uncertain generalisability of these findings, it would be prudent for malaria control programmes to evaluate the cost-effectiveness of deploying the combination.

Trial registration

www.ClinicalTrials.gov {"type":"clinical-trial","attrs":{"text":"NCT01697852","term_id":"NCT01697852"}}NCT01697852 Please see later in the article for the Editors'' Summary     

Climate change and annual survival in a temperate passerine: partitioning seasonal effects and predicting future patterns

Predicting climate change impacts on population size requires detailed understanding of how climate influences key demographic rates, such as survival. This knowledge is frequently unavailable, even in well‐studied taxa such as birds. In temperate regions, most research into climatic effects on annual survival in resident passerines has focussed on winter temperature. Few studies have investigated potential precipitation effects and most assume little impact of breeding season weather. We use a 19‐year capture–mark–recapture study to provide a rare empirical analysis of how variation in temperature and precipitation throughout the entire year influences adult annual survival in a temperate passerine, the long‐tailed tit Aegithalos caudatus. We use model averaging to predict longer‐term historical survival rates, and future survival until the year 2100. Our model explains 73% of the interannual variation in survival rates. In contrast to current theory, we find a strong precipitation effect and no effect of variation in winter weather on adult annual survival, which is correlated most strongly to breeding season (spring) weather. Warm springs and autumns increase annual survival, but wet springs reduce survival and alter the form of the relationship between spring temperature and annual survival. There is little evidence for density dependence across the observed variation in population size. Using our model to estimate historical survival rates indicates that recent spring warming has led to an upward trend in survival rates, which has probably contributed to the observed long‐term increase in the UK long‐tailed tit population. Future climate change is predicted to further increase survival, under a broad range of carbon emissions scenarios and probabilistic climate change outcomes, even if precipitation increases substantially. We demonstrate the importance of considering weather over the entire annual cycle, and of considering precipitation and temperature in combination, in order to develop robust predictive models of demographic responses to climate change. Synthesis Prediction of climate change impacts demands understanding of how climate influences key demographic rates. In our 19‐year mark‐recapture study of long‐tailed tits Aegithalos caudatus, weather explained 73% of the inter‐annual variation in adult survival; warm springs and autumns increased survival, wet springs reduced survival, but winter weather had little effect. Robust predictions thus require consideration of the entire annual cycle and should not focus solely on temperature. Unexpectedly, survival appeared not to be strongly density‐dependent, so we use historical climate data to infer that recent climate change has enhanced survival over the four decades in which the UK long‐tailed tit population has more than doubled. Furthermore, survival rates in this species are predicted to further increase under a wide range of future climate scenarios.     

The contrasting role of male relatedness in different mechanisms of sexual selection in red junglefowl

In structured populations, competition for reproductive opportunities should be relaxed among related males. The few tests of this prediction often neglect the fact that sexual selection acts through multiple mechanisms, both before and after mating. We performed experiments to study the role of within‐group male relatedness across pre‐ and postcopulatory mechanisms of sexual selection in social groups of red junglefowl, Gallus gallus, in which two related males and one unrelated male competed over females unrelated to all the males. We confirm theoretical expectations that, after controlling for male social status, competition over mating was reduced among related males. However, this effect was contrasted by other sexual selection mechanisms. First, females biased male mating in favor of the unrelated male, and might also favor his inseminations after mating. Second, males invested more—rather than fewer—sperm in postcopulatory competition with relatives. A number of factors may contribute to explain this counterintuitive pattern of sperm allocation, including trade‐offs between male investment in pre‐ versus postcopulatory competition, differences in the relative relatedness of pre‐ versus postcopulatory competitors, and female bias in sperm utilization in response to male relatedness. Collectively, these results reveal that within‐group male relatedness may have contrasting effects in different mechanisms of sexual selection.     

Bee venom secretory phospholipase A2 and phosphatidylinositol-homologues cooperatively disrupt membrane integrity,abrogate signal transduction and inhibit proliferation of renal cancer cells

Bee venom secretory phospholipase A2 (bv-sPLA2) and phosphatidylinositol-(3,4)-bisphosphate (PtdIns(3,4)P2) act synergistically to induce cell death in tumour cells of various origins with concomitant stimulation of the immune system. Here, we investigated the mechanisms involved in such actions and examined structural requirements of PtdIns-homologues to inhibit tumour cells in combination with bv-sPLA2. Renal cancer cells were treated with bv-sPLA2 alone or in combination with PtdIns-homologues. Inhibitory effects on [³H] thymidine incorporation and intracellular signal transduction pathways were tested. Reaction products generated by bv-sPLA2 interaction with PtdIns(3,4)P2 were identified by mass spectrometry. Among the tested PtdIns-homologues those with a phosphate esterified to position 3 of the inositol head group, were most efficient in cooperating with bv-sPLA2 to block tumour cell proliferation. Growth inhibition induced by the combined action of bv-sPLA2 with either PtdIns(3,4)bisphosphate or PtdIns(3,4,5)trisphosphate were synergistic and accompanied by potent cell lysis. In contrast, PtdIns, which lacked the phosphate group at position 3, failed to promote synergistic growth inhibition. The combined administration of PtdIns(3,4)P2 and bv-sPLA2 abrogated signal transduction mediated by extracellular signal regulated kinase 1 and 2 and prevented transduction of survival signals mediated by protein kinase B. Surface expression of the epidermal growth factor (EGF)-receptor was reduced after PtdIns(3,4)P2-bv-sPLA2 administration and associated with a blockade of EGF-induced signalling. In addition, mass spectroscopy revealed that bv-sPLA2 cleaves PtdIns(3,4)P2 to generate lyso-PtdIns(3,4)P2. In conclusion, we suggest that the cytotoxic activity mediated by PtdIns(3,4)P2 and bv-sPLA2 is due to cell death that results from disruption of membrane integrity, abrogation of signal transduction and the generation of cytotoxic lyso-PtdIns(3,4)P2. This work was supported by a grant to MT of the kompetenzzentrum medizin tirol (kmt), a centre of excellence.     

The aluminium content of breast tissue taken from women with breast cancer

The aetiology of breast cancer is multifactorial. While there are known genetic predispositions to the disease it is probable that environmental factors are also involved. Recent research has demonstrated a regionally specific distribution of aluminium in breast tissue mastectomies while other work has suggested mechanisms whereby breast tissue aluminium might contribute towards the aetiology of breast cancer. We have looked to develop microwave digestion combined with a new form of graphite furnace atomic absorption spectrometry as a precise, accurate and reproducible method for the measurement of aluminium in breast tissue biopsies. We have used this method to test the thesis that there is a regional distribution of aluminium across the breast in women with breast cancer. Microwave digestion of whole breast tissue samples resulted in clear homogenous digests perfectly suitable for the determination of aluminium by graphite furnace atomic absorption spectrometry. The instrument detection limit for the method was 0.48 μg/L. Method blanks were used to estimate background levels of contamination of 14.80 μg/L. The mean concentration of aluminium across all tissues was 0.39 μg Al/g tissue dry wt. There were no statistically significant regionally specific differences in the content of aluminium. We have developed a robust method for the precise and accurate measurement of aluminium in human breast tissue. There are very few such data currently available in the scientific literature and they will add substantially to our understanding of any putative role of aluminium in breast cancer. While we did not observe any statistically significant differences in aluminium content across the breast it has to be emphasised that herein we measured whole breast tissue and not defatted tissue where such a distribution was previously noted. We are very confident that the method developed herein could now be used to provide accurate and reproducible data on the aluminium content in defatted tissue and oil from such tissues and thereby contribute towards our knowledge on aluminium and any role in breast cancer.     

Cell Cycle Phase Sensitivity to Cis-Dichloro-Bis (Isopropylamine) Trans-Dihydroxy Platinum (Iv) (Chip)

Abstract. Cis-dichloro-bis (isopropylamine) trans-dihydroxy platinum (IV) (CHIP) is a second generation platinum coordination complex now in Phase II clinical trials. In vitro studies with Chinese Hamster Ovary cell cultures show that CHIP is a phase-sensitive drug, being most cytotoxic to cells in early G₁ phase and least toxic to late S and G₁ phase cells. the dose-modifying factor between the drug sensitivity of cells treated in G₁ and in late S phase is 1.6. These findings and their clinical significance are discussed with respect to the phase sensitivity of other cytotoxic agents.