HIV-1 with Multiple CCR5/CXCR4 Chimeric Receptor Use Is Predictive of Immunological Failure in Infected Children

BACKGROUND: HIV-1 R5 viruses are characterized by a large phenotypic variation, that is reflected by the mode of coreceptor use. The ability of R5 HIV-1 to infect target cells expressing chimeric receptors between CCR5 and CXCR4 (R5(broad) viruses), was shown to correlate with disease stage in HIV-1 infected adults. Here, we ask the question whether phenotypic variation of R5 viruses could play a role also in mother-to-child transmission (MTCT) of HIV-1 and pediatric disease progression. METHODOLOGY/PRINCIPAL FINDINGS: Viral isolates obtained from a total of 59 HIV-1 seropositive women (24 transmitting and 35 non transmitting) and 28 infected newborn children, were used to infect U87.CD4 cells expressing wild type or six different CCR5/CXCR4 chimeric receptors. HIV-1 isolates obtained from newborn infants had predominantly R5(narrow) phenotype (n = 20), but R5(broad) and R5X4 viruses were also found in seven and one case, respectively. The presence of R5(broad) and R5X4 phenotypes correlated significantly with a severe decline of the CD4+ T cells (CDC stage 3) or death within 2 years of age. Forty-three percent of the maternal R5 isolates displayed an R5(broad) phenotype, however, the presence of the R5(broad) virus was not predictive for MTCT of HIV-1. Of interest, while only 1 of 5 mothers with an R5X4 virus transmitted the dualtropic virus, 5 of 6 mothers carrying R5(broad) viruses transmitted viruses with a similar broad chimeric coreceptor usage. Thus, the maternal R5(broad) phenotype was largely preserved during transmission and could be predictive of the phenotype of the newborn's viral variant. CONCLUSIONS/SIGNIFICANCE: Our results show that R5(broad) viruses are not hampered in transmission. When transmitted, immunological failure occurs earlier than in children infected with HIV-1 of R5(narrow) phenotype. We believe that this finding is of utmost relevance for therapeutic interventions in pediatric HIV-1 infectio

Assessment of terrain elevation estimates from ICESat-2 and GEDI spaceborne LiDAR missions across different land cover and forest types

Accurate measurements of terrain elevation are crucial for many ecological applications. In this study, we sought to assess new global three-dimensional Earth observation data acquired by the spaceborne Light Detection and Ranging (LiDAR) missions Ice, Cloud, and Land Elevation Satellite-2 (ICESat-2) and Global Ecosystem Dynamics Investigation (GEDI). For this, we examined the “ATLAS/ICESat-2 L3A Land and Vegetation Height”, version 5 (20 × 14 m and 100 × 14 m segments) and the “GEDI Level 2A Footprint Elevation and Height Metrics”, version 2 (25 m circle). We conducted our analysis across four land cover classes (bare soil, herbaceous, forest, savanna), and six forest types (temperate broad-leaved, temperate needle-leaved, temperate mixed, tropical upland, tropical floodplain, and tropical secondary forest). For assessment of terrain elevation estimates from spaceborne LiDAR data we used high resolution airborne data. Our results indicate that both LiDAR missions provide accurate terrain elevation estimates across different land cover classes and forest types with mean error less than 1 m, except in tropical forests. However, using a GEDI algorithm with a lower signal end threshold (e.g., algorithm 5) can improve the accuracy of terrain elevation estimates for tropical upland forests. Specific environmental parameters (terrain slope, canopy height and canopy cover) and sensor parameters (GEDI degrade flags, terrain estimation algorithm; ICESat-2 number of terrain photons, terrain uncertainty) can be applied to improve the accuracy of ICESat-2 and GEDI-based terrain estimates. Although the goodness-of-fit statistics from the two spaceborne LiDARs are not directly comparable since they possess different footprint sizes (100 × 14 m segment or 20 × 14 m segment vs. 25 m circle), we observed similar trends on the impact of terrain slope, canopy cover and canopy height for both sensors. Terrain slope strongly impacts the accuracy of both ICESat-2 and GEDI terrain elevation estimates for both forested and non-forested areas. In the case of GEDI the impact of slope is, however, partly caused by horizontal geolocation error. Moreover, dense canopies (i.e., canopy cover higher than 90%) affect the accuracy of spaceborne LiDAR terrain estimates, while canopy height does not, when considering samples over flat terrains. Our analysis of the accuracy and precision of current versions of spaceborne LiDAR products for different vegetation types and environmental conditions provides insights on parameter selection and estimated uncertainty to inform users of these key global datasets

The carbon balance of South America: A review of the status, decadal trends and main determinants

Copyright © 2012 European Geosciences Union. This is the published version available at http://www.biogeosciences-discuss.net/9/627/2012/bgd-9-627-2012.htmlWe attempt to summarize the carbon budget of South America and relate it to its dominant controls: population and economic growth, changes in land use practices and a changing atmospheric environment and climate. Flux estimation methods which we consider sufficiently reliable are fossil fuel emission inventories, biometric analysis of old-growth rainforests, estimation of carbon release associated with deforestation based on remote sensing and inventories, and finally inventories of agricultural exports. Other routes to estimating land-atmosphere CO2 fluxes include atmospheric transport inverse modelling and vegetation model predictions but are hampered by the data paucity and the need for improved parameterisation. The available data we analyze suggest that South America was a net source to the atmosphere during the 1980s (∼0.3–0.4 Pg C yr−1) and close to neutral (∼0.1 Pg C yr−1) in the 1990s with carbon uptake in old-growth forests nearly compensating carbon losses due to fossil fuel burning and deforestation. Annual mean precipitation over tropical South America measured by Amazon River discharge has a long-term upward trend, although over the last decade, dry seasons have tended to be drier and longer (and thus wet seasons wetter), with the years 2005 and 2010 experiencing strong droughts. It is currently unclear what the effect of these climate changes on the old-growth forest carbon sink will be but first measurements suggest it may be weakened. Based on scaling of forest census data the net carbon balance of South America seems to have been an increased source roughly over the 2005–2010 period (a total of ∼1 Pg C of dead tree biomass released over several years) due to forest drought response. Finally, economic development of the tropical forest regions of the continent is advancing steadily with exports of agricultural products being an important driver and witnessing a strong upturn over the last decade

Estimation of Isolation Times of the Island Species in the Drosophila simulans Complex from Multilocus DNA Sequence Data

Background: The Drosophila simulans species complex continues to serve as an important model system for the study of new species formation. The complex is comprised of the cosmopolitan species, D. simulans, and two island endemics, D. mauritiana and D. sechellia. A substantial amount of effort has gone into reconstructing the natural history of the complex, in part to infer the context in which functional divergence among the species has arisen. In this regard, a key parameter to be estimated is the initial isolation time (t) of each island species. Loci in regions of low recombination have lower divergence within the complex than do other loci, yet divergence from D. melanogaster is similar for both classes. This might reflect gene flow of the lowrecombination loci subsequent to initial isolation, but it might also reflect differential effects of changing population size on the two recombination classes of loci when the low-recombination loci are subject to genetic hitchhiking or pseudohitchhiking Methodology/Principal Findings: New DNA sequence variation data for 17 loci corroborate the prior observation from 13 loci that DNA sequence divergence is reduced in genes of low recombination. Two models are presented to estimate t and other relevant parameters (substitution rate correction factors in lineages leading to the island species and, in the case of the 4-parameter model, the ratio of ancestral to extant effective population size) from the multilocus DNA sequence data. Conclusions/Significance: In general, it appears that both island species were isolated at about the same time, here estimated at,250,000 years ago. It also appears that the difference in divergence patterns of genes in regions of low an

Population transcriptomics of Drosophila melanogaster females

<p>Abstract</p> <p>Background</p> <p>Variation at the level of gene expression is abundant in natural populations and is thought to contribute to the adaptive divergence of populations and species. Gene expression also differs considerably between males and females. Here we report a microarray analysis of gene expression variation among females of 16 <it>Drosophila </it><it>melanogaster </it>strains derived from natural populations, including eight strains from the putative ancestral range in sub-Saharan Africa and eight strains from Europe. Gene expression variation among males of the same strains was reported previously.</p> <p>Results</p> <p>We detected relatively low levels of expression polymorphism within populations, but much higher expression divergence between populations. A total of 569 genes showed a significant expression difference between the African and European populations at a false discovery rate of 5%. Genes with significant over-expression in Europe included the insecticide resistance gene <it>Cyp6g1</it>, as well as genes involved in proteolysis and olfaction. Genes with functions in carbohydrate metabolism and vision were significantly over-expressed in the African population. There was little overlap between genes expressed differently between populations in females and males.</p> <p>Conclusions</p> <p>Our results suggest that adaptive changes in gene expression have accompanied the out-of-Africa migration of <it>D. melanogaster</it>. Comparison of female and male expression data indicates that the vast majority of genes differing in expression between populations do so in only one sex and suggests that most regulatory adaptation has been sex-specific.</p

HIV-1 co-receptor usage:influence on mother-to-child transmission and pediatric infection

Viral CCR5 usage is not a predictive marker of mother to child transmission (MTCT) of HIV-1. CXCR4-using viral variants are little represented in pregnant women, have an increased although not significant risk of transmission and can be eventually also detected in the neonates. Genetic polymorphisms are more frequently of relevance in the child than in the mother. However, specific tissues as the placenta or the intestine, which are involved in the prevalent routes of infection in MTCT, may play an important role of selective barriers

Evolution of a supergene that regulates a trans-species social polymorphism

Supergenes are clusters of linked genetic loci that jointly affect the expression of complex phenotypes, such as social organization. Little is known about the origin and evolution of these intriguing genomic elements. Here we analyse whole-genome sequences of males from native populations of six fire ant species and show that variation in social organization is under the control of a novel supergene haplotype (termed Sb), which evolved by sequential incorporation of three inversions spanning half of a 'social chromosome'. Two of the inversions interrupt protein-coding genes, resulting in the increased expression of one gene and modest truncation in the primary protein structure of another. All six socially polymorphic species studied harbour the same three inversions, with the single origin of the supergene in their common ancestor inferred by phylogenomic analyses to have occurred half a million years ago. The persistence of Sb along with the ancestral SB haplotype through multiple speciation events provides a striking example of a functionally important trans-species social polymorphism presumably maintained by balancing selection. We found that while recombination between the Sb and SB haplotypes is severely restricted in all species, a low level of gene flux between the haplotypes has occurred following the appearance of the inversions, potentially mitigating the evolutionary degeneration expected at genomic regions that cannot freely recombine. These results provide a detailed picture of the structural genomic innovations involved in the formation of a supergene controlling a complex social phenotype

Multiple carbon accounting to support just and effective climate policies

Negotiating reductions in greenhouse gas emission involves the allocation of emissions and of emission reductions to specific agents, and notably, within the current UN framework, to associated countries. As production takes place in supply chains,increasingly extending over several countries, there are various options available in which emissions originating from one and the same activity may be attributed to different agents along the supply chain and thus to different countries. In this way, several distinct types of national carbon accounts can be constructed. We argue that these accounts will typically differ in the information they provide to individual countries on the effects their actions have on global emissions; and they may also, to varying degrees, prove useful in supporting the pursuit of an effective and just climate policy. None of the accounting systems, however, prove 'best' in achieving these aims under real-world circumstances; we thus suggest compiling reliable data to aid in the consistent calculation of multiple carbon accounts on a global level

The carbon balance of South America: A review of the status, decadal trends and main determinants

We summarise the contemporary carbon budget of South America and relate it to its dominant controls: population and economic growth, changes in land use practices and a changing atmospheric environment and climate. Component flux estimate methods we consider sufficiently reliable for this purpose encompass fossil fuel emission inventories, biometric analysis of old-growth rainforests, estimation of carbon release associated with deforestation based on remote sensing and inventories, and agricultural export data. Alternative methods for the estimation of the continental-scale net land to atmosphere CO2 flux, such as atmospheric transport inverse modelling and terrestrial biosphere model predictions, are, we find, hampered by the data paucity, and improved parameterisation and validation exercises are required before reliable estimates can be obtained. From our analysis of available data, we suggest that South America was a net source to the atmosphere during the 1980s (∼ 0.3-0.4 Pg C a&minus;1) and close to neutral (∼ 0.1 Pg C a&minus;1) in the 1990s. During the latter period, carbon uptake in old-growth forests nearly compensated for the carbon release associated with fossil fuel burning and deforestation. Annual mean precipitation over tropical South America as inferred from Amazon River discharge shows a long-term upward trend. Although, over the last decade dry seasons have tended to be drier, with the years 2005 and 2010 in particular experiencing strong droughts. On the other hand, precipitation during the wet seasons also shows an increasing trend. Air temperatures have also increased slightly. Also with increases in atmospheric CO2 concentrations, it is currently unclear what effect these climate changes are having on the forest carbon balance of the region. Current indications are that the forests of the Amazon Basin have acted as a substantial long-term carbon sink, but with the most recent measurements suggesting that this sink may be weakening. Economic development of the tropical regions of the continent is advancing steadily, with exports of agricultural products being an important driver and witnessing a strong upturn over the last decade

Accuracy assessment of terrain and canopy height estimates from ICESat-2 and GEDI LiDAR missions in temperate and tropical forests: first results

Two new NASA spaceborne Light Detection and Ranging (LiDAR) missions launched in late 2018 the Ice, Cloud, and land Elevation Satellite 2 (ICESat-2) and the Global Ecosystem Dynamics Investigation (GEDI) produce a new set of three dimensional data of Earth’s land surface. In this study we assessed the accuracy and precision of terrain and canopy height estimates from these two new LiDAR missions by examing the ICESat-2 ATL08 land and vegetation product, version 3 (Neuenschwander and Pitts 2019; Neuenschwander et al. 2020) and the GEDI L2A footprint elevation and canopy height metrics, version 1 (Dubayah et al. 2020a, Dubayah et al. 2020b). We conducted our analysis over temperate broadleaved and needleleaved forests, and tropical rainforest. For assessment of terrain and canopy height estimates from spaceborne LiDAR data we used high resolution airborne LiDAR (ALS) data