Predictive factors of virological success to salvage regimens containing protease inhibitors in HIV-1 infected children

<p>Abstract</p> <p>Background</p> <p>The impact of HIV drug resistance mutations in salvage therapy has been widely investigated in adults. By contrast, data available of predictive value of resistance mutations in pediatric population is scarce.</p> <p>Methods</p> <p>A multicenter, retrospective, observational study was conducted in children who received rescue salvage antiretroviral therapy after virologic failure. CD4 counts and viral load were determined at baseline and 6 months after rescue intervention. Genotypic HIV-1 resistance test and virtual phenotype were assessed at baseline.</p> <p>Results</p> <p>A total of 33 children met the inclusion criteria and were included in the analysis. The median viral load (VL) and median percentage of CD4+ at baseline was 4.0 HIV-RNA log copies/ml and 23.0% respectively. The median duration that children were taking the new rescue regimen was 24.3 weeks (23.8–30.6). Overall, 47% of the 33 children achieved virological response at 24 weeks. When we compared the group of children who achieved virological response with those who did not, we found out that mean number of PI related mutations among the group of responders was 3.8 <it>vs</it>. 5.4 (p = 0.115). Moreover, the mean number of susceptible drugs according to virtual phenotype clinical cut-off for maximal virologic response was 1.7 <it>vs</it>. 0.8 and mean number of susceptible drugs according to virtual phenotype cut-off for minimal virlologic response was 2.7 <it>vs</it>. 1.3 (p < 0.01 in all cases). Eighteen children were rescued with a regimen containing a boosted-PI and virological response was significantly higher in those subjects compared with the others (61.1% <it>vs</it>. 28.6%, p < 0.01).</p> <p>Conclusion</p> <p>Salvage treatment containing ritonavir boosted-PIs in children with virological failure was very efficient. The use of new tools as virtual phenotype could help to improve virologic success in pediatric population.</p

Viral Evolution and Cytotoxic T Cell Restricted Selection in Acute Infant HIV-1 Infection

Antiretroviral therapy-naive HIV-1 infected infants experience poor viral containment and rapid disease progression compared to adults. Viral factors (e.g. transmitted cytotoxic T- lymphocyte (CTL) escape mutations) or infant factors (e.g. reduced CTL functional capacity) may explain this observation. We assessed CTL functionality by analysing selection in CTL-targeted HIV-1 epitopes following perinatal infection. HIV-1 gag, pol and nef sequences were generated from a historical repository of longitudinal specimens from 19 vertically infected infants. Evolutionary rate and selection were estimated for each gene and in CTL-restricted and non-restricted epitopes. Evolutionary rate was higher in nef and gag vs. pol, and lower in infants with non-severe immunosuppression vs. severe immunosuppression across gag and nef. Selection pressure was stronger in infants with non-severe immunosuppression vs. severe immunosuppression across gag. The analysis also showed that infants with non-severe immunosuppression had stronger selection in CTL-restricted vs. non-restricted epitopes in gag and nef. Evidence of stronger CTL selection was absent in infants with severe immunosuppression. These data indicate that infant CTLs can exert selection pressure on gag and nef epitopes in early infection and that stronger selection across CTL epitopes is associated with favourable clinical outcomes. These results have implications for the development of paediatric HIV-1 vaccines

Effect of Population, Collection Year, After-Ripening and Incubation Condition on Seed Germination of \u3cem\u3eStipa bungeana\u3c/em\u3e

Knowledge of the germination behavior of different populations of a species can be useful in the selection of appropriate seed sources for restoration. The aim of this study was to test the effect of seed population, collection year, after-ripening and incubation conditions on seed dormancy and germination of Stipa bungeana, a perennial grass used for revegetation of degraded grasslands on the Loess Plateau, China. Fresh S. bungeana seeds were collected from eight locally-adapted populations in 2015 and 2016. Dormancy and germination characteristics of fresh and 6-month-old dry-stored seeds were determined by incubating them over a range of alternating temperature regimes in light. Effect of water stress on germination was tested for fresh and 6-month-old dry-stored seeds. Seed dormancy and germination of S. bungeana differed with population and collection year. Six months of dry storage broke seed dormancy, broadened the temperature range for germination and increased among-population differences in germination percentage. The rank order of germination was not consistent in all germination tests, and it varied among populations. Thus, studies on comparing seed dormancy and germination among populations must consider year of collection, seed dormancy states and germination test conditions when selecting seeds for grassland restoration and management

The final piece of the Triangle of U: Evolution of the tetraploid Brassica carinata genome

Background: Brassica carinata (Ethiopian mustard) is an ancient crop from the Ethiopian highlands with remarkable heat and drought tolerance that has potential as a sustainable oil source for biofuel production. The resilience of this species might be due to hybrid vigor, as B. carinata is a species derived from a hybridization between Brassica nigra (black mustard) and Brassica oleracea (kale, broccoli, etc.). Thus, the B. carinata genome is allotetraploid with two parental genomes, or subgenomes, merged in one nucleus. We present a high-quality, chromosome-scale reference assembly of the B. carinata genome, which is the last of six genomes comprising the classic Triangle of U model used to study hybridization and polyploid evolution. Question: Here, we compare B. carinata to the other Triangle of U genomes for insight into the remarkable heat and drought tolerance of this crop. We investigate the evolutionary trajectory of the B. carinata genome as it returns to the diploid state to elucidate the mechanisms that act on duplicated genes, such as functional divergence of gene families and the biased fractionation of one subgenome. Findings: The B. carinata genome is the largest among the Triangle of U with notable expansions in repetitive DNA sequences and gene families related to transcriptional regulation and stress tolerance. We characterized patterns of subgenome bias, finding that the subgenome derived from B. nigra is likely dominant over the subgenome from B. oleracea. Furthermore, we comprehensively characterize subgenomic bias in homoeologous exchanges, or meiotic crossover between subgenomes, in the Triangle of U allotetraploids. Next steps: The presented B. carinata genome is a crucial resource for its expanded use as a biofuel feedstock and insight into polyploid evolution. Unraveling the genomic basis of the stress resilience of B. carinata provides an opportunity to introgress these traits to other cruciferous vegetables, which are used worldwide as vegetable and oil sources.Ethiopian mustard (Brassica carinata) is an ancient crop with remarkable stress resilience and a desirable seed fatty acid profile for biofuel uses. Brassica carinata is one of six Brassica species that share three major genomes from three diploid species (AA, BB, and CC) that spontaneously hybridized in a pairwise manner to form three allotetraploid species (AABB, AACC, and BBCC). Of the genomes of these species, that of B. carinata is the least understood. Here, we report a chromosome scale 1.31-Gbp genome assembly with 156.9-fold sequencing coverage for B. carinata, completing the reference genomes comprising the classic Triangle of U, a classical theory of the evolutionary relationships among these six species. Our assembly provides insights into the hybridization event that led to the current B. carinata genome and the genomic features that gave rise to the superior agronomic traits of B. carinata. Notably, we identified an expansion of transcription factor networks and agronomically important gene families. Completion of the Triangle of U comparative genomics platform has allowed us to examine the dynamics of polyploid evolution and the role of subgenome dominance in the domestication and continuing agronomic improvement of B. carinata and other Brassica species.We gratefully acknowledge the support of the Nevada Agricultural Experiment Station (Grant No. NEV00384) and VPRI research funding (University of Nevada, Reno).The Pires lab is funded by the National Science Foundation (NSF IOS 1339156) and the Department of Energy Defense Threat Reduction Agency (HDTRA 1-16-1-0048). The Edger lab is funded by the National Science Foundation (NSF IOS 2029959). The Mason lab is partially funded by the Deutsche Forschungsgemeinschaft (DFG, German Research Foundation) under Germany’s Excellence Strategy (EXC 2070 - 390732324). The Alvarez-Ponce lab is funded by the National Science Foundation (NSF MCB 1818288)

Robust estimation of bacterial cell count from optical density

Optical density (OD) is widely used to estimate the density of cells in liquid culture, but cannot be compared between instruments without a standardized calibration protocol and is challenging to relate to actual cell count. We address this with an interlaboratory study comparing three simple, low-cost, and highly accessible OD calibration protocols across 244 laboratories, applied to eight strains of constitutive GFP-expressing E. coli. Based on our results, we recommend calibrating OD to estimated cell count using serial dilution of silica microspheres, which produces highly precise calibration (95.5% of residuals &lt;1.2-fold), is easily assessed for quality control, also assesses instrument effective linear range, and can be combined with fluorescence calibration to obtain units of Molecules of Equivalent Fluorescein (MEFL) per cell, allowing direct comparison and data fusion with flow cytometry measurements: in our study, fluorescence per cell measurements showed only a 1.07-fold mean difference between plate reader and flow cytometry data

Discordant Impact of HLA on Viral Replicative Capacity and Disease Progression in Pediatric and Adult HIV Infection

HLA class I polymorphism has a major influence on adult HIV disease progression. An important mechanism mediating this effect is the impact on viral replicative capacity (VRC) of the escape mutations selected in response to HLA-restricted CD8+ T-cell responses. Factors that contribute to slow progression in pediatric HIV infection are less well understood. We here investigate the relationship between VRC and disease progression in pediatric infection, and the effect of HLA on VRC and on disease outcome in adult and pediatric infection. Studying a South African cohort of >350 ART-naïve, HIV-infected children and their mothers, we first observed that pediatric disease progression is significantly correlated with VRC. As expected, VRCs in mother-child pairs were strongly correlated (p = 0.004). The impact of the protective HLA alleles, HLA-B*57, HLA-B*58:01 and HLA-B*81:01, resulted in significantly lower VRCs in adults (p<0.0001), but not in children. Similarly, in adults, but not in children, VRCs were significantly higher in subjects expressing the disease-susceptible alleles HLA-B*18:01/45:01/58:02 (p = 0.007). Irrespective of the subject, VRCs were strongly correlated with the number of Gag CD8+ T-cell escape mutants driven by HLA-B*57/58:01/81:01 present in each virus (p = 0.0002). In contrast to the impact of VRC common to progression in adults and children, the HLA effects on disease outcome, that are substantial in adults, are small and statistically insignificant in infected children. These data further highlight the important role that VRC plays both in adult and pediatric progression, and demonstrate that HLA-independent factors, yet to be fully defined, are predominantly responsible for pediatric non-progression