Viral evolution during structured treatment interruptions in chronically human immunodeficiency virus-infected individuals

We analyzed the evolution of the human immunodeficiency virus type 1 (HIV-1) env gene in 12 chronically infected individuals who underwent structured treatment interruptions (STIs). Analyses of length variation and of clonal sequences demonstrated highly unpredictable evolution, which may limit the strengthening of HIV-specific immune responses by STIs because of the variability in exposure to viral antigens.     

HIV reservoirs and immune surveillance evasion cause the failure of structured treatment interruptions: a computational study

Continuous antiretroviral therapy is currently the most effective way to treat HIV infection. Unstructured interruptions are quite common due to side effects and toxicity, among others, and cannot be prevented. Several attempts to structure these interruptions failed due to an increased morbidity compared to continuous treatment. The cause of this failure is poorly understood and often attributed to drug resistance. Here we show that structured treatment interruptions would fail regardless of the emergence of drug resistance. Our computational model of the HIV infection dynamics in lymphoid tissue inside lymph nodes, demonstrates that HIV reservoirs and evasion from immune surveillance themselves are sufficient to cause the failure of structured interruptions. We validate our model with data from a clinical trial and show that it is possible to optimize the schedule of interruptions to perform as well as the continuous treatment in the absence of drug resistance. Our methodology enables studying the problem of treatment optimization without having impact on human beings. We anticipate that it is feasible to steer new clinical trials using computational models.     

HLA-A*2402-restricted HIV-1-specific cytotoxic T lymphocytes and escape mutation after ART with structured treatment interruptions

Although a limited duration of immune activation of structured treatment interruptions (STIs) has been reported, the immune escape mechanism during STIs remains obscure. We therefore investigated the role of three immunodominant cytotoxic T lymphocyte (epitopes) in 12 HLA-A*2402-positive patients participating longitudinally during the clinical study of early antiretroviral treatment (ART) with five series of structured treatment interruptions (STIs). The frequency of HLA-A*2402-restricted CTLs varied widely and a sustained CTL response was rarely noted. However, a Y-to-F substitution at the second position in an immunodominant CTL epitope Nef138-10 (Nef138-2F), which was previously demonstrated as escape mutation, was frequently detected in seven patients primarily and emerged in the remaining five patients thereafter, and the existence of escape mutations was correlated with high pVL levels early in the clinical course. These findings suggest that escape mutation in the immunodominant CTL epitope may be one of the mechanisms to limit HIV-1-specific immune control in STIs.     

Structured treatment interruptions in HIV/AIDS therapy

Structured treatment interruption (STI) has been investigated for three distinct clinical scenarios: during acute infection with the goal of immune reconstitution and auto immunization; during chronic infection, to decrease the amount and toxicity of antiretroviral drugs; and during virologic failure to restore response to subsequent antiretroviral therapy. The potential costs and benefits of STI should be determined.     

Preliminary studies on differential defense responses induced during plant communication

We compared the expression patterns of three representative genes in undamaged tomato and tobacco plants in response to exposure to either tomato or tobacco fed on by Helicoverpa armigera (cotton bollworm). When tomato and tobacco, two species of one family, were incubated in the chambers with the tomato plants damaged by the cotton bollworm, the expression of the PR1, BGL2, and PAL genes was up-regulated in leaves of both plants. However, the levels of gene expression were significantly higher in the tomato than that in the tobacco. In addition, the activities of enzymes, peroxidase, polyphenol oxidase, and lipoxygenase were found to be higher in the tomato than those in the tobacco. Similar results were obtained when the damaged plants were replaced by the tobacco.     

Persistant immunodominant anti-gag SLYNTVATL responses in HIV-patients with up to 7 years of HAART

We analyzed Gag-specific CD8+ T-cells in HIV-patients on long-term HAART and in untreated chronically-infected patients by using iTAg MHC class I tetramers (HLA-A*0201) specific for SLYNTVATL. Gag SLYNTVATL-specific CD8+ T-cells were detectable in 18 of 26 treated patients (median 5.2 years of HAART) and in 10 of 14 untreated patients. Median percentage of Gag SLYNTVATL-specific CD8+ T-cells in treated patients was 0.10 (range 0.00-0.70%). Median number of Gag SLYNTVATL-specific CD8+ T-cells per 50,000 CD8+ T-cells was 56.0 cells (range 2.0-344.0 cells) and was not significantly different compared with untreated patients (p = 0.978). Numbers of Gag SLYNTVATL-specific CD8+ T-cells were inversely correlated with the duration of undetectable plasma viremia (p = 0.02, Rho = -0.430). Chronically-infected HIV-patients on HAART (for up to 7.7 years) maintained a stable subpopulation of Gag SLYNTVATL-specific CD8+ T-cells. This finding is relevant for the analysis of treatment-induced immune reconstitution and, possibly, for future therapeutic strategies in HIV-disease.     

Medullary substrate and differential cardiovascular responses during stimulation of specific acupoints

Electroacupuncture (EA) at P5-P6 acupoints overlying the median nerve reduces premotor sympathetic cardiovascular neuronal activity in the rostral ventral lateral medulla (rVLM) and visceral reflex pressor responses. In previous studies, we have noted different durations of influence of EA comparing P5-P6 and S36-S37 acupoints, suggesting that point specificity may exist. The purpose of this study was to evaluate the influence of stimulating P5-P6 (overlying the median nerve), LI4-L7 (overlying branches of the median nerve and the superficial radial nerve), LI6-LI7 (overlying the superficial radial nerve), LI10-LI11 (overlying the deep radial nerves), S36-S37 (overlying the deep peroneal nerves), or K1-B67 (overlying terminal branches of the tibial nerves) specific acupoints, overlying deep and superficial somatic nerves, on the excitatory cardiovascular reflex and rVLM responses evoked by stimulation of chemosensitive receptors in the cat's gallbladder with bradykinin (BK) or direct splanchnic nerve (SN) stimulation. We observed point-specific differences in magnitude and duration of EA inhibition between P5-P6 or LI10-LI11 and LI4-L7 or S36-S37 in responses to 30-min stimulation with low-frequency, low-current EA. EA at LI6-LI7 and K1-B67 acupoints as well as direct stimulation of the superficial radial nerve did not cause any cardiovascular or rVLM neuronal effects. Cardiovascular neurons in the rVLM, a subset of which were classified as premotor sympathetic cells, responded to brief (30 s) stimulation of the SN as well as acupoints P5-P6, LI10-LI11, LI4-L7, S36-S37, LI6-LI7, or K1-B67, or underlying somatic pathways in a fashion similar to the reflex responses. In fact, we observed a significant linear relationship (r(2) = 0.71) between the evoked rVLM response and reflex change in mean arterial blood pressure. In addition, EA stimulation at P5-P6 and LI4-L7 decreased rVLM neuronal activity by 41 and 12%, respectively, for >1 h, demonstrating that prolonged input into the medulla during stimulation of somatic nerves, depending on the degree of convergence, leads to more or less inhibition of activity of these cardiovascular neurons. Thus EA at acupoints overlying deep and superficial somatic nerves leads to point-specific effects on cardiovascular reflex responses. In a similar manner, sympathetic cardiovascular rVLM neurons that respond to both visceral (reflex) and somatic (EA) nerve stimulation manifest graded responses during stimulation of specific acupoints, suggesting that this medullary region plays a role in site-specific inhibition of cardiovascular reflex responses by acupuncture.     

Trophoblast cells exhibit differential responses to laminin isoforms

Extracellular matrix (ECM) has specific effects on cell behavior that influence many aspects of early development. In the early postimplantation mouse embryo the ECM component laminin promotes polarization and survival of the embryonic ectoderm and formation of Reichert's membrane. In addition, dynamic patterns of laminins 1 and 10/11 expression in the embryo and the uterus correlate with the progression of implantation. In the implanting blastocyst, laminin 1 is strongly expressed in the trophectoderm basement membrane, whereas laminin 10/11 is expressed only in the inner cell mass and polar trophectoderm. In the uterus, laminin 10/11 is strongly expressed in the decidualizing matrix of the stroma. We show here that laminins 1 and 10/11 have distinct effects on trophoblast cell behavior that influence the process of implantation. Laminin 1 promotes random migration and decreases spreading, whereas laminin 10/11 promotes both spreading and persistent migration. When presented as adjacent substrates, cells stop at the boundary and do not enter the region containing laminin 1. Laminin 1 also affects cell-cell adhesion through changes in the localization of vascular endothelial (VE) cadherin. Cultured cells and primary trophoblast explants become single cells or very small groups on laminin 1 and VE-cadherin localization at regions of cell-cell contact decreases dramatically. In contrast, trophoblast cells maintain strong cell-cell contacts on substrates of laminins 10/11, and exhibit strong staining of VE-cadherin in all regions of cell-cell contact. These effects, and the localization of laminin 1 in Reichert's membrane and laminin 10/11 in the surrounding decidual matrix, suggest that these laminin isoforms influence the direction and quality of invasion of trophoblast cells during implantation, and provide epigenetic cues that drive the morphogenesis of the yolk sac placenta.     

Predicting genomic selection efficiency to optimize calibration set and to assess prediction accuracy in highly structured populations

Key message

We propose a criterion to predict genomic selection efficiency for structured populations. This criterion is useful to define optimal calibration set and to estimate prediction reliability for multiparental populations.

Abstract

Genomic selection refers to the use of genotypic information for predicting the performance of selection candidates. It has been shown that prediction accuracy depends on various parameters including the composition of the calibration set (CS). Assessing the level of accuracy of a given prediction scenario is of highest importance because it can be used to optimize CS sampling before collecting phenotypes, and once the breeding values are predicted it informs the breeders about the reliability of these predictions. Different criteria were proposed to optimize CS sampling in highly diverse panels, which can be useful to screen collections of genotypes. But plant breeders often work on structured material such as biparental or multiparental populations, for which these criteria are less adapted. We derived from the generalized coefficient of determination (CD) theory different criteria to optimize CS sampling and to assess the reliability associated to predictions in structured populations. These criteria were evaluated on two nested association mapping (NAM) populations and two highly diverse panels of maize. They were efficient to sample optimized CS in most situations. They could also estimate at least partly the reliability associated to predictions between NAM families, but they could not estimate differences in the reliability associated to the predictions of NAM families using the highly diverse panels as calibration sets. We illustrated that the CD criteria could be adapted to various prediction scenarios including inter and intra-family predictions, resulting in higher prediction accuracies.

     

Predicting observed and latent responses to BLUP selection involving logistic variates

Multivariate BLUPs can be derived when data are a mixture of continuous traits and observed discrete traits controlled by logistic latent traits. Algorithms were developed for predicting discrete responses to BLUP selection, and latent responses when the selection process included additional culling on scores. These algorithms were Taylor expansions using well-known expressions such as the probabilities and the two first moments of the truncated multinormal distribution, after appropriate re-parametrizations. They were compared to very accurate quadrature integrations. The test examples were suggested by a situation found in chickens where selection can involve body weight and leg deformity described by two logistic latent variates. Quadratic Taylor expansions generally provided a good accuracy. Therefore, they could be recommended when quadrature methods are too demanding, e.g., for complex breeding schemes.