Re-evaluating causal modeling with mantel tests in landscape genetics

The predominant analytical approach to associate landscape patterns with gene flow processes is based on the association of cost distances with genetic distances between individuals. Mantel and partial Mantel tests have been the dominant statistical tools used to correlate cost distances and genetic distances in landscape genetics. However, the inherent high correlation among alternative resistance models results in a high risk of spurious correlations using simple Mantel tests. Several refinements, including causal modeling, have been developed to reduce the risk of affirming spurious correlations and to assist model selection. However, the evaluation of these approaches has been incomplete in several respects. To demonstrate the general reliability of the causal modeling approach with Mantel tests, it must be shown to be able to correctly identify a wide range of landscape resistance models as the correct drivers relative to alternative hypotheses. The objectives of this study were to (1) evaluate the effectiveness of the originally published causal modeling framework to support the correct model and reject alternative hypotheses of isolation by distance and isolation by barriers and to (2) evaluate the effectiveness of causal modeling involving direct competition of all hypotheses to support the correct model and reject all alternative landscape resistance models. We found that partial Mantel tests have very low Type II error rates, but elevated Type I error rates. This leads to frequent identification of support for spurious correlations between alternative resistance hypotheses and genetic distance, independent of the true resistance model. The frequency in which this occurs is directly related to the degree of correlation between true and alternative resistance models. We propose an improvement based on the relative support of the causal modeling diagnostic tests

Expansion of a subset of CD14(high)CD16(neg)CCR2(low/neg) monocytes functionally similar to myeloid-derived suppressor cells during SIV and HIV infection

Monocytes have been categorized in three main subpopulations based on CD14 and CD16 surface expression. Classical monocytes express the CD14(++)CD16(-) CCR2(+) phenotype and migrate to inflammatory sites by quickly responding to CCL2 signaling. Here, we identified and characterized the expansion of a novel monocyte subset during HIV and SIV infection, which were undistinguishable from classical monocytes, based on CD14 and CD16 expression, but expressed significantly lower surface CCR2. Transcriptome analysis of sorted cells demonstrated that the CCR2(low/neg) cells are a distinct subpopulation and express lower levels of inflammatory cytokines and activation markers than their CCR2(high) counterparts. They exhibited impaired phagocytosis and greatly diminished chemotaxis in response to CCL2 and CCL7. In addition, these monocytes are refractory to SIV infection and suppress CD8(+) T cell proliferation in vitro. These cells express higher levels of STAT3 and NOS2, suggesting a phenotype similar to monocytic myeloid-derived cells, which suppress expansion of CD8(+) T cells in vivo. They may reflect an antiproliferative response against the extreme immune activation observed during HIV and SIV infections. In addition, they may suppress antiviral responses and thus, have a role in AIDS pathogenesis. Antiretroviral therapy in infected macaque and human subjects caused this population to decline, suggesting that this atypical phenotype is linked to viral replication. J. Leukoc. Biol. 91: 803-816; 2012.National Institutes of HealthNational Institutes of Health [MH070306, NS055648, MH085554]Ministry of Health [914/BRA/3014-UNESCO/Kallas]Ministry of HealthSao Paulo City Health Department [2004-0.168.922-7/Kallas]Sao Paulo City Health DepartmentFundacao de Amparo a Pesquisa do Estado de Sao PauloFundacao de Amparo a Pesquisa do Estado de Sao Paulo [04/15856-9/Kallas]Coordenacao de Aperfeicoamento de Pessoal de Nivel Superior (CAPES)Coordenacao de Aperfeicoamento de Pessoal de Nivel Superior (CAPES)Brazilian Ministry of EducationBrazilian Ministry of EducationBrazilian Program for STD and AIDSBrazilian Program for STD and AID

Dual Role of Novel Ingenol Derivatives from <i>Euphorbia tirucalli</i> in HIV Replication: Inhibition of <i>De Novo</i> Infection and Activation of Viral LTR

<div><p>HIV infection is not cleared by antiretroviral drugs due to the presence of latently infected cells that are not eliminated with current therapies and persist in the blood and organs of infected patients. New compounds to activate these latent reservoirs have been evaluated so that, along with HAART, they can be used to activate latent virus and eliminate the latently infected cells resulting in eradication of viral infection. Here we describe three novel diterpenes isolated from the sap of <i>Euphorbia tirucalli,</i> a tropical shrub. These molecules, identified as ingenols, were modified at carbon 3 and termed ingenol synthetic derivatives (ISD). They activated the HIV-LTR in reporter cell lines and human PBMCs with latent virus in concentrations as low as 10 nM. ISDs were also able to inhibit the replication of HIV-1 subtype B and C in MT-4 cells and human PBMCs at concentrations of EC₅₀ 0.02 and 0.09 µM respectively, which are comparable to the EC₅₀ of some antiretroviral currently used in AIDS treatment. Control of viral replication may be caused by downregulation of surface CD4, CCR5 and CXCR4 observed after ISD treatment <i>in vitro</i>. These compounds appear to be less cytotoxic than other diterpenes such as PMA and prostratin, with effective dose versus toxic dose TI>400. Although the mechanisms of action of the three ISDs are primarily attributed to the PKC pathway, downregulation of surface receptors and stimulation of the viral LTR might be differentially modulated by different PKC isoforms.</p></div

Platelet factor 4 mediates inflammation in experimental cerebral malaria

Cerebral malaria (CM) is a major complication of Plasmodium falciparum infection in children. The pathogenesis of CM involves vascular inflammation, immune stimulation, and obstruction of cerebral capillaries. Platelets have a prominent role in both immune responses and vascular obstruction. We now demonstrate that the platelet-derived chemokine, platelet factor 4 (PF4)/CXCL4, promotes the development of experimental cerebral malaria (ECM). Plasmodium-infected red blood cells (RBCs) activated platelets independently of vascular effects, resulting in increased plasma PF4. PF4 or chemokine receptor CXCR3 null mice had less severe ECM, including decreased T cell recruitment to the brain, and platelet depletion or aspirin treatment reduced the development of ECM. We conclude that Plasmodium-infected RBCs can directly activate platelets, and platelet-derived PF4 then contributes to immune activation and T cell trafficking as part of the pathogenesis of ECM

ING-B blocks HIV <i>de novo</i> replication through downregulation of surface receptors.

<p>CD4+ T cells from three healthy donors were stimulated with PHA/IL-2 for 5 days and then treated with different concentrations of ING-B for 24 h. A portion of the cells was used for cytometry evaluation (A), and the graph depicts the mean and standard deviation of three independent experiments. The remaining cells were infected with HIV NL4-3-Luc for 24 h and cell lysates were analyzed by luciferase activity (B). Results are shown as relative light units (RLU). ZVD 1 µM was used as positive control and DMSO 1% as vehicle control. Results are representative of mean and standard deviation of triplicates for each blood donor.</p

ISDs reduce HIV replication in a dose-dependent manner.

<p>Lymphocytic cell line MT-4 (A and B) and human PBMCs (C and D) were infected with HIV subtype B NL-4.3 (A and C) or HIV subtype C ZM247Fv-1 (B and D) and treated with different concentrations of ISDs. After six days, cell viability was evaluated using the Cell Titer blue kit. Curves were derived by non-linear regression (dose-response curve by Hill for 3 parameters), and dotted lines represent EC₅₀. Experiments were done in triplicate for PBMCs and sextuplicate for MT-4. ZVD was used as positive control.</p

Baseline characteristics of study subjects.

<p>(*) Time on HAART with documented continuous suppression of plasma viremia (< 50 copies/mL); (**) Drug abbreviations: ZDV, zidovudine; 3TC, lamivudine; EFV, efavirenz; TDF, tenofovir disoproxil fumarate.</p

CC₅₀ and EC₅₀ of ISDs and ZVD in MT-4 cells and primary CD4+ T lymphocytes infected with different HIV subtypes (see Figure 5).

<p>CC₅₀ and EC₅₀ values are presented in µM. Therapeutic index (TI) was defined as the ratio CC₅₀/EC₅₀. NA: non applicable. (*) Value estimated by extrapolation.</p

ISDs modulate surface expression of CD4, CXCR4, CCR5 and activation markers.

<p>MT-4 cells (A) and CD4+ T lymphocytes (B) were stimulated with ISDs (ING-A, ING-B, ING-C), bryostatin (bryo), prostratin (prost) and PMA for 48 h. Surface marker expression was evaluated by cytometry. CD4+ T cells were also evaluated for the activation markers CD25, CD38, HLA-DR (C) and CD69 (D). Results are representative of the mean and standard deviation of three independent experiments. DMSO 1% was used as vehicle control.</p

ISDs upregulate HIV-LTR-driven GFP expression in J-Lat clones.

<p>GFP expression (A) and viability (B) in J-Lat clone 9.2 were measured after cells were treated with ISDs, prostratin and PMA in different concentrations for 48 h. Similar experiment was done in J-Lat clone 10.6 (C and D). E) Comparison of GFP expression in four different J-Lat clones, all treated with 1 µM of each compound for 48 h. J-Lat clone 15.4 is depicted in a different graph (F). Graphs show mean and standard deviation of 3 separate tests. In all experiments, TNF-α 10 ng/mL was used as positive control.</p