am nat dryad ctdata

am nat dryad ctdat

GundersonLeal15_AmNat_Anole_Data

Activity data for Anolis cristatellu

Genetic diversity of Anolis krugi

Genetic diversity of Anolis krug

Electronic supplementary tables and figures. from Thermal niche evolution across replicated <i>Anolis</i> lizard adaptive radiations

Contains Supplementary Tables S1-S2 and Supplementary Figures S1-S4

A. pulchellus and A. krugi ND2 sequences

Alligned ND2 sequences in a fasta format for Anolis krugi, Anolis pulchellus and outgroups

A. pulchellus and A. krugi nuclear DNAH3 sequences

Alligned and phased nuclear DNAH3 sequences for A. pulchellus, A. krugi and outgroup

PD-1 and CTLA-4 expression on PPD-specific CD4 T-cells in response to TB treatment.

<p><b>A.</b> Representative plot showing the gating scheme used to identify PD-1, CTLA-4, and 2B4 expression on PPD-specific CD4 T-cells. Single, live, CD3⁺, CD4⁺ cells were gated for CD27 and CD45RO. The naïve CD4 T cell population was identified (CD27⁺CD45RO^-) and selected to set gates for PD-1, CTLA-4 and 2B4 as this population typically does not express inhibitory molecules. These gates were then applied to PPD-specific and total CD4 T-cell populations. <b>B.</b> Expression of PD-1, CTLA-4, and 2B4 on PPD-specific CD4 T-cells in untreated and treated TB disease. <b>C.</b> Correlation between baseline CD4 T-cell count and frequency of PD-1 and CTLA-4 expression on PPD-specific CD4 T-cells in untreated and treated TB disease. Lines of best fit, along with Spearman’s rank correlation coefficient and corresponding p-values are shown <b>D.</b> Expression of PD-1, CTLA-4, and 2B4 on CMV-specific CD4 T-cells in untreated and treated TB disease in our HIV-TB and TB cohorts. <b>E</b>. Expression of PD-1, CTLA-4, and 2B4 on total CD4 T-cells in untreated and treated TB disease in our HIV-TB and TB cohorts. <b>F</b>. Bar graph depicts the co-expression patterns of PD-1, CTLA-4, and 2B4 on PPD-specific CD4 T-cells in untreated and treated TB disease in our HIV-TB and TB cohorts. To assess expression of inhibitory molecules on PPD and CMV-specific CD4 T-cells, only samples with at least 50 cytokine positive cells and 2-fold higher responses than negative control samples were included to allow for a statistically valid analysis. * denotes p<0.05, ** p<0.01, *** p<0.001 by Wilcoxon matched-pairs signed rank test. $denotes p<0.05,$ $p<0.01,$ $$ p<0.001 by Mann-Whitney test.</p

Characteristics of ACTG 5221 (A5221) Study Population.

<p>Characteristics of ACTG 5221 (A5221) Study Population.</p

TB therapy alters maturation phenotype of PPD-specific CD4 T-cells.

<p><b>A.</b> Representative example of differentiation marker expression on PPD-specific CD4 T-cells. PPD-specific CD4 T-cells (red dots) are overlaid onto density plots of CD27 and CD45RO and CD27 and CD57, gated on total CD4 T-cells. <b>B.</b> Frequency of PPD-specific CD4 T-cells expressing CD27⁺CD45RO⁺ (CM), CD27^-CD45RO⁺ (EM), and CD57⁺ (TD) phenotypes. <b>C.</b> Correlation between baseline CD4 T-cell count and frequency of PPD-specific CD4 T-cells expressing CM and TD phenotypes in untreated and treated TB disease. Lines of best fit, along with Spearman’s rank correlation coefficient and corresponding p-values are shown <b>D.</b> Frequency of CMV-specific CD4 T-cells expressing CM, EM, and TD phenotypes in our HIV-TB and TB cohorts. <b>E.</b> Frequency of naïve, CM, EM, and TD subsets on total CD4 T-cells in untreated and treated TB disease in our HIV-TB and TB cohorts. To assess maturation phenotype on PPD and CMV-specific CD4 T-cells, only samples with at least 50 cytokine positive cells and 2-fold higher responses than negative control samples were included to allow for a statistically valid analysis. The Wilcoxon matched-pairs signed rank test was used for paired comparisons (HIV-TB cohort) while the Mann-Whitney test was used to analyze unpaired data (TB cohort and comparisons between cohorts). * denotes p<0.05, ** p<0.01, *** p<0.001 by Wilcoxon matched-pairs signed rank test. $denotes p<0.05,$ $p<0.01,$ $$ p<0.001 by Mann-Whitney test.</p

TB therapy alters the functional profile of PPD-specific CD4 T-cells.

<p><b>A.</b> Representative plot showing the gating scheme used to identify cytokine/chemokine positive cells. Single, live, CD3⁺, CD4⁺ T cells were gated for CD27 and CD45RO to identify the total CD4 memory population. Cytokine/chemokine gates were then applied to the total CD4 memory population to identify cytokine/chemokine positive cells. <b>B.</b> Total frequency of IFN-γ, TNF-α, IL-2, and MIP-1β produced by memory CD4 T-cells in untreated and treated TB disease within our HIV-TB and TB cohorts. Background cytokine/chemokine production from the negative control sample was subtracted. <b>C.</b> Pie graph displaying the proportion of cytokine/chemokine⁺ CD4 T-cells producing all 4 cytokines/chemokines (light grey wedge) or any combination of 3 cytokines/chemokines (medium gray), 2 cytokines/chemokines (dark grey), or a single cytokine/chemokine (black wedge) in untreated and treated TB disease. The bar graph depicts the relative contribution of each cytokine/chemokine producing subset to the overall PPD-specific CD4 T-cell response. “G” denotes IFN-γ, “2” denotes IL-2, “T” denotes TNF-α, and “M” denotes MIP-1β. For all bar graphs bars represent the interquartile range (IQR), horizontal lines denote the median, and whiskers the 10^th and 90^th percentiles. Solid bars represent our HIV-TB cohort, patterned bars represent our TB cohort. Light gray represents untreated TB disease while dark gray represents treated TB disease. Statistical analysis was performed using the Wilcoxon matched-pairs signed rank test for paired data (HIV-TB cohort) and the Mann-Whitney test for unpaired data (TB cohort or comparisons between cohorts).* denotes p<0.05, ** p<0.01, *** p<0.001 by Wilcoxon matched-pairs signed rank test. $denotes p<0.05,$ $p<0.01,$ $$ p<0.001 by Mann-Whitney test.</p