Macaca nemestrina
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ABSTRACT:
PROVIDER: PRJNA223294 | ENA |
REPOSITORIES: ENA
Similar Datasets
Project description:miRNA profiling of Macaca nemestrina plasma samples: before SIV infection and during acute infection
| PRJNA135565 | ENA
Project description:Monocytes have been categorized in three main subpopulations based on CD14 and CD16 surface expression. Classical monocytes are the most abundant subset in the blood. They express a CD14+CD16-CCR2+ phenotype, which confers on them the ability to migrate to inflammatory sites by quickly responding to CCL2 signaling. Here we identified and characterized the surge and expansion of a novel monocyte subset during SIV and HIV infection. They were undistinguishable from classical monocytes regarding CD14 and CD16 expression, but did not express surface CCR2. Transcriptome analysis of sorted cells confirmed that they represent a distinct subpopulation that expresses lower levels of inflammatory cytokines and activation markers than their CCR2+ counterparts. They exhibited impaired phagocytosis and deficient chemotaxis in response to CCL2 and CCL7, besides being refractory to SIV infection. We named these cells atypical CCR2- classical (ACC) monocytes, and believe they play an important role in AIDS pathogenesis, possibly reflecting an anti-inflammatory response against the extreme immune activation observed during SIV and HIV infection. Antiretroviral therapy caused this population to decline in both macaque and human subjects, suggesting that this atypical phenotype may be induced by viral replication. Expression profiling by NanoString nCounter gene expression system. Classical monocytes (CD14++CD16-) from six SIV-infected macaques (day 14 post inoculation) were sorted in two groups according to CCR2 expression.
2012-03-01 | E-GEOD-27559 | biostudies-arrayexpress
Project description:Monocytes have been categorized in three main subpopulations based on CD14 and CD16 surface expression. Classical monocytes are the most abundant subset in the blood. They express a CD14+CD16-CCR2+ phenotype, which confers on them the ability to migrate to inflammatory sites by quickly responding to CCL2 signaling. Here we identified and characterized the surge and expansion of a novel monocyte subset during SIV and HIV infection. They were undistinguishable from classical monocytes regarding CD14 and CD16 expression, but did not express surface CCR2. Transcriptome analysis of sorted cells confirmed that they represent a distinct subpopulation that expresses lower levels of inflammatory cytokines and activation markers than their CCR2+ counterparts. They exhibited impaired phagocytosis and deficient chemotaxis in response to CCL2 and CCL7, besides being refractory to SIV infection. We named these cells atypical CCR2- classical (ACC) monocytes, and believe they play an important role in AIDS pathogenesis, possibly reflecting an anti-inflammatory response against the extreme immune activation observed during SIV and HIV infection. Antiretroviral therapy caused this population to decline in both macaque and human subjects, suggesting that this atypical phenotype may be induced by viral replication. Expression profiling by NanoString nCounter gene expression system.
2012-03-01 | GSE27559 | GEO
Project description:This study describes a circulating miRNA signature of acute retroviral infection, which may include candidate diagnostic or prognostic miRNAs for lentivirus-associated neurologic conditions. Plasma samples were taken from six macaques prior to infection and at ten days post-infection. Three macaques each went on to develop no or severe encephalitis. miRNA profiles were generated for each animal before and 10 days after SIV infection.
2011-09-14 | E-GEOD-26057 | biostudies-arrayexpress
Project description:Expression profiling by NanoString nCounter gene expression system Inflammatory response genes play an important role during acute HIV and SIV infection. Using an SIV macaque model for AIDS and CNS disease, we measured mRNA expression of 92 genes before and at multiple time points during acute SIV infection in three tissues: Peripheral blood mononuclear cells, mesenteric lymph nodes (MLN) and peripheral blood mononuclear cells (PBMC). Studying the overall changes of mRNA expressions over time or analyzing the correlation between the gene measurements and SIV RNA in plasma can result in limited interpretations. This is due to several reasons including but not limited to: 1) lack of prior information on how cells react to changes in gene expressions; and 2) biological responses typically involve many genes working together. To approach this problem, we combine multiple preprocessing methods with two multivariate analysis methods, namely principal component analysis and partial least square regression, to create a multiplexed set of 12 “judges”. Each of the judges simultaneously observes all the variables and emphasizes a unique type of gene expression response that could be significant, for example, depending on whether the cell responds to the absolute or relative size of gene expression changes. By incorporating multiple potential biological models of response, it is possible to identify genes that are consistently ranked as high “contributing” genes in different scenarios, i.e., genes that have a higher weight when we classify the data based on different classification schemes. We then use statistical analysis to verify that the consistently high-ranking genes are also statistically significant. We also investigate whether genes are tissue-specific, identify clusters of genes that co-vary together and study their correlation with regard to other gene clusters. The multiplex component analysis method introduced in this paper is a powerful tool to analyze complex gene datasets, identify significant genes, and generate testable hypotheses. In this study we inoculated 20 pig-tailed macaques with two SIV strains (SIV/17E-Fr and the swarm SIV/DeltaB670), and mock-inoculated 4 animals for control. Infected animals were sacrificed at 4 time points, as following: 6 animals sacrificed at 4 days, 6 at 7 days, 6 at 14 days and 2 at 21 days post-infection. Animals were perfused before necropsy to decrease blood contamination in the tissues. Organs were then culled, and RNA was extraction for NanosString analysis using a set of 92 probes specifically generated for macaque genes. Data were then analyzed by multiple preprocessing methods with two multivariate analysis methods. The following files contains raw data for the listed samples, respectively; GAMA Nanostring RAW MLN.xlsx - all MLN samples GAMA Nanostring RAW PBMC.xlsx - all PBMC samples GAMA Nanostring RAW Spleen 1.xls - PT01-04SP, PT71-74SP, PT141-144SP GAMA Nanostring RAW Spleen 2.xls - PT41-44SP, PT75-76SP, PT145-146SP, PT211-212SP GAMA Nanostring RAW Spleen 3.xls - PT45-46SP Please note that, in the associated publication, we describe a multiplexed component analysis to identify genes that highly contribute to inflammation during SIV acute infection. This analysis was done by compiling results generated by different types of data transformations and data normalizations (more than 12 for each tissue) and the relevant algorithms/mathematical processes will be discussed in detail. Therefore, only raw data is presented in this record (i.e. each sample data table contains raw data).
2015-05-22 | E-GEOD-51488 | biostudies-arrayexpress
Project description:Expression profiling by NanoString nCounter gene expression system Inflammatory response genes play an important role during acute HIV and SIV infection. Using an SIV macaque model for AIDS and CNS disease, we measured mRNA expression of 92 genes before and at multiple time points during acute SIV infection in three tissues: Peripheral blood mononuclear cells, mesenteric lymph nodes (MLN) and peripheral blood mononuclear cells (PBMC). Studying the overall changes of mRNA expressions over time or analyzing the correlation between the gene measurements and SIV RNA in plasma can result in limited interpretations. This is due to several reasons including but not limited to: 1) lack of prior information on how cells react to changes in gene expressions; and 2) biological responses typically involve many genes working together. To approach this problem, we combine multiple preprocessing methods with two multivariate analysis methods, namely principal component analysis and partial least square regression, to create a multiplexed set of 12 “judges”. Each of the judges simultaneously observes all the variables and emphasizes a unique type of gene expression response that could be significant, for example, depending on whether the cell responds to the absolute or relative size of gene expression changes. By incorporating multiple potential biological models of response, it is possible to identify genes that are consistently ranked as high “contributing” genes in different scenarios, i.e., genes that have a higher weight when we classify the data based on different classification schemes. We then use statistical analysis to verify that the consistently high-ranking genes are also statistically significant. We also investigate whether genes are tissue-specific, identify clusters of genes that co-vary together and study their correlation with regard to other gene clusters. The multiplex component analysis method introduced in this paper is a powerful tool to analyze complex gene datasets, identify significant genes, and generate testable hypotheses.
2015-05-22 | GSE51488 | GEO
Project description:Transcriptome comparison between CCR2+ and CCR2- classical monocytes in SIV-infected Macaca nemestrina
| PRJNA138395 | ENA
Project description:Probiotic and Prebiotic Supplementation of Antiretroviral Therapy Improves Gastrointestinal Immunity in SIV-infected Macaques
| PRJNA179375 | ENA
Project description:Intra-amniotic Balloon Inflation Induces an Inflammatory “Pulse” and Labor in Nonhuman Primates
| PRJNA267264 | ENA
Project description:Primates have evolved a variety of restriction factors that prevent retroviral replication. One such factor, TRIM5alpha, mediates a postentry restriction in many Old World primates. Among New World primates, Aotus trivirgatus exerts a similar early restriction mediated by TRIMCyp, a TRIM5-cyclophilin A (CypA) chimera resulting from a CypA retrotransposition between exons 7 and 8 of the TRIM5 gene. Macaca nemestrina do not express TRIM5alpha; therefore, we asked whether these animals and related Old World primates express TRIMCyp. RT-PCR of total RNA from M. nemestrina and Macaca fascicularis yielded three TRIMCyp amplification products, one of which is predicted to encode a TRIMCyp chimera containing a full-length CypA. Unlike A. trivirgatus, genomic sequencing of M. nemestrina and M. fascicularis identifies a CypA retrotransposition in the 3' untranslated region of the TRIM5 locus. There is approximately 78% homology between the predicted protein sequences of Old World and New World primate TRIMCyp, with most of the differences found in the TRIM5-derived sequence. Notably, exon 7 is absent from both M. nemestrina and M. fascicularis TRIMCyp. Neither M. nemestrina nor M. fascicularis TRIMCyp could restrict HIV-1 or simian immunodeficiency virus SIVmac in an in vitro infectivity assay. The discovery of TRIMCyp in both M. nemestrina and M. fascicularis indicates that TRIMCyp expression may be more common among Old World primates than previously believed. Convergent evolution of TRIMCyp in both Old World and New World primates suggests that TRIMCyp may have provided evolutionary advantages.
| S-EPMC2265124 | biostudies-literature