Project description:Cellular proteins in central nervous system involved in avian neurotropic virus infection remains completely unknown. To investigate host gene expression profile in NDV infected SPF chicken brains, The microarray initial analysis was performed at LC-Bio (Hangzhou, China). A 44K Agilent chicken whole genome chip (43,803 probes) (Agilent Technologies, USA) was used for gene microarray analysis from F48E9-, LaSota-infected and mock-infected brains through intraocular-nasal routes.The chicken brains were collected at 5 day post infection. The significance analysis was used to evaluate the differences in gene expression. P and fold change (FC) values represent the alteration tendency of gene expression between experimental and control groups. The genes (FC>2) were input in Gene Ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway analysis for DEGs. Overall design: F48E9-, LaSota-infected and PBS (control)-infected brains through intraocular-nasal routes in 100000 pfu/100μl/chicken were collected at 5 day post infection.The data from F48E9- and LaSota-infected brains were compared to mock (PBS)-infection.
Project description:Isolation of bacteria in infected brains in patients with Parkinson's disease. Here we used next generation sequencing of 16S ribosomal RNA gene PCR amplicons (NGS 16S amplicon analysis).
Project description:We report the transcriptional profiles from individual Drosophila melanogaster (whole bodies or dissected brains) to Entomophthora muscae at 24 time points following fungal exposure. In whole fruit fly bodies, a significant immune response is observed following exposure to the fungus. In brains, few differences are consistently observed between infected and uninfected animals. Overall design: Three mock vials and three exposure vials were started with 25 CantonS Wolbachia-free flies 0-1 days old (RT-PCR, whole flies) or 1-2 days old (dissected brains) with either zero (mock) or six (exposure) Entomophthora muscae-killed D. melanogaster cadavers. For whole bodies, three uninfected females were individually collected at 24, 48, 72, 96 and 120 hours following mock exposure. Six exposed female flies were individually collected at each 24, 48 and 72 hours; three exposed females were collected at 96 hours and three fresh female cadavers were collected at each 96 and 120 hours. For dissected brains, three uninfected and three exposed female brains were individually collected at 24, 48 and 72 hours following mock exposure or exposure, respectively.
Project description:Cannabinoid administration before and after simian immunodeficiency virus (SIV)-inoculation ameliorated disease progression and decreased inflammation in male rhesus macaques. Δ9-tetrahydrocannabinol (Δ9-THC) did not increase viral load in brain tissue or produce additive neuropsychological impairment in SIV-infected macaques. To determine if the neuroimmunomodulation of Δ9-THC involved differential microRNA (miR) expression, miR expression in the striatum of uninfected macaques receiving vehicle (VEH) or Δ9-THC (THC) and SIV-infected macaques administered either vehicle (VEH/SIV) or Δ9-THC (THC/SIV) was profiled using next generation deep sequencing. Overall design: Brains were removed, flash frozen on dry ice, and RNA was harvested using Norgen RNA extraction kit. Illumina TruSeq RNA Sample Prep Kit was used with 500 ng of total RNA for the construction of sequencing libraries.
Project description:Project for the study of spatial and temporal alterations in organelle proteins during HCMV infection. Two datasets are included, one for label-free quantification and one for TMT quantification. Samples were collected at 5 time points of infection (24, 48, 72, 96, and 120 hours) and subject to organelle fractionation. One non-infected sample was included for the label-free analysis, and 5 non-infected samples (one per time point) were included for the TMT dataset. The nucleus and cytosolic fractions were removed by differential centrifugation, leaving a crude organelle fraction. The crude organelle fraction was further fractionated by density gradient ultracentrifugation into sicx fractions.
Project description:This SuperSeries is composed of the following subset Series: GSE26269: Genome-wide identification and analysis of microRNA expression in brains of mice infected with FJDRV, a street rabies virus with high virulence, and ERA, a laboratory-adapted virus with lower virulence GSE26270: Genome-wide identification and analysis of gene expression in brains of mice infected with FJDRV, a street rabies virus with high virulence, and ERA, a laboratory-adapted virus with lower virulence Refer to individual Series
Project description:The experiment describes the dynamic transcriptional alterations in brains of ME7- infected, and age-matched, mock-inoculated mice immediatly before inoculation, at two important preclinical time points and at terminal stages.
Project description:HIV-infected slow-progressors (SP) represent a heterogeneous group of subjects who spontaneously control HIV infection without treatment for several years while showing moderate signs of disease progression. Here we determined the frequency of SP subjects who showed loss of HIV control within our Canadian Cohort of HIV+ Slow-Progressors and identified the proinflammatory cytokine IL-32 as a robust biomarker for control failure. Overall design: Total cellular RNA was extracted from PBMC from 5 donors at two time points ('V1' before and 'V2' after loss of control, and only Long Term Non Progressors (LTNP) were part of the case study), along with 2 control Leuka914 and Aging106032 samples.
Project description:We have used cDNA microarrays to compare gene expression profiles in brains from normal mice to those infected with the Anka strain of Plasmodium berghei, a model of cerebral malaria. For each of three brains in each group, we computed ratios of all quantifiable genes with a composite reference sample and then computed ratios of gene expression in infected brains with untreated controls. Of the almost 12,000 unigenes adequateluy quantified in all arrays, about 3% were significantly downregulated (p<0.05, >50% fold change) and about 7% were upregulated. Upon inspection of the lists of regulated genes, we identified a high number encoding proteins of importance to normal brain function or associated with neuropathology. These results emphasize the important impact of malarial infection on gene expression in brain and provide tentative target biomarkers that might provide novel therapeutic targets for neurological sequelae of disease. Overall design: We have used a previously published protocol (Iacobas et al., Physiol Genomics 2005) and a composite reference RNA sample (R) prepared in sufficient quantity for the entire experiment from ten adult mouse tissues (aorta, brain, heart, kidney, liver, lung, ovary/testicles, spleen, and stomach - equal amounts from males and females). This combination of source tissues provided a high diversity of genes expressed in the midrange of the detection system for the AECOM mouse cDNA microarrays. Briefly, 60μg total RNA, extracted in Trizol® (Invitrogen, Carlsbad, CA) from brains of three infected (I) and three control (C) mice, purified with RNeasy® mini kit (Qiagen, Valencia, CA), were reverse transcribed into cDNA incorporating fluorescent Cy3-dUTP. The composite reference was reverse transcribed to incorporate Cy5-dUTP. Each of the six Cy3-labeled brain extracts was co-hybridized overnight at 50°C against the Cy5-labeled reference with AECOM 32k Mouse oligonucleotide arrays, MO3 printing series (platform described in http://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GPL5371). After hybridization, the slides were washed at room temperature, using solutions containing 0.1% sodium dodecyl sulfate (SDS) and 1% SSC (3M NaCl + 0.3M sodium citrate) to remove the non-hybridized cDNAs.
Project description:Transcriptional profiling of WT and myd88-/- macrophages infected with WT and hly- L. monocytogenes for 30, 60, 120, or 180 minutes Keywords: Timecourse, cell type comparison, bacteria strain comparison. Overall design: Timecourse experiment in different genetic backgrounds, with both WT and mutant bacteria. Multiple biological replicates (see array names), with one replicate per array.