Baseline expression of symptomatic and asymptomatic subjects after YF17D vaccination in Trial 2
ABSTRACT: This study investigates how the baseline expression level of genes impact symptomatic outcome of flaviviral infection. Before given the YF17D vaccine, whole blood was extracted into tempus tubes from vaccinated subjects. Thereafter, the subjects were assessed if they experienced adverse events (or symptoms). 35 subjects (n=12 symptomatic, n=23 asymptomatic) were processed according to manufacturer's protocol. Transcript expression was then evaluated by nCounter RNA Cancer Metabolism (#VRXC-CM1-12) or a custom Unfolded Protein Response codeset and its respective probesets.
Project description:The effect of pre and periconceptional multiple micronutrient supplementation on methylation of CpG loci within CpG islands associated with 14,000 genes across the human genome has been investigated in the offspring of a cohort of Gambian women participating in a controlled double blinded trial. Methylation levels in placebo and micronutrient supplemented cohorts were compared in genomic DNA from cord blood (35 placebo and 21 micronutrient supplemented) and in circulating blood samples (14 placebo and 9 micronutrient supplemented) drawn from the same cohort at 9 months old. A small number of differentially methylated CpG loci were identified in cord blood (14 in males and 21 in females) and a larger number in the 9 month infant comparison (108 in males and 106 in females). Seven differentially methylated loci in males and 8 in females persisted from cord to infant. These findings indicate that micronutrient supplementation pre-conception or early in embryonic development is potentially associated with programming of gene activity at birth, which is maintained into early infanthood. Strikingly, the loci affected by micronutrient supplementation differed between males and females, with no shared changes in cord blood and only 5 shared changes at 9 months. Additionally, a large number of CpG loci showed variation in methylation level when comparing 9-month samples to cord blood samples. These postnatal changes were more consistent between sexes, with 85% of female alterations being found as a subset of male changes in the placebo cohort and 62% of the female changes shared with males in the supplemented cohort. Taken together, the results suggest that there is a core developmental program shared between the sexes that is unaffected by nutrient supplementation, but that there are also sex-specific developmental changes which are altered under conditions of micronutrient supplementation and deficiency. Bisulphite converted DNA from 59 cord (36 placebo and 23 treated) and 25 infant peripheral blood (15 placebo and 10 treated) samples were hybridised to the Illumina Infinium 27k Human Methylation Beadchip v1.2. (For further analysis, five were excluded during quality control leaving 56 cord (35 placebo and 21 treated) and 23 infant peripheral blood (14 placebo and 9 treated) samples. Full data set of 84 samples were submitted to GEO)
Project description:The aim of the experiment was to determine the effects of 48 hours of treatment with oxidized low density lipoprotein (oxLDL) on gene expression in primary human monocyte-derived macrophages. 6 independent biological replicates were processed. From each replicate half of the cells were treated with oxLDL and the other half were treated with the control buffer. For foam cell formation (after 7 days) macrophages were treated with oxLDL (50mcg/ml, enodtoxin free, Copper oxidized). Control macrophages were treated with a matching buffer without oxLDL. Treatment duration - 48 hours.
Project description:Embryonic mouse skin samples were halved, one half separated into epidermis and dermis and RNA isolated, and the other half immersed in medium containing Actinomycin D (Act D) to halt transcription. After 30, 60 or 120 minutes at 37 degrees C the Actinomycin D treated samples were separated into epidermis and dermis and RNA isolated from these. Resulting RNA samples were sequenced to quantify transcript abundances.
Project description:The â??small perturbationâ?? approach is critical in studying the â??steady stateâ?? of a biological system. In our experiments, small perturbations were generated by applying a series of repeating intermittent small doses of ultraviolet radiation to a human keratinocyte cell line, HaCaT. The biological response was assessed by monitoring the gene expression profiles using a high reliability and high resolution cDNA microarray system. Following intermittent 10 J/m2 UVB small perturbations, two opposite classes of genes, down-regulated and up-regulated, exhibited an immediate response followed by relaxation between each small perturbation, but were prolonged down- or up-regulated without relaxation while larger doses (233 or 582.5 J/m2) of UVB were applied. A repeated cycle pattern of gene expression following small perturbations is an indication of the existence of steady states. This cycle pattern is suppressed when large perturbations are applied. We believe that this is a universal phenomenon. In our experiments, the functions of up-regulated genes were mainly associated with anti-proliferation, anti-mitogenesis, and apoptosis. On the other hand, down-regulated genes were mainly related to proliferation, mitogenesis, and anti-apoptosis. In conclusion, this study experimentally proves the concept of steady state at the transcription level and demonstrates the feasibility of using small perturbation approaches for investigating steady states. This study could also set a foundation of computational systems biology, which has implicitly used the concept of steady state. Keywords: time course Three UVB exposures are indicated by UV at time points of 0, 8 and 16 hours. T1, T2, T3, T4, T5, and T6 denote the sampling time points. T1, T3 and T5 are allocated 30 minutes after the corresponding UVB irradiation. T2, T4 and T6 are allocated 8 hours after each UVB irradiation. At each sampling time point, two samples (control and UV-irradiated) are collected. See supplementary file Loop_design.pdf for further explanation.
Project description:The extracellular matrix (ECM) of the ocular trabecular meshwork (TM) builds resistance to aqueous humor outflow, thereby regulating intraocular pressure (IOP). Glaucoma, a leading cause of blindness worldwide, is associated with changes in the ECM of the TM. The elastic modulus indicates glaucomatous TM is more rigid than age-matched normal TM; however, the biomechanical properties of segmental low (LF) and high flow (HF) TM regions in response to elevated pressure, are unknown. In this study, we measured the elastic modulus by atomic force microscopy (AFM) and measured protein expression differences in perfused human TM tissues by proteomics analyses. The elastic modulus of LF regions was 2.3-fold stiffer than HF regions at physiological (1x) pressure, and 7.4-fold or 3.5-fold stiffer than HF regions at elevated (2x) pressure after 24 or 72 hours, respectively. Quantitative proteomics using isobaric tandem mass tags (TMT), multi-notch isolation, high resolution, and extended multiplexing were used to compare protein expression levels between normal, LF, and HF regions at the two pressures. A total of 3730 proteins (2 peptides per protein) were identified from the ECM samples, and 2637 proteins were quantified. Statistically significant ECM proteins over expressed in LF compared with HF regions at 2x, and in HF regions at 1x compared with 2x pressure were determined. A sub-set of ECM proteins, including decorin, TGFβ-induced protein, keratocan, lumican, dermatopontin and thrombospondin 4, were common differential candidates in both comparisons. These data suggest a correlation between the biomechanical properties of TM regions and differential levels of specific ECM proteins in response to elevated pressure.
Project description:Healthy young males (n=13) attended in this controlled laboratory experiment stimulating a workin week with reduced sleep. After baseline, the experimental group (n=9) were partially sleep deprived for 5 nights (time in bed 4 h/night) and had a recovery period of two nights (8 h/night). The control group (n= 4) spent the time in the same laboratory conditions but sleeping normally (8 h/night). RNA expression was detected in peripheral blood mononuclear cells (PBMC) taken in the morning after baseline (BL), sleep restriction (SR), and recovery (REC) periods.
Project description:The Arabidopsis thaliana DRINK ME gene (bZIP30; AT2G21230) is a member of the bZIP transcription factor family. Overexpression of DKM leads to a dwarf plant phenotype and defects in meristematic and reproductive tissues. This experiment aims at identifying the differentially experessed genes between wild type (Ws-3) and 35S::DKM inflorescences (with closed buds).
Project description:affy_genomic_poplar - affy_genomic_poplar - The project aims to identify genes of interest for water deficit acclimation in poplar. We look for genes and gene expression networks related to drought stress in two hybrid cultivars, differing in their drought tolerance in field. Affymetrix poplar genome array was designed on several Populus species. In order to deal with comparative approaches, we checked the convenience of the array by hybridizing genomic DNA of the two hybrid cultivars (Populus deltoides × Populus nigra, namely ‘cv Carpaccio’ and ‘cv Soligo’). This point is important as transcript sequence might have diverged in the two genomes (Fossati et al, 2005), which could lead to absence of hybridization without physiological meaning. -Two poplar cultivars, Soligo (S) and Carpacio (C) were grown in controlled conditions. Mature leaves were collected and genomic DNA was extracted from leaves in CTAB buffer. gDNA was fragmented with DNAse1. DNA fragments were labelled with Biotin N6-ddATP and hybridized on Affymetrix poplar genome array. Two technical replicates per genotype were performed. Keywords: genomic comparison,gain of fuction epimutation 4 arrays - poplar
Project description:Transcriptional expression of a restricted set of cancer signal transduction-related gesen were comparatively quantified in HER2/neu transgenic mammary tumors, mesenchymal and epithelial tumor cell lineages, both estabilished from HER-2/neu transgenic tumors, and syngeneic mesenchymal stem cells. In the study presented here, HER-2/neu transgenic mouse mammary tumors, previously described (Galie et al Carcinogenesis 2005 26(11):1868) mesenchymal (A17) and epithelial (BB1) cell lineages estabilished from murine HER-2/neu transgenic mammary tumors, and syngeneic mesenchymal stem cells, underwent transcriptional analysis using microarrays containing probes for 112 signal transduction-related genes and controls (GEArray Q Series Mouse Signal Transduction in Cancer Gene Array, MM-044, Superarray, Friederick, MD, USA).