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Metabolomics,Unknown,Transcriptomics,Genomics,Proteomics

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Transcriptional profiling of UV-B response of Populus alba.

ABSTRACT: Microarray technology was used to assess transcriptome changes in poplar (Populus alba L.) under a realistic simulation of increased UV-B radiation. Plants were UV-Bbe (UV-B biologically effective radiation) supplemented with a dose of 6 kJ/m2/day for 12 hours per day and allowed to recover during the night. Poplar plants were UV-B treated using a refined controlled environment able to guarantee a realistic simulation of natural conditions, especially for light parameters such as presence of background UV-B radiation for control plants and balanced PAR/UV-A/UV-B ratio. A time course experiment was planned to look both at the rapid and delayed response of poplar to UVB; two time points after 3 h (T3h) and 30 h (6th hour of the third day of treatment, T30h) were considered. 4 independent biological replicates were analysed for each time point. Competitive hybridisations were carried out using the PICME 28K microarray. Keywords: Time course experiment, stress response Two condition experiment: UVB supplemented plants vs normal UV-B level plants. Biological replicates: 4 UVB suplemented plants, 4 control plants, two time points, one replicate per array. Dye swap between replicates.

ORGANISM(S): Populus alba

SUBMITTER: Giovanni Emiliani

PROVIDER: E-GEOD-9470 | biostudies-arrayexpress |

REPOSITORIES: biostudies-arrayexpress

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Transcriptional profiling of UV-B response of Populus alba.

Project description:Microarray technology was used to assess transcriptome changes in poplar (Populus alba L.) under a realistic simulation of increased UV-B radiation. Plants were UV-Bbe (UV-B biologically effective radiation) supplemented with a dose of 6 kJ/m2/day for 12 hours per day and allowed to recover during the night. Poplar plants were UV-B treated using a refined controlled environment able to guarantee a realistic simulation of natural conditions, especially for light parameters such as presence of background UV-B radiation for control plants and balanced PAR/UV-A/UV-B ratio. A time course experiment was planned to look both at the rapid and delayed response of poplar to UVB; two time points after 3 h (T3h) and 30 h (6th hour of the third day of treatment, T30h) were considered. 4 independent biological replicates were analysed for each time point. Competitive hybridisations were carried out using the PICME 28K microarray. Keywords: Time course experiment, stress response

2013-12-01 | GSE9470 | GEO

Studying Gene Expression Profiles of UV-Irradiated Human Keratinocytes by cDNA Microarray

2008-11-18 | GSE4223 | GEO

Studying Gene Expression Profiles of UV-Irradiated Human Keratinocytes by cDNA Microarray

Project description:The goal of this thesis is to study the response of a human keratinocyte cell line (HaCaT cells) after UVB irradiation. In order to develop a system for UV irradiation, we firtstly studied the UV illumination system to find out a stable and reliable condition for UV irradiation experiments. Further, we found out the proper dose of UVB radiation and time points after UVB irradiation by performing MTT assay and trypan blue viability test. According to the results of MTT assay and trypan blue viability test, the cellular activity as well as survival rate of UVB-irradiated cells were in proportion to the radiation doses within a lower UVB dose range. We wanted to find out the possible reasons for this phenomenon by using cDNA microarray. We hope the thesis could be a guide for the following researches, and be useful in the clinical studies about the UV damage. Keywords: dose response and time course Loop-designed microarray experiments were performed in our study. Twenty-one samples are arranges as seven small loops and one large loop, with three and seven microarray slides for each small and large loop, respectively. This set of loop-designed microarray experiment contains one control untreated (non UVB-treated) samples and two UVB-treated samples (one low dose and one high dose UVB-treated) at each time point (total seven time points).

2010-05-16 | E-GEOD-4223 | biostudies-arrayexpress

UV Photoprotection and Long-lasting Pigmentation from UVA and/or UVB

Project description:To test whether there is a photoprotective benefit after different types of suberythemal repetitive UV, a 1.5 MED challenge dose was applied 1 week after the initial 2 weeks of repetitive irradiation. To determine what different mechanisms and/or factors might be involved in physiological pigmentary responses of the skin to different types of UV, we used whole human genome microarrays and immunohistochemical analyses to characterize human skin in situ to examine how melanocyte-specific proteins and paracrine melanogenic factors are regulated by repetitive exposure to suberythemal doses of different types of UV (UVA and/or UVB). Seven volunteers with skin type II-III were irradiated with UVA, UVB or UVA+UVB radiation for 2 weeks (5 times per week, 10 times total) after preliminary determination of their MEDs. A UVA+UVB challenge dose of 1.5X the MED was applied 1 week later. Biopsies were taken before the challenge dose, immediately after the challenge dose, 4 days after the challenge, and 15 weeks after the challenge.

2014-12-12 | E-GEOD-56754 | biostudies-arrayexpress

Changes of lncRNA expression in primary human skin fibroblasts after irradiation with UVA or UVB

Project description:In response to ultraviolet radiation (UVR), cells alter gene expression, switching on a variety of damage response pathways. Long non-coding RNA (lncRNA) is thought to play critical roles in regulating expression of protein-coding genes. We hypothesized that lncRNAs also regulate gene expression following UV exposure and screened for changes in lncRNA expression in human primary fibroblasts after irradiation with longwave UV (UVA) or shortwave UV (UVB).

2016-10-21 | GSE89005 | GEO

Regulation of human skin pigmentation in situ by repetitive UV exposure - Molecular characterization of responses to UVA, UVB and SSR

Project description:To test the hypothesis that different mechanisms and/or factors might be involved in physiological pigmentary responses of the skin to different types of UV, we used whole human genome microarrays and immunohistochemical analyses to characterize human skin in situ to examine how melanocyte-specific proteins and paracrine melanogenic factors are regulated by repetitive exposure to suberythemal doses of different types of UV (UVA, UVB or SSR). Six volunteers with skin type II-III were irradiated with SSR, UVA or UVB radiation for 2 weeks (5 times per week, 10 times total) after preliminary determination of their MEDs. Biopsies were taken 3 days after the last irradiation.

2010-08-18 | E-GEOD-21429 | biostudies-arrayexpress

UV effects in mouse melanocytes

Project description:Ultraviolet (UV) radiation is a major melanoma risk factor, yet underlying mechanisms remain poorly understood. Here we introduce a mouse model permitting fluorescence-aided melanocyte imaging and isolation following in vivo UV irradiation. We use expression profiling to show that activated neonatal skin melanocytes isolated following a melanomagenic UVB dose bear a distinct, persistent interferon-response signature, including genes associated with immunoevasion. UVB-induced melanocyte activation, characterized by aberrant growth and migration, was abolished by antibody-mediated systemic blockade of interferon-gamma (IFN-gamma), but not type-I interferons. IFN-gamma was produced by macrophages recruited to neonatal skin by UVB-induced chemokine receptor Ccr2 ligands. Admixed recruited skin macrophages enhanced transplanted melanoma growth by inhibiting apoptosis; notably, IFN-gamma blockade abolished macrophage-associated melanoma growth and survival. IFN-gamma-producing macrophages were identified in 70% of human melanomas examined. Our data reveal an unanticipated role for IFN-gamma in promoting melanocytic cell survival/immunoevasion, and suggest IFN-gamma-R signaling represents a novel therapeutic melanoma target. Biologic replicates of UVA- and UVB-treated mouse melanocytes, as well as untreated mouse melanocytes and mouse keratinocytes, were used to define melanocyte expression signatures associated with UV treatment.

2011-01-01 | E-GEOD-25164 | biostudies-arrayexpress

MiRNAs expression in supernatant after ultraviolet irradiation

Project description:To investigate the mechanism of radiation induced bystander effect, we explored miRNAs expression in supernatant of human skin fibroblasts after culturing for 24h post UV irradiation. Primary human skin fibroblasts were obtained from healthy volunteers by means of a foreskin circumcision. Human skin fibroblasts was irradiated with 20J/cm2 UVA or 60mJ/cm2 UVB. Expression of miRNAs were tested by microarray between radiation and control samples.

2018-03-07 | GSE111444 | GEO

Anti-inflammatory effects of differential molecular weight hyaluronic acids on UVB-induced calprotectin-mediated keratinocyte inflammation

Project description:Background: The biological functions of HA are related to its molecular weight and binding to its receptor TLR4 or CD44. Recent studies have shown that LMW-HA exhibits proinflammatory effects, while HMW-HA functions as an anti-inflammatory factor. UVB-induced epidermal inflammation is mainly mediated by endogenous molecules, such as DAMPs, that cause severe skin damage by activating TLR signaling pathways. Objective: Since both LMW- and HMW-HA have inhibitory functions on TLR-mediated macrophage inflammation, HA is assumed to suppress UVB-induced DAMP-mediated inflammation in the skin. In this study, both uLMW-HA and HMW-HA were found to inhibit UVB-induced keratinocyte inflammation. Methods: To elucidate whether HAs have anti-inflammatory effects on inflammation induced by UVB exposure, we performed whole transcriptome analysis in HaCaT cells treated with or without HAs after UVB exposure. Results: UV radiation induced upregulation or downregulation of genes (FC>1.2 or FC<0.8, q<0.05) were obtained. We analyzed network of these genes with Ingenuity Pathway analysis using information collected from databases on protein interactions. IL-6 was detected as an upstream factor of HA suppressing UV-radiation effects on HaCaT cells. Canonical pathway analysis also shows uLMW-HA downregulated NF-κB, which is located downstream of TLR4 signaling pathway, although HMW-HA did not show downregulation of NF-κB signaling pathway. Conclusions: Both uLMW-HA and HMW-HA were found to inhibit UVB-induced keratinocyte inflammation.

2022-08-05 | GSE201850 | GEO

UVB irradiation does not directly induce detectable changes of DNA methylation in human keratinocytes

Project description:Unprotected exposure to UVB radiation from the sun and the resulting DNA damage are thought to be responsible for physiological changes in the skin and for a variety of skin cancers, including basal cell and squamous cell carcinoma and malignant melanoma. Although the mutagenic effects of UVB have been well documented and studied mechanistically, there is only limited information as to whether UV light may also be responsible for inducing epigenetic changes in the genome of exposed cells. DNA methylation is a stable epigenetic modification involved in gene control. To study the effects of UVB radiation on DNA methylation, we repeatedly exposed normal human keratinocytes to a UVB light source. After a recovery period, we analyzed global DNA methylation patterns in the irradiated and control cells using the methylated-CpG island recovery assay (MIRA) method in combination with high-resolution microarrays. Bioinformatics analysis revealed only a limited number of possible differences between UVB-exposed and control cells. However, these minor apparent changes could not be independently confirmed by bisulfite sequencing-based approaches. This study reveals that UVB irradiation of keratinocytes has no recognizable global effect on DNA methylation patterns and suggests that changes in DNA methylation, as observed in skin cancers, are not immediate consequences of human exposure to solar UVB irradiation. DNA methylation analysis of control and UVB irradiated keratinocytes. The MIRA assay was used for enrichment of methylated DNA. NimbleGen CpG island plus promoter arrats were used.

2013-01-30 | E-GEOD-42943 | biostudies-arrayexpress

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