Ontology highlight
ABSTRACT:
PROVIDER: PRJNA1187297 | ENA |
REPOSITORIES: ENA
Dataset's files
| Action | DRS | |||
|---|---|---|---|---|
| SRR31372829_1.fastq.gz | Fastqsanger.gz | |||
| SRR31372829_2.fastq.gz | Fastqsanger.gz | |||
| SRR31372830_1.fastq.gz | Fastqsanger.gz | |||
| SRR31372830_2.fastq.gz | Fastqsanger.gz |
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Project description:Aim: To identify the genes and non-coding RNAs (ncRNAs) involved in the neuroprotective actions of a dietary anti-oxidant (saffron) and of photobiomodulation. Methods: We used a previously published assay of photoreceptor damage, in which albino Sprague Dawley rats raised in dim cyclic illumination (12h 5 lux, 12h darkness) are challenged by 24h exposure to bright (1,000 lux) light. Experimental groups were protected against light damage by pretreatment with dietary saffron (1mg/kg/day for 21d) or photobiomodulation (10 J/cm2 at the eye, daily for 5d). RNA from 1 eye of each of 4 animals in each of the 6 experimental groups (control, light damage (LD), saffron, photobiomodulation (PBM), saffronLD, and PBMLD) was hybridized to Affymetrix rat genome ST arrays. Quantitative real-time PCR analysis of 14 selected genes was used to validate microarray results. Results: LD caused the regulation of 175 entities (genes and ncRNAs) beyond criterion levels (P < 0.05 in comparisons with controls, fold-change >2). PBM pretreatment reduced the expression of 126 of these 175 LD-regulated entities below criterion; saffron pretreatment reduced the expression of 53 entities (50 in common with PBM). In addition, PBM pretreatment regulated the expression of 67 entities not regulated by LD, while saffron pretreatment regulated 122 entities not regulated by LD (48 in common with PBM). PBM and saffron, given without LD, regulated genes and ncRNAs beyond criterion levels, but in lesser numbers than during their protective action. A high proportion of the entities regulated by LD (>90%) were known genes; by contrast, ncRNAs where prominent among the entities regulated by PBM and saffron in their neuroprotective roles (73% and 62% respectively). Conclusions: Given alone, saffron and (more prominently) PBM both regulated significant numbers of genes and ncRNAs. Given prior to retinal exposure to damaging light, thus while exerting their neuroprotective action, they regulated much larger numbers of entities, among which ncRNAs were prominent. Further, the downregulation of known genes and of ncRNAs was prominent in the protective actions of both neuroprotectants. These comparisons provide an overview of gene expression induced by two neuroprotectants and provide a basis for more focused study of their mechanisms. The were 3 biological repliactes of each of the following groups: Control, Saffron pretreated, Photobiomodulation pretreated, Light Damage, Saffron Light Damage and Photobiomodulation Light Damage. 18 chips in total were performed.
2010-07-16 | E-GEOD-22818 | biostudies-arrayexpress
Project description:This work represents the first epigenomic study carried out on saffron crocus. Five accessions of saffron, showing differences in tepal pigmentation, yield of saffron and flowering time, were analysed at the epigenetic level by applying a methylation-sensitive restriction enzyme-sequencing (MRE-seq) approach. Five accession-specific hypomethylomes plus a reference hypomethylome, generated by combining the sequence data from the single accessions, were obtained. Assembled sequences were annotated against existing online databases. In the absence of the Crocus genome, the rice genome was mainly used as the reference as it is the best annotated genome among monocot plants. Comparison of the hypomethylomes revealed many differentially methylated regions, confirming the high epigenetic variability present among saffron accessions, including sequences encoding for proteins that could be good candidates to explain the accessions’ alternative phenotypes. In particular, transcription factors involved in flowering process (MADS-box and TFL) and for the production of pigments (MYB) were detected. Finally, by comparing the generated sequences of the different accessions, a high number of SNPs, likely having arisen as a consequence of the prolonged vegetative propagation, were detected, demonstrating surprisingly high genetic variability. Gene ontology (GO) was performed to map and visualise sequence polymorphisms located within the GOs and to compare their distributions among different accessions. As well as suggesting the possible existence of alternative phenotypes with a genetic basis, a clear difference in polymorphic GO is present among accessions based on their geographic origin, supporting a possible signature of selection in the Indian accession with respect to the Spanish ones.
2021-03-24 | GSE166350 | GEO
Project description:Aim: To identify the genes and non-coding RNAs (ncRNAs) involved in the neuroprotective actions of a dietary anti-oxidant (saffron) and of photobiomodulation. Methods: We used a previously published assay of photoreceptor damage, in which albino Sprague Dawley rats raised in dim cyclic illumination (12h 5 lux, 12h darkness) are challenged by 24h exposure to bright (1,000 lux) light. Experimental groups were protected against light damage by pretreatment with dietary saffron (1mg/kg/day for 21d) or photobiomodulation (10 J/cm2 at the eye, daily for 5d). RNA from 1 eye of each of 4 animals in each of the 6 experimental groups (control, light damage (LD), saffron, photobiomodulation (PBM), saffronLD, and PBMLD) was hybridized to Affymetrix rat genome ST arrays. Quantitative real-time PCR analysis of 14 selected genes was used to validate microarray results. Results: LD caused the regulation of 175 entities (genes and ncRNAs) beyond criterion levels (P < 0.05 in comparisons with controls, fold-change >2). PBM pretreatment reduced the expression of 126 of these 175 LD-regulated entities below criterion; saffron pretreatment reduced the expression of 53 entities (50 in common with PBM). In addition, PBM pretreatment regulated the expression of 67 entities not regulated by LD, while saffron pretreatment regulated 122 entities not regulated by LD (48 in common with PBM). PBM and saffron, given without LD, regulated genes and ncRNAs beyond criterion levels, but in lesser numbers than during their protective action. A high proportion of the entities regulated by LD (>90%) were known genes; by contrast, ncRNAs where prominent among the entities regulated by PBM and saffron in their neuroprotective roles (73% and 62% respectively). Conclusions: Given alone, saffron and (more prominently) PBM both regulated significant numbers of genes and ncRNAs. Given prior to retinal exposure to damaging light, thus while exerting their neuroprotective action, they regulated much larger numbers of entities, among which ncRNAs were prominent. Further, the downregulation of known genes and of ncRNAs was prominent in the protective actions of both neuroprotectants. These comparisons provide an overview of gene expression induced by two neuroprotectants and provide a basis for more focused study of their mechanisms.
2010-07-16 | GSE22818 | GEO
Project description:Ulcerative colitis is a chronic inflammatory disorder for which a definitive cure is still missing. This is characterized by an overwhelming inflammatory milieu in the colonic tract where a composite set of immune and non-immune cells orchestrate its pathogenesis. Over the last years, a growing body of evidence has been pinpointing gut virome dysbiosis as underlying its progression. Nonetheless, its role during the early phases of chronic inflammation is far from being fully defined. Here we show the gut virome-associated Hepatitis B virus protein X, most likely acquired after an event of zoonotic spillover, to be associated with the early stages of ulcerative colitis and to induce colonic inflammation in mice. It acts as a transcriptional regulator in epithelial cells, provoking barrier leakage and altering mucosal immunity at the level of both innate and adaptive immunity. This study paves the way to the comprehension of the aetiopathogenesis of intestinal inflammation and encourages further investigations of the virome as a trigger also in other scenarios. Moreover, it provides a brand-new standpoint that looks at the virome as a target for tailored treatments, blocking the early phases of chronic inflammation and possibly leading to better disease management.
2023-02-20 | GSE204665 | GEO
Project description:This work investigates the effects of a prebiotic mix containing lutein, zeaxanthin, and saffron, recognized for their anti-inflammatory properties, on ophthalmological and microbial parameters in neovascular AMD (nAMD) patients.
2024-12-05 | GSE261732 | GEO
Project description:With nearly 140 α-glycosidases in 14 different families, plants are well equipped with enzymes that can break the α-glucosidic bonds in a large diversity of molecules. Here, we introduce activity profiling of α-glycosidases in plants using α-configured cyclophellitol aziridine probes carrying various fluorophores or biotin. In Arabidopsis, these probes label members of the GH31 family of Glycosyl Hydrolases, including ER-resident α-glucosidase-II RSW3/PSL5 and Golgi-resident α-mannosidase-II HGL1, which both trim N-glycans on glycoproteins. We also detect the active state of extracellular α-glycosidases such as α-xylosidase XYL1, which acts on xyloglucan in the cell wall to promote cell expansion, and α-glucosidase AGLU1, which acts in starch hydrolysis and can suppress fungal invasion. α-glycosidase labelling causes specific signals at 100-130 kDa that are pH-dependent and can be supressed by α-glycosidase inhibitors miglitol and acarbose. The α-glycosidase probes display similar miglitol-sensitive signals in leaf extracts of in a broad range of plant species. To show its use on a non-model plant, we applied glycosidase activity profiling on Crocus sativa, a cash crop for the production of saffron spice. Using a combination of biotinylated glycosidase probes, we identified and quantified 70 active glycosidases in stigma stages 1 and 4 of saffron (Crocus sativa L.), ten of which are differentially active. We also uncover massive changes in hydrolase activities in corms upon infection with Fusarium oxysporum using multiplex fluorescent labelling in combination with probes for serine hydrolases and cysteine proteases. These experiments demonstrate the ease by which active α-glycosidases and other hydrolases can be displayed in non-model plants.
2018-05-17 | PXD009014 | Pride