Rattus norvegicus
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PROVIDER: PRJNA210869 | ENA |
REPOSITORIES: ENA
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Project description:In our previous study, we reported that a diet rich in antioxidants such as coral calcium hydride (CCH) increased the endogenous antioxidant ability in the hippocampus of rats. We conducted this study to test the hypothesis that diet supplementation with CCH would change the gene expression in rats and to understand how CCH enhances antioxidant ability. We used a DNA array to compare the expression levels in the hippocampus of rats fed with CCH for 2 weeks with those of rats fed a normal diet. Immune response-related genes were down-regulated, while nuclear respiratory factor 2 and aldehyde dehydrogenase 3A were up-regulated. Our findings about the changes in the mRNA levels of these genes well explain the physiological finding of enhanced antioxidant ability in rat brain.
2013-12-31 | GSE48623 | GEO
Project description:In our previous study, we reported that a diet rich in antioxidants such as coral calcium hydride (CCH) increased the endogenous antioxidant ability in the hippocampus of rats. We conducted this study to test the hypothesis that diet supplementation with CCH would change the gene expression in rats and to understand how CCH enhances antioxidant ability. We used a DNA array to compare the expression levels in the hippocampus of rats fed with CCH for 2 weeks with those of rats fed a normal diet. Immune response-related genes were down-regulated, while nuclear respiratory factor 2 and aldehyde dehydrogenase 3A were up-regulated. Our findings about the changes in the mRNA levels of these genes well explain the physiological finding of enhanced antioxidant ability in rat brain. CCH was obtained from ICB, Ltd., Sendai, Japan, and coral calcium (CC) was purchased from Coralbio, Okinawa, Japan. Male Wistar rats were acquired from Kyudo, Co., Ltd. and maintained at the Experimental Animal Center of the University of Miyazaki at a controlled ambient temperature of 23 ± 1 °C and 50 ± 10% relative humidity. The Committee for Ethics on Animal Experiments, Faculty of Medicine, University of Miyazaki, Japan, reviewed and approved the experimental design. Six-week-old male Wistar rats (n = 8) were assigned to 2 groups: standard diet-fed group (CE-2, Clea Japan, Inc., Tokyo, Japan) and CCH-fed group. The CCH diet was standard CE-2 feed supplemented with 0.1% CCH powder. Inhibition of accelerated aging and an increase in the in vivo antioxidant ability was observed in SAM/P-8 mice fed a diet supplemented with 0.1% CCH. In accordance with these reports, the CCH concentration used in our study was set at 0.1%.The animals were killed by cervical dislocation at the age of 8 weeks. They were decapitated and the hippocampi were removed and rapidly frozen in liquid nitrogen. The hippocampi were then homogenized with a conventional rotor-stator homogenizer. Total RNA was then extracted from the tissues by using the RNeasy Lipid Tissue Mini Kit (Qiagen, Valencia, CA).
2013-12-31 | E-GEOD-48623 | biostudies-arrayexpress
Project description:Hippocampal gene network analysis to determine the effects of coral calcium hydride in an experimental model of accelerated senescence
| PRJNA145587 | ENA
Project description:Recent studies strongly support the hypothesis that antioxidant diet inhibits the pathological aging process as shown in senescence-accelerated mouse prone 8 (SAM/P-8). In our previous study, we reported that a diet rich in antioxidants inhibits the pathological aging process, as shown coral calcium hydride (CCH) increased the endogenous antioxidant ability and contributed to prolonging the life-span of SAM/P-8. In order to test the hypothesis that antioxidant CCH supplementation to SAM/P-8 mice would change the gene expression and understand how CCH reverses the acceleration of aging in SAM/P-8 mice, in the current study, we used a DNA array to compare the expression levels in the hippocampus of the brains from 16-week-old SAM/P-8 mice treated or not treated with CCH. The most significant up regulated changes in the gene network of SAM/P-8 mice were free radical scavenging and molecular transport, and genes associated with cell death, cancer, and cell cycle were downregulated. Our findings about changes in these mRNA might be associated with that inhibition of the acceleration of aging is observed in SAM/P-8 mice fed a CCH-diet. Eight-week-old male SAM/P-8 and SAM/R-1 mice were assigned to two groups: the CCH-fed group (fed with CCH for 8 weeks with CE-2 (rodent diet, Clea Japan, Inc., Tokyo, Japan) containing 0.1% CCH) and the control group (fed with CE-2 for 8 weeks).
2011-09-22 | E-GEOD-31606 | biostudies-arrayexpress
Project description:Recent studies strongly support the hypothesis that antioxidant diet inhibits the pathological aging process as shown in senescence-accelerated mouse prone 8 (SAM/P-8). In our previous study, we reported that a diet rich in antioxidants inhibits the pathological aging process, as shown coral calcium hydride (CCH) increased the endogenous antioxidant ability and contributed to prolonging the life-span of SAM/P-8. In order to test the hypothesis that antioxidant CCH supplementation to SAM/P-8 mice would change the gene expression and understand how CCH reverses the acceleration of aging in SAM/P-8 mice, in the current study, we used a DNA array to compare the expression levels in the hippocampus of the brains from 16-week-old SAM/P-8 mice treated or not treated with CCH. The most significant up regulated changes in the gene network of SAM/P-8 mice were free radical scavenging and molecular transport, and genes associated with cell death, cancer, and cell cycle were downregulated. Our findings about changes in these mRNA might be associated with that inhibition of the acceleration of aging is observed in SAM/P-8 mice fed a CCH-diet.
2011-09-23 | GSE31606 | GEO
Project description:The surprising observation that virtually the entire human genome is transcribed means we know very little about the function of many emerging classes of RNAs, except their astounding diversity. Traditional RNA function prediction methods rely on sequence or alignment information, which are limited in their ability to classify classes of non-coding RNAs (ncRNAs). To address this, we developed CoRAL, a machine learning-based approach for classification of RNA molecules. CoRAL uses biologically interpretable features including fragment length, cleavage specificity, and antisense transcription to distinguish between different ncRNA classes. We evaluated CoRAL using genome-wide small RNA sequencing (smRNA-seq) datasets from two human tissue types (brain and skin [GSE31037]), and were able to classify six different types of RNA transcripts with 79~80% accuracy in cross-validation experiments, and with 71~73% accuracy when CoRAL uses one tissue type for training and the other as validation. Analysis by CoRAL revealed that long intergenic ncRNAs, small cytoplasmic RNAs, and small nuclear RNAs show more tissue specificity, while microRNAs, small nucleolar, and transposon-derived RNAs are highly discernible and consistent across the two tissue types. The ability to consistently annotate loci across tissue types demonstrates the potential of CoRAL to characterize ncRNAs using smRNA-seq data in less characterized organisms. Four samples were sequenced, each one coming from frozen brain tissue (frontal cortex) of a deceased female human patient with no remarkable pathology.
2013-07-07 | E-GEOD-43335 | biostudies-arrayexpress
Project description:The purpose of the study was to determine the potential role of ATF4 in gene regulation by brain derived neurotrophic factor (BDNF). To achieve this, we compared gene regulation by BDNF in cultured rat hippocampal neurons with or without prior ATF4 knockdown with shRNA. We surveyed cultures after 0,2,4,8 and 16 hrs of exposure to BDNF.
2017-09-09 | E-MTAB-6046 | biostudies-arrayexpress
Project description:Micorarray analysis was performed on RNA samples from hippocampal cultures infected with either Ad-aCaN or Ad-LacZ or uninfected. Each sample was applied to its own GeneChip (Rat RG-U34A; n=7-9 chips/group). Chips were then processed and scanned using Agilent Affymetrix GeneArray Scanner. MAS5 was used to determine signal intensity and presence/absence calls for the data. Keywords = bioinformatics Keywords = gene expression Keywords = calcineurin Keywords = calcium Keywords = Alzheimer's Keywords = inflamation Keywords = Adenovirus Keywords = astrocytes Keywords = microarray Keywords: parallel sample
2005-05-06 | GSE1978 | GEO
Project description:The surprising observation that virtually the entire human genome is transcribed means we know very little about the function of many emerging classes of RNAs, except their astounding diversity. Traditional RNA function prediction methods rely on sequence or alignment information, which are limited in their ability to classify classes of non-coding RNAs (ncRNAs). To address this, we developed CoRAL, a machine learning-based approach for classification of RNA molecules. CoRAL uses biologically interpretable features including fragment length, cleavage specificity, and antisense transcription to distinguish between different ncRNA classes. We evaluated CoRAL using genome-wide small RNA sequencing (smRNA-seq) datasets from two human tissue types (brain and skin [GSE31037]), and were able to classify six different types of RNA transcripts with 79~80% accuracy in cross-validation experiments, and with 71~73% accuracy when CoRAL uses one tissue type for training and the other as validation. Analysis by CoRAL revealed that long intergenic ncRNAs, small cytoplasmic RNAs, and small nuclear RNAs show more tissue specificity, while microRNAs, small nucleolar, and transposon-derived RNAs are highly discernible and consistent across the two tissue types. The ability to consistently annotate loci across tissue types demonstrates the potential of CoRAL to characterize ncRNAs using smRNA-seq data in less characterized organisms.
2013-07-07 | GSE43335 | GEO
Project description:Coral reefs are based on the symbiotic relationship between corals and photosynthetic dinoflagellates of the genus Symbiodinium. We followed gene expression of coral larvae of Acropora palmata and Montastraea faveolata after exposure to Symbiodinium strains that differed in their ability to establish symbioses. We show that the coral host transcriptome remains almost unchanged during infection by competent symbionts, but is massively altered by symbionts that fail to establish symbioses. Our data suggest that successful coral-algal symbioses depend mainly on the symbionts' ability to enter the host in a stealth manner rather than a more active response from the coral host.
2009-04-01 | GSE14923 | GEO