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Metabolomics,Unknown,Transcriptomics,Genomics,Proteomics

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Characterization of a Medicago truncatula P450 monooxygenase mutant

ABSTRACT: The aim of the experiment was to characterise a P450 monooxygenase mutant involved in the biosynthetic pathway of haemolytic saponins. Saponins are a group of glycosidic compounds with an antimicrobial function. The gene CYP716A12 is responsible for an early step in saponin biosythesis. Transcriptome analysis of a CYP716A12 mutant was performed to investigate its function. 6 samples were used in the experiment: 3 biological replicates of CYP716A12 mutant plants and 3 biological replicates of wild-type plants.

ORGANISM(S): Medicago truncatula

SUBMITTER: Ornella Calderini

PROVIDER: E-GEOD-22835 | biostudies-arrayexpress |

REPOSITORIES: biostudies-arrayexpress

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Characterization of a Medicago truncatula P450 monooxygenase mutant

Project description:The aim of the experiment was to characterise a P450 monooxygenase mutant involved in the biosynthetic pathway of haemolytic saponins. Saponins are a group of glycosidic compounds with an antimicrobial function. The gene CYP716A12 is responsible for an early step in saponin biosythesis. Transcriptome analysis of a CYP716A12 mutant was performed to investigate its function.

2010-12-29 | GSE22835 | GEO

Molecular analysis of heterosis in alfalfa

Project description:The aim of the experiment was to investigate the transcriptome changes in a double hybrid of alfala. The transcriptomes of a double hybrid (B2xB5) was compared to the two parental lines. 9 samples were used in the experiment, 3 biologcal replicates of the double hybrid and two parental lines.

2010-12-29 | E-GEOD-25034 | biostudies-arrayexpress

Transcriptome profiling of irg1 mutant leaf of Medicago truncatula

Project description:To gain a molecular understanding of the loss-of-function mutation of a transcription factor involved in leaf morphogenesis impacts symmetric cuticular wax loading in M. truncatula, we compared the transcript profiles of wild-type R108 and three independent irg1/palm1 homozygous null mutant lines (irg1-1, irg1-2, and irg1-5).

2012-03-01 | E-MEXP-3190 | biostudies-arrayexpress

RNA-sequencing analysis of NGN3-GFP positive and negative cells purified from differentiating human embryonic stem cells

Project description:NGN3-eGFP could be used to mark endocrine progenitor cells and their progeny in differentiating hESCs, suggesting that profiling analysis of NGN3-eGFP+ cells could lead to the discovery of novel gene participation. Six batches of NGN3-eGFP+ and NGN3-eGFP -cells purified by FACS from a reporter hES cell line cell cultures at stage 4 were pooled together, respectively. RNA-seq-based analysis of the two cell fractions identified a total of 3976 differentially expressed genes (P-value<0.05; Fold >2), of which 72% are enriched in NGN3-GFP+ cells. As expected, all the genes expressed in pancreatic progenitor cells are enriched in NGN3-eGFP-cells; while all endocrine-associated genes are enriched in NGN3-eGFP+ cells. Among the 3976 genes, 195 have potential transcriptional factor activity and 453 are potential non-coding RNA genes, most of which have not been well investigated in pancreatic endocrine cells. The gene ontology term M-bM-^@M-^Xintegral to membraneM-bM-^@M-^Y GO: 0016021 identified 1003 differentially expressed genes that encoded ion channels, adhesion molecules and transporters. NGN3-eGFP Postive and negtive cells were purified at stage 4 and subjected to RNA-sequncing

2014-09-12 | E-GEOD-54879 | biostudies-arrayexpress

Cytochrome P450 Monooxygenase Mediated Metabolic Utilization of Benzo(a)pyrene by Fungi

Project description:Cytochrome P450 Monooxygenase Mediated Metabolic Utilization of Benzo(a)pyrene by Fungi

| PRJNA480272 | ENA

Cytochrome P450 Monooxygenase Mediated Metabolic Utilization of Benzo(a)pyrene by Fungi

Project description:Soil dwelling Aspergillus fungi possess the versatile metabolic capability to utilize complex organic compounds which are toxic to humans, yet the mechanisms they employ remain largely unknown. Benzo(a)pyrene is a common carcinogenic contaminant, posing a significant concern for human health. Here, we report that Aspergillus fungi can degrade benzo(a)pyrene effectively. In Aspergillus nidulans, exposure to benzo(a)pyrene results in transcriptomic and metabolic changes associated with cellular growth and energy generation, implying that the fungus utilizes benzo(a)pyrene as a food. Importantly, we identify and characterize the conserved bapA gene encoding a cytochrome P450 monooxygenase that exerts the first step in the degradation of benzo(a)pyrene. We further demonstrate that the fungal NF-κB-type global regulators VeA and VelB are required for benzo(a)pyrene degradation in A. nidulans, which occurs through expression control of bapA in response to nutrient limitation. Our study illuminates fundamental knowledge of fungal benzo(a)pyrene metabolism and provides novel insights into enhancing bioremediation potential.

2018-07-10 | GSE116804 | GEO

Medicago truncatula

Project description:Characterization of a Medicago truncatula P450 monooxygenase mutant

| PRJNA127891 | ENA

RNA-Seq analysis of Medicago truncatula hairy root lines treated with methyl jasmonate

Project description:In hairy roots of the model legume Medicago truncatula the saponin production can be elicited by methyl jasmonate treatment. To identify genes potentially involved in saponin biosynthesis or its regulation we carried out transcript profiling by RNA-Seq of M. truncatula hairy roots treated with 100 μM of methyl jasmonate (dissolved in ethanol) for two or 24 hours. As control, M. truncatula hairy roots treated with an equivalent amount of ethanol were profiled.

2020-01-27 | E-MTAB-8697 | biostudies-arrayexpress

Dietary soyasaponin and prebiotics modulate intestinal health and function in the cleaner fish Ballan wrasse (Labrus bergylta)

Project description:This paper presents data from a 5-week feeding trial in which Ballan wrasse was fed either a reference diet, or the identical diet supplemented with i) the antinutrient soya saponin (0.7%) ii) a commercial prebiotic (Aquate™ SG, 0.4%) or iii) a combination of soya saponin and prebiotics. Blood, tissue and gut content from four separate intestinal segments were sampled from 6 fish per duplicate tank. Gut health and digestive functions were evaluated by various endpoint measurements employing biochemical and histomorphological tools as well as global gene expression profiling. No significant differences in fish growth were seen between the four dietary groups. Saponin supplementation, both alone and in combination with prebiotics, increased weight indices of two mid gut segments (IN2 and IN3) and decreased blood plasma glucose, cholesterol and total protein. Dry matter of intestinal content and activity of digestive enzymes were not affected by diet. Histomorphological analyses revealed clear structural alterations in the gut of fish fed saponin, both alone and in combination with prebiotics. The results indicated a progressing inflammation with increased infiltration by immune cells particularly into the distal parts of the intestine. Gene expression profiles obtained by RNA sequencing and quantitative PCR mirrored the histological and biochemical changes induced by the saponin load. The work has provided novel basic knowledge on the anatomy, digestive and immune function of the Ballan wrasse intestine. Additionally, the study demonstrated that Ballan wrasse gut health and digestive function may be markedly affected by diet composition.

2021-06-15 | GSE152475 | GEO

Analysis of gene expression changes when KIM1 is overexpressed in human PC3 cells

Project description:KIM1 was overexpressed using an adenoviral delivery system. Overexpression was confirmed post infection by RT-PCR and Western Blot analysis. Codelink Whole genome microarrays were used to analyse changes in expression resulting from KIM1 overexpression.

2015-07-09 | E-MTAB-3225 | biostudies-arrayexpress

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