Gene expression profiling predicts processing properties in short-term imbibition of wheat
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PROVIDER: PRJNA480650 | ENA |
REPOSITORIES: ENA
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Project description:Objective: Germination of wheat maximizes phytochemical content and antioxidant activity while altering chemical composition, gluten content, and pasting properties. We previously reported marked changes in gene expression in soybean prior to germination before the radicle had grown from a seed. The present study investigated whether imibibition induces similar changes in wheat. Methods: Changes in gene expression profiles of wheat during short-term imbibition (0, 16, and 24 h) were evaluated by DNA microarray analysis. Gene Ontology (GO) analysis was carried out to categorize the function of genes with altered expression. The expression of genes encoding enzymes associated with starch breakdown was evaluated by quantitative real-time PCR, and changes in enzymatic activity were assessed with functional assays. Pasting properties of flour made from wheat seeds imbibed for different times were examined with a Rapid Visco Analyzer. The protein profile was determined by sodium dodecyl sulfate polyacrylamide gel electrophoresis, and gluten content was quantified. Results: The GO analysis revealed that genes related to cellulose and cell wall synthesis were upregulated by imbibition for 16 h whereas those associated with polysaccharide catabolism and nucleosome assembly were upregulated in the subsequent 8 h. α-Amylase expression was highest after 24-h imbibition, with a corresponding increase in enzymatic activity. The pasting properties of wheat flour decreased when seeds were imbibed for over 16 h. Gluten was not degraded until 48 h imbibition. Conclusion: Short-term imbibition of wheat can produce a new type of starch with improved physical and functional properties that may be more appealing to consumers.
2018-09-01 | GSE116933 | GEO
Project description:Mitotic chromosome binding predicts transcription factor properties in interphase
| PRJNA490284 | ENA
Project description:Mitotic chromosome binding predicts transcription factor properties in interphase [ChIP-Seq]
| PRJNA490289 | ENA
Project description:Mitotic chromosome binding predicts transcription factor properties in interphase [ATAC-Seq]
| PRJNA490288 | ENA
Project description:<p>During seed imbibition, lipids are engaged in membrane reorganization while facing free radical-mediated oxidative injury. In the present work, we explored changes in lipid components at different timepoints of imbibition (0.5, 2, 4, 6, and 8 h) in the legume Medicago truncatula, by combining biochemical approaches with targeted lipidomics and untargeted metabolomics. ROS and RNS (reactive oxygen and nitrogen species) accumulation was observed throughout the tested timepoints whereas lipid peroxidation increased at 4 h of imbibition. The seed response to oxidative damage was evidenced by a significant increase in tocopherols starting from 0.5 h of imbibition as well as by the reduction in total thiol content occurring at 2 h of imbibition. Since under physiological conditions, the proper functions of the cell membranes are strongly dependent on the qualitative and quantitative balance of fatty acid residues in phospholipids, the investigation was expanded to the fatty acid cohort of Medicago truncatula seeds. Total saturated fatty acids (SFAs), monounsaturated fatty acids (MUFAs), polyunsaturated fatty acids (PUFAs), omega-3 and omega-6 fatty acids showed fluctuations during seed imbibition. The most remarkable finding was the profile of the omega-3 PUFA docosopentaenoic acid (DPA, 7 cis, 10 cis, 13 cis, 16 cis, 19 cis-22:5) that showed a peak (up to 1.0% of the total fatty acid content) at 0.5 and 8 h of imbibition, respectively, concomitant with the peaks observed in tocopherol levels. It is possible that the observed changes in DPA alter the physical properties of membranes, as reported in animal cells, triggering signaling pathways relevant for the cell defence against oxidative injury. Furthermore, the content and balance between tocopherols and PUFAs is regarded as a determinant of storage stability. No enhancement in trans-fatty acids occurred throughout imbibition, suggesting for a proper antioxidant response carried by the seed. Fatty acids profiles were integrated with data from untargeted metabolomics showing changes in lipid sub-pathways, among which fatty acid amide, lyso-phospholipids and phospholipid metabolism. The emerging lipid profiles and dynamics are discussed in view of the overall imbibition damage generated during M. truncatula seed imbibition.</p>
2019-10-14 | MTBLS181 | MetaboLights
Project description:In order to study the role of SlLBD40 and WRKY37 in seed germination, we established two gene knockout lines respectively. We then used RNA-seq data from seeds 6 h after imbibition of WT and two gene knockout lines for gene expression profiling.
2023-09-01 | GSE232485 | GEO
Project description:For production of soy-foods or supplements, imbibition of soybean seeds in the water is required step for generation of tofu, soy-milk, and other soy-products. With an aim to get new insight into effects of different imbibition temperature (4, 25, and 55℃), this study conducted integrated proteomics and metabolomics analysis of soybean seeds. For total proteome analysis, we applied TMT labeling based quantitative proteomics combined to FASP (Filter-Aided Sample Preparation) with high-throughput LC-MS/MS. A total of 2,616 proteins were identified out of which 801 proteins showed significantly difference of protein abundance (≥1.5 fold change, Benjamini-Hochberg FDR <0.05) among 4, 25, and 55℃ imbibition seeds. Functional analysis of identified proteins showed an increased abundance of proteins functioning as glycosyl hydrolase enzymes such as beta-glucosidase, alpha and beta-galactosidase, and alpha-mannosidase, or protease, and PTMs related enzymes as well. UPLC TOF-MS analysis showed around 20 fold increase in isoflavone aglycones (daidzein and genistein) while isoflavone glycosides (daidzin and genistin) were decreased in 55℃ imbibition seed, in agreement with proteomics results which we assume positively related to increase abundance of glycosyl hydrolase. A metabolomics analysis revealed 64 metabolites were significantly altered, for example, various free amino acids showed accumulation patterns by increased abundance of various protease enzymes and further confirmed the accumulation of isoflavone aglycones and degradation of raffinose and stachyose in 55℃ imbibition seeds. Based on these results, we recommend the use of 55℃ for soybean seed imbibition to increase the quality of soy-food products.
2020-09-25 | PXD014152 | Pride
Project description:In the analysis of peripheral blood gene expression, timely processing of samples is essential to ensure that measurements reflect in vivo biology, rather than ex vivo sample processing variables. The effect of processing delays on global gene expression patterns in peripheral blood mononuclear cells (PBMC) was assessed by isolating and stabilizing PBMC-derived RNA from three individuals either immediately after phlebotomy or following a 4 hour delay. RNA was labeled using NuGEN Ovation labeling and probed using the Affymetrix HG U133plus 2.0 GeneChip®. Comparison of gene expression levels (p<0.05 and ≥ 2-fold expression change) identified 327 probe sets representing genes with increased expression and 46 indicating decreased expression after 4 hours. The trends in expression patterns associated with delayed processing were also apparent in an independent set of 276 arrays of RNA from human PBMC samples with varying processing times. These data indicate that the time between sample acquisition, initiation of processing, and when the RNA is stabilized should be a prime consideration when designing protocols for translational studies involving PBMC gene expression analysis. Keywords: Technical comparison
2011-03-22 | GSE21039 | GEO
Project description: Not available
| S-EPMC4091227 | biostudies-literature
Project description:In the analysis of peripheral blood gene expression, timely processing of samples is essential to ensure that measurements reflect in vivo biology, rather than ex vivo sample processing variables. The effect of processing delays on global gene expression patterns in peripheral blood mononuclear cells (PBMC) was assessed by isolating and stabilizing PBMC-derived RNA from three individuals either immediately after phlebotomy or following a 4 hour delay. RNA was labeled using NuGEN Ovation labeling and probed using the Affymetrix HG U133plus 2.0 GeneChip®. Comparison of gene expression levels (p<0.05 and ? 2-fold expression change) identified 327 probe sets representing genes with increased expression and 46 indicating decreased expression after 4 hours. The trends in expression patterns associated with delayed processing were also apparent in an independent set of 276 arrays of RNA from human PBMC samples with varying processing times. These data indicate that the time between sample acquisition, initiation of processing, and when the RNA is stabilized should be a prime consideration when designing protocols for translational studies involving PBMC gene expression analysis. Keywords: Technical comparison 3 subjects, 3 samples each. First sample is prepared immediately, 2nd after 2 hour delay and last after a 4 hour delay.
2011-03-22 | E-GEOD-21039 | biostudies-arrayexpress