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
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Project description:Mitotic chromosome binding predicts transcription factor properties in interphase [ATAC-Seq]
| PRJNA490288 | ENA
Project description:Mitotic chromosome binding predicts transcription factor properties in interphase [ChIP-Seq]
| PRJNA490289 | ENA
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: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
Project description:One day cold treatment of wheat (Triticum aestivum L.) lines Chinese Spring, Cheyenne and two 5A chromosome substitution lines of Chinese Spring, Chinese Spring(Cheyenne 5A) and Chinese Spring(Spelta 5A)
2016-10-22 | E-MTAB-3937 | biostudies-arrayexpress
Project description:Body weight in lower animals and humans is highly stable despite a very large flux in energy intake and expenditure over time. Conversely, the existence of higher-than-average variability in weight may indicate a disruption in the mechanisms responsible for homeostatic weight regulation.In a sample chosen for weight-gain proneness, we evaluated whether weight variability over a 6-mo period predicted subsequent weight change from 6 to 24 mo.A total of 171 nonobese women were recruited to participate in this longitudinal study in which weight was measured 4 times over 24 mo. The initial 3 weights were used to calculate weight variability with the use of a root mean square error approach to assess fluctuations in weight independent of trajectory. Linear regression analysis was used to examine whether weight variability in the initial 6 mo predicted weight change 18 mo later.Greater weight variability significantly predicted amount of weight gained. This result was unchanged after control for baseline body mass index (BMI) and BMI change from baseline to 6 mo and for measures of disinhibition, restrained eating, and dieting.Elevated weight variability in young women may signal the degradation of body weight regulatory systems. In an obesogenic environment this may eventuate in accelerated weight gain, particularly in those with a genetic susceptibility toward overweight. Future research is needed to evaluate the reliability of weight variability as a predictor of future weight gain and the sources of its predictive effect. The trial on which this study is based is registered at clinicaltrials.gov as NCT00456131.
| S-EPMC4625595 | biostudies-literature
Project description:AimsA prolonged corrected QT interval (QTc) ≥500 ms is associated with high all-cause mortality in hospitalized patients. We aimed to explore any difference in short- and long-term mortality in patients with QTc ≥500 ms compared with patients with QTc <500 ms after adjustment for comorbidity and main diagnosis.Methods and resultsPatients with QTc ≥500 ms who were hospitalized at Telemark Hospital Trust, Norway between January 2007 and April 2014 were identified. Thirty-day and 3-year all-cause mortality in 980 patients with QTc ≥500 ms were compared with 980 patients with QTc <500 ms, matched for age and sex and adjusting for Charlson comorbidity index (CCI), previous admissions, and main diagnoses. QTc ≥500 ms was associated with increased 30-day all-cause mortality [hazard ratio (HR) 1.90, 95% confidence interval (CI) 1.38-2.62; P < 0.001]. There was no significant difference in mortality between patients with QTc ≥500 ms and patients with QTc <500 ms who died between 30 days and 3 years; 32% vs. 29%, P = 0.20. Graded CCI was associated with increased 3-year all-cause mortality (CCI 1-2: HR 1.62, 95% CI 1.34-1.96; P < 0.001; CCI 3-4: HR 2.50, 95% CI 1.95-3.21; P < 0.001; CCI ≥5: HR 3.76, 95% CI 2.85-4.96; P < 0.001) but was not associated with 30-day all-cause mortality.ConclusionQTc ≥500 ms is a powerful predictor of short-term mortality overruling comorbidities. QTc ≥500 ms also predicted long-term mortality, but this effect was mainly caused by the increased short-term mortality. For long-term mortality, comorbidity was more important.
| S-EPMC6680365 | biostudies-literature