Implications of transcriptomics, proteomics and metabolomics analysis of maize seeds for food safety
Ontology highlight
ABSTRACT:
ORGANISM(S): Zea mays
PROVIDER: GSE15853 | GEO | 2009/12/31
SECONDARY ACCESSION(S): PRJNA117073
REPOSITORIES: GEO
Similar Datasets
Project description:In this study we used non-targeted molecular profiling to provide insight into the extent of variation in the maize transcriptome, proteome and metabolome by analyzing replicas of two genetically modified and one isogenic maize genotype. Three white maize lines, the transgenic commercial Bt hybrid line DKC78-15 Bt (event MON810 from Monsanto), the transgenic commercial Roundup Ready (RR) line DKC78-35R (event NK603 from Monsanto) and its respective control line CRN 3505 (conventional from Monsanto) were grown in three consecutive years, and in two or three different locations in South Africa.
2010-05-16 | E-GEOD-15853 | biostudies-arrayexpress
Project description:Unintended effects of genetically modified (GM) crops may pose safety issues. Omics techniques provide researchers with useful tools to assess such unintended effects. Proteomics and metabolomics analyses were performed for three GM maize varieties, 2A-7, CC-2, and 2A-7×CC-2 stacked transgenic maize, and the corresponding non-GM parent Zheng58.Proteomics revealed 120, 271 and 135 maize differentially expressed proteins (DEPs) in the 2A-7/Zheng58, CC-2/Zheng58 and 2A-7×CC-2/Zheng58 comparisons, respectively. Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway enrichment analysis showed that most DEPs participated in metabolic pathways and the biosynthesis of secondary metabolite. Metabolomics revealed 179, 135 and 131 differentially accumulated metabolites (DAMs) in the 2A-7/Zheng58, CC-2/Zheng58 and 2A-7×CC-2/Zheng58 comparisons, respectively. Based on KEGG enrichment analysis, most DAMs are involved in the biosynthesis of secondary metabolite and metabolic pathways. According to integrated proteomics and metabolomics analysis, the introduction of exogenous EPSPS did not affect the expression levels of six other enzymes or the abundance of seven metabolites involved in the shikimic acid pathway in CC-2 and 2A-7×CC-2 seeds. Six co-DEPs annotated by integrated proteomics and metabolomics pathway analysis were further analyzed by qRT-PCR.This study successfully employed integrated proteomic and metabolomic technology to assess unintended changes in maize varieties. The results suggest that GM and gene stacking do not cause significantly unintended effects.
| S-EPMC8189116 | biostudies-literature
Project description:We study the expression level change of candidate genes associated with seed filling in maize, through RNA-seq for maize seeds in different filling stages. The results show that the change of the expression of these candidate genes would lead to the change of grain filling trajectory.
2019-05-09 | GSE130930 | GEO
Project description:The metabolic response of maize source leaves to low nitrogen supply was analyzed in maize seedlings by parallel measurements of transcriptome and metabolome profiling. Inbred lines A188 and B73 were cultivated under controlled growth chamber conditions and supplied with either sufficient (15mM) or limiting (0.15mM) nitrate supply. Leaf lamina material was harvested at day 20 and day 30 after germination with the fifth and sixth leaf representing the main source leaf respectively. Four replicates were collecetd from individual plants for each combination of genotype, growth stage and nitrogen treatment. The leaf material was frozen, homogenised and aliquoted for transcriptome and metabolome analysis. The molecular data was further supplemented by phenotypic characterisation of the maize seedlings under investigation. Limited availability of nitrogen caused strong shifts in the metabolite profile of leaves. The transcriptome was less affected by the nitrogen stress but showed strong genotype and age dependent patterns. Nitrogen starvation initiated the selective down-regulation of processes involved in nitrate reduction and amino acid assimilation; ammonium assimilation related transcripts on the other hand were not influenced. Carbon assimilation related transcripts were characterized by high transcriptional coordination and general down-regulation under low nitrogen conditions. Nitrogen deprivation caused a slight accumulation of starch, but also directed increased amounts of carbohydrates into the cell wall and secondary metabolites. The decrease in N availability also resulted in accumulation of phosphate and by strong down-regulation of genes usually involved in phosphate starvation response, underlining the great importance of phosphate homeostasis control under stress conditions. Maize inbred lines A188 and B73 were cultivated in pots containing nutrient poor peat soil under the controlled conditions of a growth chamber. The plants were fertilized with modified Hoagland solutions containing either 15mM (high N) or 0.15mM nitrate (low N). Source leaf lamina were harvested at day 20 and day 30 after start of germination for parallel analysis of transcriptome and metabolome profiles. The molecular data is further supplemented by phenotypic characterization of the maize seedlings under investigation.
2012-11-01 | E-GEOD-40678 | biostudies-arrayexpress
Project description:This study looked for signals produced in UV-B irradiated leaves, and possibly induced in shielded leaves, that modulate physiological responses in maize. Transcriptome and proteomics profiling tracked changes in exposed and shielded organs. Metabolic profiling was examined for signaling molecules. Exposure of just the top leaf substantially alters the transcriptome of both irradiated and shielded organs, with greater changes as an additional 1-2 leaves are irradiated. Transcriptome, proteome and metabolome changes are UV-B regulated in shielded organs. Early steps in signal transduction and possible signal molecules are identified utilizing a time course experiment. Keywords: UVB, maize, leaves, ears
2011-02-01 | GSE25038 | GEO
Project description:Foodborne bacteria interconnect food and human health. Despite significant progress in food safety regulation, bacterial contamination is still a serious public health concern and the reason for significant commercial losses. The screening of the microbiome in meals is one of the main aspects of food production safety influencing the health of the end-consumers. Our research provides an overview of proteomics findings in the field of food safety made over the last decade. It was believed that proteomics offered an accurate snapshot of the complex networks of the major biological machines called proteins. The proteomic methods for the detection of pathogens were armed with bioinformatics algorithms, allowing us to map the data onto the genome and transcriptome. The mechanisms of the interaction between bacteria and their environment were elucidated with unprecedented sensitivity, specificity, and depth. Using our web-based tool ScanBious for automated publication analysis, we analyzed over 48,000 scientific articles on antibiotic and disinfectant resistance and highlighted the benefits of proteomics for the food safety field. The most promising approach to studying safety in food production is the combination of classical genomic and metagenomic approaches and the advantages provided by proteomic methods with the use of panoramic and targeted mass spectrometry.
| S-EPMC9966529 | biostudies-literature
Project description:To investigate the developmental gradient of the third maize leaf, the light exposed area of the leaf (corresponding to 18cm of leaf) and 2cm shaded by the sheath were sampled in ten slices. Four replicates were collected, immediately shock frozen in liquid nitrogen and subsequently cut into 2cm slices. At least 10 plants were pooled for each biological replicate. We have systematically analyzed a developmental gradient of the third maize leaf from the point of emergence into the light to the tip in ten continuous leaf slices to study organ development and physiological and biochemical functions. Transcriptome analysis, oxygen sensitivity of photosynthesis, delta-13C values, and photosynthetic rate measurements showed that the maize leaf undergoes a sink to source transition without an intermediate phase of C3 photosynthesis or operation of a photorespiratory carbon pump. Metabolome and transcriptome analysis, chlorophyll and protein measurements, as well as dry weight determination showed continuous gradients for all analyzed items. The absence of binary on-off switches and regulons pointed to a morphogradient along the leaf as the determining factor of developmental stage. Analysis of transcription factors for differential expression along the leaf gradient defined a list of putative regulators orchestrating the sink-to-source transition and establishment of C4 photosynthesis. Finally, transcriptome and metabolome analysis, as well as enzyme activity measurements, and absolute quantification of selected metabolites revised the current model of maize C4 photosynthesis. All datasets are included within the publication to serve as a resource for maize leaf systems biology. For the transcriptional analysis, the goal of the study was to (i) identify whether the leaf contains binary switches for genes involved in photosynthesis, (ii)characterize the patterns of gene expression in the leaf, (iii) provide independent validation of maize leaf expression experiments published in Li et al. (2011) and (iv) determine transcripts co-expressed with key transcripts of C4 photosynthesis. To this end, changed transcripts were determined by ANOVA and characterized by K-means and hierachical clustering.
2011-12-21 | GSE33861 | GEO
Project description:To investigate the developmental gradient of the third maize leaf, the light exposed area of the leaf (corresponding to 18cm of leaf) and 2cm shaded by the sheath were sampled in ten slices. Four replicates were collected, immediately shock frozen in liquid nitrogen and subsequently cut into 2cm slices. At least 10 plants were pooled for each biological replicate. We have systematically analyzed a developmental gradient of the third maize leaf from the point of emergence into the light to the tip in ten continuous leaf slices to study organ development and physiological and biochemical functions. Transcriptome analysis, oxygen sensitivity of photosynthesis, delta-13C values, and photosynthetic rate measurements showed that the maize leaf undergoes a sink to source transition without an intermediate phase of C3 photosynthesis or operation of a photorespiratory carbon pump. Metabolome and transcriptome analysis, chlorophyll and protein measurements, as well as dry weight determination showed continuous gradients for all analyzed items. The absence of binary on-off switches and regulons pointed to a morphogradient along the leaf as the determining factor of developmental stage. Analysis of transcription factors for differential expression along the leaf gradient defined a list of putative regulators orchestrating the sink-to-source transition and establishment of C4 photosynthesis. Finally, transcriptome and metabolome analysis, as well as enzyme activity measurements, and absolute quantification of selected metabolites revised the current model of maize C4 photosynthesis. All datasets are included within the publication to serve as a resource for maize leaf systems biology. For the transcriptional analysis, the goal of the study was to (i) identify whether the leaf contains binary switches for genes involved in photosynthesis, (ii)characterize the patterns of gene expression in the leaf, (iii) provide independent validation of maize leaf expression experiments published in Li et al. (2011) and (iv) determine transcripts co-expressed with key transcripts of C4 photosynthesis. To this end, changed transcripts were determined by ANOVA and characterized by K-means and hierachical clustering. Four replicates were collected for each of the ten consecutive leaf slices resulting in 40 one color arrays. Slice 1 represents the tip of the leaf, slice 10 the lowermost slice which is shaded by the sheath with all slices in between consecutively numbered.
2011-12-21 | E-GEOD-33861 | biostudies-arrayexpress
Project description:This study looked for signals produced in UV-B irradiated leaves, and possibly induced in shielded leaves, that modulate physiological responses in maize. Transcriptome and proteomics profiling tracked changes in exposed and shielded organs. Metabolic profiling was examined for signaling molecules. Exposure of just the top leaf substantially alters the transcriptome of both irradiated and shielded organs, with greater changes as an additional 1-2 leaves are irradiated. Transcriptome, proteome and metabolome changes are UV-B regulated in shielded organs. Early steps in signal transduction and possible signal molecules are identified utilizing a time course experiment. Keywords: UVB, maize, leaves, ears Compared irradiated leaves in a time course, irradiated leaves versus shielded leaves, and shielded ears on plants with irradiated leaves. Also compared different number of leaves being irradiated. Spike-in controls were included.
2011-02-01 | E-GEOD-25038 | biostudies-arrayexpress
Project description:The metabolic response of maize source leaves to low nitrogen supply was analyzed in maize seedlings by parallel measurements of transcriptome and metabolome profiling. Inbred lines A188 and B73 were cultivated under controlled growth chamber conditions and supplied with either sufficient (15mM) or limiting (0.15mM) nitrate supply. Leaf lamina material was harvested at day 20 and day 30 after germination with the fifth and sixth leaf representing the main source leaf respectively. Four replicates were collecetd from individual plants for each combination of genotype, growth stage and nitrogen treatment. The leaf material was frozen, homogenised and aliquoted for transcriptome and metabolome analysis. The molecular data was further supplemented by phenotypic characterisation of the maize seedlings under investigation. Limited availability of nitrogen caused strong shifts in the metabolite profile of leaves. The transcriptome was less affected by the nitrogen stress but showed strong genotype and age dependent patterns. Nitrogen starvation initiated the selective down-regulation of processes involved in nitrate reduction and amino acid assimilation; ammonium assimilation related transcripts on the other hand were not influenced. Carbon assimilation related transcripts were characterized by high transcriptional coordination and general down-regulation under low nitrogen conditions. Nitrogen deprivation caused a slight accumulation of starch, but also directed increased amounts of carbohydrates into the cell wall and secondary metabolites. The decrease in N availability also resulted in accumulation of phosphate and by strong down-regulation of genes usually involved in phosphate starvation response, underlining the great importance of phosphate homeostasis control under stress conditions.
2012-11-01 | GSE40678 | GEO