Transcriptome profiling of Festuca arundinacea exposed to different glyphosate doses using the Wheat Affymetrix Gene Chip
Ontology highlight
ABSTRACT:
ORGANISM(S): Festuca arundinacea
SUBMITTER: Hikmet Budak
PROVIDER: E-MEXP-1655 | biostudies-arrayexpress |
REPOSITORIES: biostudies-arrayexpress
Similar Datasets
Project description:<br>Three Festuca species were grown in greenhouse in two replications for control and different dose applications of glyphosate. Plants were sprayed with two different rates (5% and 20%) of isopropylamine salt of glyphosate at three leaf stage. Affymetrix Wheat Genome array was used for transcriptional profiling.<br>
2008-08-01 | E-MEXP-1647 | biostudies-arrayexpress
Project description:Glyphosate is known to inhibit 5-enolpyruvylshikimate-3-phosphate synthase of the chorismate biosynthetic pathway, and chorismate is a precursor to aromatic amino acids, auxin, and many other secondary products. Although the perennial weed leafy spurge (Euphorbia esula L.) is considered glyphosate tolerant, glyphosate is often used as part of an integrated pest management program in non-cultivated ecosystems of North America. Part of its tolerance is attributed to escape through an abundance of underground adventitious buds (UABs). Sub-lethal concentrations of foliar applied glyphosate leads to new shoot growth from UABs that have a stunted and/or bushy phenotype after growth-inducing decapitation. To gain insights into glyphosateM-bM-^@M-^Ys impact on molecular mechanisms associated with the stunted and bushy phenotype, we obtained global transcriptome abundance using RNAseq from a subsequent generation of aerial shoots derived from crown buds of glyphosate-treated and -untreated leafy spurge. We further correlated transcript abundance to accumulation of shikimate and phytohormones from the same samples to elucidate interactions. Abundance of shikimate was similar in subsequent generations of aerial shoots generated from crown buds of treated and untreated plants and is likely not a direct factor leading to the stunted and bushy phenotype. However, the results do suggest that transcripts involved in auxin transport and signaling and crosstalk with other phytohormones likely play a role in the bushy phenotype. The results of this study provide some insights for identifying new targets for manipulation of plant growth and development. Transcriptome and metabolite profiling are obtained for aerial tissues derived from crown buds of foliar glyphosate-treated and control (2.24 or 0 kg/ha active ingredient glyphosate + 0.25% v/v surfactant) leafy spurge plants. Each experiment included 4 biological replicates.
2014-04-15 | E-GEOD-56509 | biostudies-arrayexpress
Project description:This submission contains the RNAseq data from a study of leafy spurge crown buds transitioning through a seasonal dormancy time course following glyphosate treatments where buds transitioned from paradoprmancy to endodormancy and then to ecodormancy. The sequences in this study were mapped to an assembled transcriptome built from sequences from this study along with sequences from : 1) A study of leafy spurge crown buds through a time course for paradormancy release induced by excision of the aerial portion of the shoot (Series GSE71317). 2) A study identical to this study but where leafy spurge plants were not treated with glyphosate (Series GSE71321). 3) A previously submitted study of leafy spurge shoots following treament with glyphosate was also used to assemble the transcriptome (Series GSE56509). This crown buds transitioning through a seasonal dormancy time course following a glyphosate treatment study has 4 biological replicates collected at each of the three dormancy states (paradormant, endodormant, and ecodormant).
2015-08-05 | E-GEOD-71406 | biostudies-arrayexpress
Project description:Glyphosate (GLY) is an effective antimetabolite that acts against the shikimate pathway 5-enolpyruvylshikimate 3-phosphate (EPSP) synthase, However, little is known about the genome-scale transcriptional responses of bacteria after glyphosate shock. To investigate further the mechanisms by which E. coli response to a glyphosate shock, a DNA-based microarray was used for transcriptional analysis of E. coli exposed to 200 mM glyphosate. RNA extracted from cells of E. coli K-12 JM109 cells after 4 h of growth to OD600 achieve 0.4, or cells after 200 mM glyphosate shock for 1 h when their OD600 achieved 0.4.
2011-07-21 | E-GEOD-30838 | biostudies-arrayexpress
Project description:Glyphosate is one of the most widely used herbicides globally. It acts by inhibiting an enzyme in an aromatic amino synthesis pathway specific to plants and microbes, leading to view that glyphosate poses no risk to other organisms. However, there is growing concern that glyphosate is associated with detrimental health effects in humans, and an ever-increasing body of evidence suggests that glyphosate affects other animals including pollinating insects such as bees. Although pesticides have long been considered a contributing factor in the decline of wild bee populations most research on bees has focussed on demonstrating and understanding the effects (particularly sublethal ones) of insecticides. To assess whether glyphosate poses a potential risk to bees we characterised the changes in survival, behaviour, digestive tract proteome and microbiome in the bumblebee Bombus terrestris after chronic exposure to field relevant doses of glyphosate alone and as part of the commercially available product RoundUp Optima+®. Regardless of source, changes in response to herbicide exposure in important cellular and physiological processes in the digestive tract of B. terrestris were observed, with the abundances of proteins associated with oxidative stress regulation, metabolism, cellular adhesion, the extracellular matrix, and various signalling pathways being altered. Interestingly, endocytosis, oxidative phosphorylation, the TCA cycle, and carbohydrate, lipid, and amino acid metabolism were differentially altered depending on whether the exposure source was glyphosate AI or RoundUp Optima+®. In addition, RoundUp Optima+®, but not the active ingredient glyphosate, impacted fungal diversity in the digestive tract microbiota. Our research provides new insights into the potential mode of action and consequences of glyphosate exposure at the molecular and cellular levels in bumblebees and highlights issues with current regulatory measures involving commercial formulations of pesticides where the impact of the co-formulants on non-target organisms are generally overlooked.
2023-07-01 | PXD036578 | Pride
Project description:Total transcript amplification (TTA) from single eukaryotic cells for transcriptome analysis is established, but TTA from a single prokaryotic cell presents additional challenges with much less starting material and lack of poly(A)-tails. We described, here, a novel method for single bacterium TTA, using a Burkholderia thailandensis model exposed to subinhibitory concentration of the antibacterial agent, glyphosate. Utilizing B. thialandensis microarray to assess the TTA method showed little gene bias (< 2 fold-change) and absence (~5-6%) when compared to the larger scale non-amplified RNA samples. B. thailandensis genes important to possibly recuperate and balance the intracellular amino acid pool were induced (or repressed) by the aromatic amino acid biosynthesis inhibitor, glyphosate. We validated our single-cell microarray data at the multi-cells and single-cell levels with lacZ and gfp reporter-gene fusions, respectively. This novel method will rejuvenate and expand the prokaryotic transcriptomic field. Two identical cultures of B. thailandensis wildtype strain E264 were grown in 1x M9 minimal medium supplemented with 1% Brij-58 and 20 mM glucose (MG) to mid-log phase. One culture was induced by final concentration of 0.01% (w/v) glyphosate for 30 minutes. Total RNA was then purified from B. thailandensis uninduced and induced samples, converted to cDNA and hybridized onto B. thailandensis 70mer triplicate array
2010-08-05 | E-GEOD-23419 | biostudies-arrayexpress
Project description:Glyphosate (GLY) is an effective antimetabolite that acts against the shikimate pathway 5-enolpyruvylshikimate 3-phosphate (EPSP) synthase, However, little is known about the genome-scale transcriptional responses of bacteria after glyphosate shock. To investigate further the mechanisms by which E. coli response to a glyphosate shock, a DNA-based microarray was used for transcriptional analysis of E. coli exposed to 200 mM glyphosate.
2011-07-22 | GSE30838 | GEO
Project description:This submission contains the RNAseq data from a study of leafy spurge crown buds transitioning through a seasonal dormancy time course where buds transitioned from paradoprmancy to endodormancy and then to ecodormancy. The sequences in this study were mapped to an assembled transcriptome built from sequences from this study along with sequences from : 1) A study of leafy spurge crown buds through a time course for paradormancy release induced by excision of the aerial portion of the shoot (Series GSE71317). 2) A study identical to this study but where leafy spurge plants were first treated with glyphosate (Series GSE71406). 3) A previously submitted study of leafy spurge shoots following treatment with glyphosate was also used to assemble the transcriptome (Series GSE56509). This crown buds transitioning through a seasonal dormancy time course study has 4 biological replicates collected at each of the three dormancy states (paradormant, endodormant, and ecodormant).
2015-08-05 | E-GEOD-71321 | biostudies-arrayexpress
Project description:Background: Herbicides are environmental contaminants that have gained much attention due to the potential hazards they pose to human health. Glyphosate, the active ingredient in many commercial herbicides, is the most heavily applied herbicide worldwide. The recent rise in glyphosate application to corn and soy crops correlates positively with increased death rates due to Alzheimer's disease and other neurodegenerative disorders. Glyphosate has been shown to cross the blood-brain barrier in in vitro models, but has yet to be verified in vivo. Additionally, reports have shown that glyphosate exposure increases pro-inflammatory cytokines in blood plasma, particularly TNFα. Methods: Here, we examined whether glyphosate infiltrates the brain and elevates TNFα levels in 4-month-old C57BL/6J mice. Mice received either 125, 250, or 500 mg/kg/day of glyphosate, or a vehicle via oral gavage for 14 days. Urine, plasma, and brain samples were collected on the final day of dosing for analysis via UPLC-MS and ELISAs. Primary cortical neurons were derived from amyloidogenic APP/PS1 pups to evaluate in vitro changes in Aβ40-42 burden and cytotoxicity. RNA sequencing was performed on C57BL/6J brain samples to determine changes in the transcriptome. Results: Our analysis revealed that glyphosate infiltrated the brain in a dose-dependent manner and upregulated TNFα in both plasma and brain tissue post-exposure. Notably, glyphosate measures correlated positively with TNFα levels. Glyphosate exposure in APP/PS1 primary cortical neurons increases levels of soluble Aβ40-42 and cytotoxicity. RNAseq revealed over 200 differentially expressed genes in a dose-dependent manner and cell-type-specific deconvolution analysis showed enrichment of key biological processes in oligodendrocytes including myelination, axon ensheathment, glial cell development, and oligodendrocyte development. Conclusions: Collectively, these results show for the first time that glyphosate infiltrates the brain, elevates both the expression of TNFα and soluble Aβ, and disrupts the transcriptome in a dose-dependent manner, suggesting that exposure to this herbicide may have detrimental outcomes regarding the health of the general population.
2024-01-15 | GSE253299 | GEO
Project description:Transcriptomic profiling of glyphosate-treated seedlings comparing Arabidopsis wild-type (Ler) versus gcn2 mutant line
2015-03-10 | GSE56146 | GEO