Tef Zinc levels
Ontology highlight
ABSTRACT:
INSTRUMENT(S): Illumina HiSeq 2500
ORGANISM(S): Eragrostis tef
SUBMITTER: Matthew Milner
PROVIDER: E-MTAB-8827 | biostudies-arrayexpress |
REPOSITORIES: biostudies-arrayexpress
Similar Datasets
Project description:Alkaline soils such as those found in some Mediterranean areas typically have a low phosphorus (P) and zinc (Zn) phytoavailability that detracts from plant growth and yield. We examined the effects of P and Zn fertilization individually and in combination on growth, yield and grain protein content in maize grown in pots filled with three Mediterranean soils. P and Zn translocation was impaired, and yield reduced by 8–85%, in plants treated with Zn or P alone. In contrast, joint fertilization with P and Zn enhanced translocation to grain and nutrient use efficiency, thereby increasing plant growth, yield (31–121%) and grain Zn availability. Fertilization with P or Zn also influenced the abundance of specific proteins affecting grain quality (viz., storage, lys-rich and cell wall proteins), which were more abundant in mature grains from plants fertilized with Zn alone and, to a lesser extent, P + Zn.
2021-09-09 | PXD021503 | Pride
Project description:We conducted a genome-wide transcriptomic analysis in soybean leaves and roots treated with zinc (Zn) deficiency using RNA sequencing (RNA-seq) technology. Two biological replicates of RNA-seq were included for Zn-sufficient leaves (ZSL), Zn-deficient leaves (ZDL), Zn-sufficient roots (ZSR), and Zn-deficient roots (ZDR). Therefore a total of eight libraries were constructed. Using a 2-fold change and a P-value ≤0.05 as the cut-off for selecting the differentially expressed transcripts, we globally identified Zn-deficiency responsive genes. At least 20 genes that are potentially involved Zn homeostasis were significantly changed by Zn deficiency, including 7 ZIP (ZRT, IRT-related protein) transporter genes, 3 nicotianamine synthase genes, and 7 metallothionein genes. At least 48 genes encoding likely Zn-binding proteins were found to be responsive to Zn deficiency in leaves or roots. Eighty-five transcription factor genes were significantly changed by Zn deficiency in leaves or roots, including 5 bZIP members and 10 Golden 2-like members. In addition, some other groups of genes which are possibly related to reactive oxygen species scavenging, calcium and hormone signaling, and protein phosphorylation and dephosphorylation also differentially expressed under Zn deficiency.
2019-03-30 | GSE111799 | GEO
Project description:Zinc is indispensable for the catalytic activity and structural stability of many proteins, and its deficiency can have severe consequences for microbial growth in natural and industrial environments. For example, Zn depletion in wort negatively affects beer fermentation and quality. Several studies have investigated yeast adaptation to low Zn supply, but were all performed in batch cultures, where specific growth rate depends on Zn availability. The transcriptional responses to growth-rate and Zn availability are then intertwined, which obscures result interpretation. In the present study, transcriptional responses of Saccharomyces cerevisiae to Zn availability were investigated at a fixed specific growth rate under Zn limitation and excess in chemostat culture. To investigate the context-dependency of this transcriptional response, yeast was grown under several chemostat regimes resulting in various carbon (glucose), nitrogen (ammonium) and oxygen supplies. A robust set of genes that responded consistently to Zn limitation was identified and enabled the definition of a Zn-specific Zap1 regulon comprising of 26 genes and characterized by a broader ZRE consensus (MHHAACCBYNMRGGT) than so far described. Most surprising was the Zn-dependent regulation of genes involved in storage carbohydrate metabolism. Their concerted down-regulation was physiologically relevant as revealed by a substantial decrease in glycogen and trehalose cellular content under Zn limitation. An unexpectedly large amount of genes were synergistically or antagonistically regulated by oxygen and Zn availability. This combinatorial regulation suggested a more prominent involvement of Zn in mitochondrial biogenesis and function than hitherto identified. Experiment Overall Design: Zinc is indispensable for the catalytic activity and structural stability of many proteins, and its deficiency can have severe consequences for microbial growth in natural and industrial environments. For example, Zn depletion in wort negatively affects beer fermentation and quality. Several studies have investigated yeast adaptation to low Zn supply, but were all performed in batch cultures, where specific growth rate depends on Zn availability. The transcriptional responses to growth-rate and Zn availability are then intertwined, which obscures result interpretation. In the present study, transcriptional responses of Saccharomyces cerevisiae to Zn availability were investigated at a fixed specific growth rate under Zn limitation and excess in chemostat culture. To investigate the context-dependency of this transcriptional response, yeast was grown under several chemostat regimes resulting in various carbon (glucose), nitrogen (ammonium) and oxygen supplies. A robust set of genes that responded consistently to Zn limitation was identified and enabled the definition of a Zn-specific Zap1 regulon comprising of 26 genes and characterized by a broader ZRE consensus (MHHAACCBYNMRGGT) than so far described. Most surprising was the Zn-dependent regulation of genes involved in storage carbohydrate metabolism. Their concerted down-regulation was physiologically relevant as revealed by a substantial decrease in glycogen and trehalose cellular content under Zn limitation. An unexpectedly large amount of genes were synergistically or antagonistically regulated by oxygen and Zn availability. This combinatorial regulation suggested a more prominent involvement of Zn in mitochondrial biogenesis and function than hitherto identified.
2008-06-15 | E-GEOD-8035 | biostudies-arrayexpress
Project description:The gasotransmitter hydrogen sulfide (H2S) is thought to be involved in the post-translational modification of cysteine residues to produce reactive persulfides. A persulfide-specific chemoselective proteomics approach with mammalian cells has identified a broad range of zinc finger (ZF) proteins as targets of persulfidation. Parallel studies with isolated ZFs show that persulfidation is mediated by Zn(II), O2, and H2S, with intermediates involving oxygen- and sulfur-based radicals detected by mass spectrometry and optical spectroscopies. A small molecule Zn(II) complex exhibits analogous reactivity with H2S and O2, giving a persulfidated product. These data show that Zn(II) is not just a biological structural element, but also plays a critical role in mediating H2S-dependent persulfidation. ZF persulfidation appears to be a general post-translational modification and a possible conduit for H2S signaling. This work has implications for our understanding of H2S-mediated signaling and the regulation of ZFs in cellular physiology and development.
2024-06-23 | PXD041310 | Pride
Project description:Durum wheat requires high nitrogen inputs to obtain the high protein concentration necessary to satisfy pasta and semolina quality criteria. Optimizing plant nitrogen use efficiency is therefore of major importance for wheat grain quality. Here, we studied the impact on grain yield, protein concentration, and for the first time on protein composition of a marine (DPI4913) and a fungal (AF086) biostimulants applied to plant leaves. Plants were grown in a greenhouse and sampled at maturity for grain analysis. The protein concentration and quantity in grains per plant were determined, as well as water-use efficiency. A large-scale quantitative proteomics study of wheat flour samples was performed to determine the effect of biostimulant treatment on grain protein composition. Grain dry biomass and protein quantity were increased by 23.9% and 24.8% respectively with DPI4913, and by 27.4% and 25.9%, respectively, with AF086. A total of 1471 proteins were identified and 1391 were quantified. Quantitative proteomics analysis revealed 26 and 38 proteins with a significantly varying abundance after DPI4913 and AF086 treatment, respectively. Among these, 14 proteins were affected by both DPI4913 and AF086 treatments. The highest variations in proteins abundances were found for proteins involved in grain technological properties such as grain hardness, in storage functions with the substantial over-representation of the gluten protein gamma-gliadin, in regulation processes with the over-representation of proteins that play a transcription regulator role, and in stress responses with the over-representation of proteins implied in biotic and abiotic stress defense. The involvement of biostimulants in the abiotic stress response is suggested by the increase in water-use efficiency for DPI4913 treatment (15.4%) and for AF086 treatment (9.9%). In conclusion, our work, performed in greenhouse, has shown that DPI4913 and AF086 treatments promote grain yield while maintaining protein concentration in grains, and positively affect protein composition in term of grain quality. This study suggests that these biostimulants could be used to optimize durum wheat production and quality in field conditions.
2019-03-29 | PXD012469 | Pride
Project description:Elucidation of molecular basis of Iron and zinc homeostasis is crucial to breed iron and zinc use efficient and iron -zinc biofortified maize cultivars. The present investigation was framed to decipher the global expression snapshot maize seedlings in response to iron and zinc starvtion. Genome-wide transcriptome assay was performed with ~18,000 transcripts distributed across the maize genome, in maize seedlings after exposing the seedlings to three Fe and Zn stress treatments (+Fe–Zn, –Fe+Zn, –Fe–Zn) along with control (+Fe+Zn). Microarrays were used to study the global gene expression pattern iron and zinc starvation responsive genes in maize.
2021-01-04 | GSE122581 | GEO
Project description:This application is from a NERC-funded consortium (Mark MacNair, Nick Smirnoff, Exeter) and (Brian Ford-Lloyd, John Newbury, Birmingham). Metal tolerance is one of the classic examples of micro-evolution. Despite extensive research the physiological bases of the adaptation in plants are largely unknown. Arabidopsis halleri is a zinc tolerant, zinc accumulating species whereas Arabidopsis petraea is non-accumulating and non-tolerant. The objective of our programme is to identify: a) those key genes that act to determine Zn tolerance and accumulation in Arabidopsis (and which account for the difference in performance of A. halleri and A. petraea grown in the presence of elevated Zn), and b) those _downstream_ genes that are expressed as part of the tolerance or accumulation response. Phase 1: Total of 24 chips: Material ready by May 2003. The results will: a) tell us how effectively material derived from other Arabidopsis species hybridises to the chips, and b) identify genes that are differentially expressed in the two species in the presence and absence of Zn stress (thus providing initial lists of genes that may be responsible for Zn tolerance or accumulation- (but see phase 2). A. halleri exposed to low and high Zn; root and leaf mRNAs extracted: 3 replicates of each: = 12 slides. A. petraea exposed to low and high Zn; root and leaf mRNAs extracted: 3 replicates of each: = 12 slides. Phase 2: Total of 48 chips: Material ready by September 2003. The results will tell us which genes, identified as having appropriate expression patterns, co-segregate with the Zn tolerance or accumulation phenotype and will provide firmer candidate genes for intensive study. Bulks will be produced from F3 progeny (from the halleri x petraea cross) following phentoypic analyses for Zn tolerance and accumulation. A bulk of F3 progeny all exhibiting high Zn tolerance: exposed to low and high Zn; leaf and root mRNAs: 3 replicates: = 12 slides. A bulk of F3 progeny all exhibiting low Zn tolerance: exposed to low and high Zn; leaf and root mRNAs: 3 replicates: = 12 slides. A bulk of F3 progeny all exhibiting high Zn accumulation: exposed to low and high Zn; leaf and root mRNAs: 3 replicates: = 12 slides. A bulk of F3 progeny all exhibiting low Zn accumulation: exposed to low and high Zn; leaf and root mRNAs: 3 replicates: = 12 slides. Experimenter name = H. John Newbury Experimenter phone = 0121 414 5581 Experimenter fax = 0121 414 5925 Experimenter institute = University of Birmingham Experimenter address = School of Biosciences Experimenter address = University of Birmingham Experimenter address = Edgbaston Experimenter address = Birmingham Experimenter zip/postal_code = B15 2TT Experimenter country = UK Keywords: stimulus_or_stress_design; organism_part_comparison_design; strain_or_line_design
2007-01-08 | GSE5738 | GEO
Project description:Zinc (Zn) deficiency is a prevalent micronutrient insufficiency. Although the gut is a vital organ for Zn utilization, and Zn deficiency is associated with impaired intestinal permeability and a global decrease in gastrointestinal health, alterations in the gut microbial ecology of the host under conditions of Zn deficiency have yet to be studied. Using the broiler chicken (Gallus gallus) model, the aim of this study was to characterize distinct cecal microbiota shifts induced by chronic dietary Zn depletion. We demonstrate that Zn deficiency induces significant taxonomic alterations and decreases overall species richness and diversity, establishing a microbial profile resembling that of various other pathological states. Through metagenomic analysis, we show that predicted Kyoto Encyclopedia of Genes and Genomes (KEGG) pathways responsible for macro- and micronutrient uptake are significantly depleted under Zn deficiency; along with concomitant decreases in beneficial short chain fatty acids, such depletions may further preclude optimal host Zn availability. We also identify several candidate microbes that may play a significant role in modulating the bioavailability and utilization of dietary Zn during prolonged deficiency. Our results are the first to characterize a unique and dysbiotic cecal microbiota during Zn deficiency, and provide evidence for such microbial perturbations as potential effectors of the Zn deficient phenotype.
Experiment setup
Upon hatching, chicks were randomly allocated into two treatment groups on the basis of body weight and gender (aimed to ensure equal distribution between groups, n = 6): 1. Zn(+): 42 µg/g zinc; 2. Zn(−): 2.5 µg/g zinc.
Research is published:
http://www.mdpi.com/2072-6643/7/12/5497/htm
2015-06-08 | ST000190 | MetabolomicsWorkbench
Project description:This application is from a NERC-funded consortium (Mark MacNair, Nick Smirnoff, Exeter) and (Brian Ford-Lloyd, John Newbury, Birmingham). Metal tolerance is one of the classic examples of micro-evolution. Despite extensive research the physiological bases of the adaptation in plants are largely unknown. Arabidopsis halleri is a zinc tolerant, zinc accumulating species whereas Arabidopsis petraea is non-accumulating and non-tolerant. The objective of our programme is to identify a) those key genes that act to determine Zn tolerance and accumulation in Arabidopsis (and which account for the difference in performance of A. halleri and A. petraea grown in the presence of elevated Zn) and b) those _downstream_ genes that are expressed as part of the tolerance or accumulation response. Phase 1: Total of 24 chips: Material ready by May 2003 The results will a) tell us how effectively material derived from other Arabidopsis species hybridises to the chips, and b) identify genes that are differentially expressed in the two species in the presence and absence of Zn stress (thus providing initial lists of genes that may be responsible for Zn tolerance or accumulation- but see phase 2)· A. halleri exposed to low and high Zn; root and leaf mRNAs extracted: 3 replicates of each: = 12 slides· A. petraea exposed to low and high Zn; root and leaf mRNAs extracted: 3 replicates of each: = 12 slides Phase 2: Total of 48 chips: Material ready by September 2003 The results will tell us which genes, identified as having appropriate expression patterns, co-segregate with the Zn tolerance or accumulation phenotype and will provide firmer candidate genes for intensive study. Bulks will be produced from F3 progeny (from the halleri x petraea cross) following phentoypic analyses for Zn tolerance and accumulation.· A bulk of F3 progeny all exhibiting high Zn tolerance: exposed to low and high Zn; leaf and root mRNAs: 3 replicates: = 12 slides· A bulk of F3 progeny all exhibiting low Zn tolerance: exposed to low and high Zn; leaf and root mRNAs: 3 replicates: = 12 slides· A bulk of F3 progeny all exhibiting high Zn accumulation: exposed to low and high Zn; leaf and root mRNAs: 3 replicates: = 12 slides· A bulk of F3 progeny all exhibiting low Zn accumulation: exposed to low and high Zn; leaf and root mRNAs: 3 replicates: = 12 slides Experimenter name = H. John Newbury Experimenter phone = 0121 414 5581 Experimenter fax = 0121 414 5925 Experimenter department = Newbury lab Experimenter institute = University of Birmingham Experimenter address = School of Biosciences Experimenter address = University of Birmingham Experimenter address = Edgbaston Experimenter address = Birmingham Experimenter zip/postal_code = B15 2TT Experimenter country = UK Keywords: stimulus_or_stress_design; organism_part_comparison_design; strain_or_line_design
2007-01-08 | GSE5613 | GEO