Furner
Ontology highlight
ABSTRACT:
ORGANISM(S): Arabidopsis thaliana
SUBMITTER: David Craigon
PROVIDER: E-NASC-9 | biostudies-arrayexpress |
REPOSITORIES: biostudies-arrayexpress
Similar Datasets
Project description:As part of an investigation into mechanisms of HDG silencing in Arabidopsis, we have produced transgenic plants containing extra copies of the chalcone synthase (CHS) gene. The CHS gene mediates an early step in the biosynthesis of the purple pigment anthocyanin. The insertion of extra copies of CHS in Arabidopsis caused the gene to be silenced in some plants. Seeds harvested from these CHS-silenced plants were mutated by treatment with ems. The progeny of these seeds were screened for "revertants" in which the effects of CHS silencing was alleviated and plants were able to produce anthocyanin. These revertants were found to contain a single recessive mutation; the trait has been termed hog1 (for homology dependant gene silencing 1). Our previous experiment used the Affymetrix 8200 chip to make comparisons between gene expression in the two genetic variants: the CHS-silenced type (ECG) and the anthocyanin-producing revertants (15B). Results showed that there were over 100 genes with at least a 10-fold increase or decrease in expression. However, the variation between 2 reps of each genetic variant was high. We would now like to carry out a modified version of this experiment using the 25K Affymetrix chip. It is intended to increase the number of reps to 4, and take samples at an earlier stage than previously in order to decrease the effect of developmental spread. To reduce the effects of interplant variability, samples will be generated from total plant tissue from a pool of 10 plants at GS 1.04. RNA will be purified using RNeasy kits from Qiagen.
2022-11-21 | E-NASC-36 | biostudies-arrayexpress
Project description:As part of an investigation into mechanisms of HDG silencing in Arabidopsis, we have produced transgenic plants containing extra copies of the chalcone synthase (CHS) gene. The CHS gene mediates an early step in the biosynthesis of the purple pigment anthocyanin. The insertion of extra copies of CHS in Arabidopsis caused the gene to be silenced in some plants. Seeds harvested from these CHS-silenced plants were mutated by treatment with ems. The progeny of these seeds were screened for "revertants" in which the effects of CHS silencing was alleviated and plants were able to produce anthocyanin. These revertants were found to contain a single recessive mutation; the trait has been termed hog1 (for homology dependant gene silencing 1). Our previous experiment used the Affymetrix 8200 chip to make comparisons between gene expression in the two genetic variants: the CHS-silenced type (ECG) and the anthocyanin-producing revertants (15B). Results showed that there were over 100 genes with at least a 10-fold increase or decrease in expression. However, the variation between 2 reps of each genetic variant was high. We would now like to carry out a modified version of this experiment using the 25K Affymetrix chip. It is intended to increase the number of reps to 4, and take samples at an earlier stage than previously in order to decrease the effect of developmental spread. To reduce the effects of interplant variability, samples will be generated from total plant tissue from a pool of 10 plants at GS 1.04. RNA will be purified using RNeasy kits from Qiagen. Experiment Overall Design: Number of plants pooled:10 Experiment Overall Design: Biological replicates: 4
2008-06-14 | E-GEOD-6166 | biostudies-arrayexpress
Project description:Plant growth and development are strongly affected by light signals perceived by phytochromes (phy) and cryptochromes (cry). The physical interaction between photoreceptors and the cross-talk among downstream signalling steps creates a network of interactions in which the action of one photoreceptor depends on the status of the others. The processes modulated by phy and or cry include seed germination, seedling de-etiolation, plant body formation and flowering. Compared to the wild type the leaves of the phyB mutant are characterised by their extended petioles and pale colour. These features resemble the phenotype of normal plants grown under the low red to far-red ratios typical of dense plant canopies thus providing support to the idea that phyB plays a key role in the perception of high red to far-red ratios. The triple mutant lacking phyA cry1 and cry2 shows little differences in leaf size and shape with the wild typebut the quadruple phyA phyB cry1 cry2 mutant shows severely impaired leaf expansion. In addition to the specific effects on leaf sizeshape and pigmentation the phyB mutation accelerates flowering in the wild type background. This effect can be observed as a reduced number of days between sowing and visible flower buds (time scale) and as a reduced final number of leaves (developmental scale). However in the phyA cry1 cry2 triple mutant background the phyB mutation accelerates flowering on a developmental scale but severely delays flowering on a time scale. The long photoperiods inducing flowering are perceived by the leaves. Flowering signals that could include hormones and sugars migrate from the leaves to the apex in response to the light stimulus. We propose to compare the following mRNA samples of expanding leaves: 1) wild type 2) phyB mutant 3) phyA cry1 cry2 triple mutant 4) phyA phyB cry1 cry2 quadruple mutant. The comparison between the wild type and the phyB mutant will help to uncover the changes in leaf mRNA patterns underlying enhanced petiole growthreduced pigmentation and early flowering in response to the absence of phyB activity. The comparison between the phyA cry1 cry2 triple mutant and the phyA phyB cry1 cry2 quadruple mutant should reveal the mRNA differences between photosynthetic leaves with dramatically different abilities to expand. The added value of the simultaneous analysis of the two comparisons is that effect of phyB is different in both genetic backgrounds and this should provide information on the mechanisms and significance of photoreceptor interactions.
2003-10-29 | E-NASC-6 | biostudies-arrayexpress
Project description:The aim of this study is to identify genes differentially expressed during the transition between dormancy and activity in axillary shoot apical meristems. We have chosen to study this by comparing mRNA populations from the axillary buds of the auxin over-responding, apically dominant axr3-1 mutant of Arabidopsis,with those from the axillary buds of the auxin resistant axr1-12 bushy mutant. Preliminary investigation using cDNA AFLP has been successful in identifying differentially expressed transcripts in the buds of these two genotypes, thus demonstrating the importance of this study, however this is a time consuming procedure. Axillary buds from axr3-1 are seen to arrest at an early stage when the buds are approximately 2mm long and harvested at this point. Buds of a similar size were harvested from axr1-12 plants and the RNA extracted using Qiagen columns.These two mRNA samples will represent the dormant and active buds to be comparedin this experiment. The plants from which these buds were harvested were grown in adjacent p40 trays in a plant growth room. Between two and three buds were harvested from each plant.
2003-10-20 | E-NASC-10 | biostudies-arrayexpress
Project description:Plastids communicate with the nucleus by means of retrograde plastid signals. The far-red (FR) light insensitive Arabidopsis mutant laf6 disrupted in a plastid-localised ABC-like protein (atABC1) accumulates the plastid signal protoporphyrin IX (proto IX) and has attenuated nuclear gene expression (Moller et al.2001 Genes Dev. 15:90-103). Our data suggests that proto IX accumulation results in hypocotyl elongation in response to FR light and we have demonstrated that by inhibiting the plastid localised protoporphyrinogen IX oxidase (PPO) using flumioxazin wild-type plants phenocopy laf6 by accumulating proto IX with a concomitant loss of hypocotyl growth inhibition in a dose-dependent manner. It is at present unclear what effect increased proto IX has on nuclear gene expression and how this is integrated with photomorphogenic responses such as hypocotyl elongation.
2022-11-21 | E-NASC-42 | biostudies-arrayexpress
Project description:Many signalling pathways are involved in controlling gene expression during plant senescence. Pathways involving SA, JA and ethylene have a role in senescence but none are essential for the senescence process to occur. The aim of this experiment is to classify senescence-enhanced genes into groups depending on the signalling pathways that regulate them. This will provide useful information on the relative importance of each signalling pathway during senescence and allow us to separate potential senescence-specific genes and pathways from the stress response pathways.Mutants in genes in the ethylene pathway (ein2) and the jasmonate pathway (coi1) and the NahG transgenic plant which is defective in the salicylic acid pathway will be grown until the mid flowering stage. Fully developed green and partially senescent leaves will be harvested from the plants at this stage. In addition, two different lines of Arabidopsis (Col-5 glabrous and Col-0) will be grown as controls. Leaves will be harvested from the two control plants before flowering (green) and at mid flowering as above. The control plants will be harvested at two stages to identify the senescence- enhanced genes. The effects of each mutation on the senescence related expression of these genes will then be studied.Mutant RNAs will be isolated in duplicate. The two control accessions will act as replicates for the wild type. Two wild type accessions will be used to reduce possible differences that could be observed the mutants due to slight differences in background.
2022-11-21 | E-NASC-17 | biostudies-arrayexpress
Project description:SKS mutant (snakeskin) vs wildtype
2022-11-21 | E-NASC-57 | biostudies-arrayexpress
Project description:Aim: To identify regulatory factors that control: (1) chloroplast protein importand (2) chloroplast-to-nucleus signalling. This project is a joint proposal from the Jarvis lab which is interested in chloroplast protein import [1] and the Moller lab which is interested in plastid-to-nucleus signalling [2]. Background: The majority of chloroplast proteins are encoded in the nucleus and imported post-translationally into chloroplasts. The abundance of chloroplast proteins may therefore be regulated at multiple levels. It is well documented that the nuclear gene expression is responsive to (largely unknown) signals from the chloroplast [23] and evidence is now emerging that protein import is also a regulated process [1]. Protein import into chloroplasts is mediated by protein complexes in the outer and inner envelope membranes called Toc and Tic respectively. Biochemical studies of pea chloroplasts identified several Toc/Tic components. These proteins are mechanistic or structural components of the import apparatus. Arabidopsis homologues of the pea Toc/Tic proteins were identified by the AGI. Pea Toc34 is represented in Arabidopsis by two genes "Toc33 and Toc34" and pea Toc75 is represented by three genes. These different Tocs have different expression patterns and are proposed to have different precursor protein recognition specificities. The factors that regulate Toc expression in concert with the needs of plastids in developmentally different cells are unknown. Proposal: Two Arabidopsis mutants will be analysed. The ppi1 mutant is null for the putative precursor protein receptor Toc33 [1]and the ppi3 mutant is null for a putative component of the protein import channel Toc75-IV (on chromosome IV). ppi1 plants are yellow-green in appearance but remarkably healthy and grow only slightly more slowly than wild type. By contrast ppi3 plants are indistinguishable from wild type by eye although analysis of the mutant's chloroplast proteome is beginning to reveal some differences (K. Lilley personal communication). Gene expression changes in ppi1 are likely to be quite extensive. Retardation of chloroplast development in ppi1 will activate retrograde signalling pathways so that many nuclear photosynthetic genes are down-regulated. Changes in the expression of photosynthetic genes and of the genes responsible for mediating these responses may therefore be observed. Any regulatory and signalling genes identified will be of interest to the Moller lab. The expression of factors that regulate Toc/Tic gene expression may also be altered in ppi1. It should be possible to distinguish these factors from those involved in the general control of chloroplast gene expression by comparing the results from the two mutants. Genes affected in both mutants are more likely to be involved in regulating chloroplast import since it is unlikely that widespread changes in gene expression will be observed in ppi3. Changes in the expression of factors that regulate import post-translationallyand of the Toc/Tic genes themselves (many are on the RNA) may also be observed. References: 1. Jarvis P. et al. (1998) Science 282: 100-103. 2. Moller S.G. et al. (2001) Genes Dev. 15:90-103. 3. Jarvis P. (2001) Curr. Biol. 11: R307-R310.
2022-11-21 | E-NASC-35 | biostudies-arrayexpress
Project description:Background: Release of the caesium radioisotope 137Cs during weapons testing and industrial activity has contaminated thousands of hectares of agricultural land. Ingesting 137Cs has damaging and, sometimes, fatal effects. Most Cs enters the food chain through plants. The generation of _safe_ crops that exclude Cs and can be cultivated on contaminated land requires knowledge about the mechanisms for Cs uptake. Caesium is chemically similar to potassium (K) and might enter plants through K+ transporters in the plasma membrane of root cells. To determine which transporters mediate Cs entry to plants, we have compared the accumulation of Cs and K by wildtype Arabidopsis with mutants lacking specific K+ transporters. Preliminary results showed that Cs concentration in the shoots of akt1-1, cngc1 and cngc4 (obtained from the Wisconsin T-DNA knockout facility) differed significantly from the Wassilewskija wildtype (Ws-2). A cursory investigation of their transcriptome, using the Affymetrix Arabidopsis 8K GeneChip, showed that the expression of several genes encoding K+ transporters differed between mutants and wildtype plants. The aim of this GarNet project is to confirm the previous observations and to identify further genes that are differentially expressed in mutant and wildtype plants and which might impact on Cs accumulation. Methods: Arabidopsis mutants akt1-1 (N3762), cngc1 and cngc4 and their parental ecotype Wassilewskija -2 (N1601) will be sown on MS agar and transferred to hydroponics 21 days after germination. Seedlings will be grown for a further 7 days on full nutrient solution under continuous light in a Saxcil growth cabinet. RNA will be extracted from roots of mutant and parent (control) plants at the same growth stage and twelve complete-genome Affymetrix GeneChips (3 biological replicates of material from wildtype and 3 mutants) are requested to determine the differences in their transcriptome under comparable environmental conditions.
2022-11-21 | E-NASC-31 | biostudies-arrayexpress
Project description:Regulation of expression of genes encoding chloroplast components is critical to the autotrophic plant and never more so than in the cotyledons of the de-etiolating seedling. Many chloroplast proteins are nuclear-encoded and a retrograde signal from the chloroplasts (the Plastid Signal) modulates nuclear transcription. However, not all chloroplast-targeted genes are subject to this control and not all plastid-dependent nuclear genes are chloroplast-targeted. We therefore aim to provide the most comprehensive screen yet of which genes are affected by plastid-signalling. To specifically knock-out positive plastid signalling in light-grown cotyledons, the herbicide Norflurazon (NF) is supplied in the growth medium, causing a carotenoid deficiency that leaves the chloroplasts vulnerable to photobleaching. This blocks the expression of a subset of nuclear genes, such as Lhcb and HEMA1. Two pairs of RNAs will directly compare the transcription in seedlings grown under continuous white light with and without NF. A third RNA will also be compared from a mutant that shows a degree of constitutive positive plastid signalling. These two mutants act synergistically to counteract the effect of NF on nuclear transcription. The gun1,gun5 double mutant maintains a significantly higher level of Lhcb and HEMA1 expression in the presence of photobeached chloroplasts than the NF-treated wild-type. This transcriptome set will therefore complement RNA1 (wild-type+NF) and indicate which of the genes identified from the RNA1/RNA2 comparison are subject to the particular gun1/gun5 plastid signalling pathway(s). The growth of conditions of the seedlings (namely on MS medium supplemented with 1.5% sucrose, for 3 days under continuous WL following 2 days germination in darkness) has been chosen from the results of our own recent studies using Northern blotting techniques that show these conditions to maximise the respective NF and gun mutant effects on Lhcb and HEMA1 gene expression. This experiment is part one of a two-part study to compare the transcriptional output of this NF-affected pathway with that of a newly discovered FR-mediated pathway. A subsequent array experiment will assess the nuclear response as affected by this FR/ phyA-input pathway and the two sets of array data will be compared and contrasted. Note: Col-0 wild-type (NASC code N1092). gun1,gun5 double mutant(obtained from Enriquez Lopez-Juez, Royal Holloway, University of London.(Mochizuki et al. 2001 PNAS 98: 2053-2058). This line cannot be donated by us as it is the IP of Joanne Chory (SALK Institute, USA). Treatment = a herbicide (Norflurazon) application which leads to chloroplast photobleaching and hence down regulation of nuclear genes dependent on plastid signalling from intact chloroplasts.
2022-11-21 | E-NASC-40 | biostudies-arrayexpress