Transcription profiling of Arabidopsis potassium-starved and caesium-treated plants
Ontology highlight
ABSTRACT:
ORGANISM(S): Arabidopsis thaliana
SUBMITTER: Nottingham Arabidopsis Stock Centre (NASC)
PROVIDER: E-GEOD-6160 | biostudies-arrayexpress |
REPOSITORIES: biostudies-arrayexpress
Similar Datasets
Project description:Background: Since chemical assays of soil nutrients are unreliable the UK horticultural and agricultural industries routinely apply large amounts of inorganic fertiliser to maintain crop yields and quality. Excessive fertiliser applications are both costly and can lead to unnecessary pollution. A possible solution to this problem is to use sensor (GM or non-GM) technologies that exploit the changes in plant gene expression profiles under incipient nutrient deficiency. The aim of this project is to identify genes upregulated in the early stages of nutrient depletion. Methods: Arabidopsis ecotype Col-5 (N1644) will be grown hydroponically using established techniques. In parallel experiments NP and K will be withdrawn individually after 21 d growth. RNA will be extracted from shoots of nutrient replete (control) and nutrient depleted plants 24 h after the removal of nutrients. Shoot nutrient content will be assayed by ICP-EMS as a reference. By comparing expression profiles we will be able to differentiate between genes that are upregulated by lack of specific nutrients and those upregulated by a universal stress-response system. Promoters and transcripts of these genes will underpin the development of novel sensor technologies and knowledge of the gene expression profiles will improve our understanding of the physiology of plant mineral nutrition. Experiment Overall Design: 4 samples
2008-06-14 | E-GEOD-6159 | 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. Experiment Overall Design: Number of plants pooled:20-40
2008-06-14 | E-GEOD-6161 | biostudies-arrayexpress
Project description:This work is part of an existing collaboration between the two laboratories, funded by the EU (EU-RTN-INTEGA). Both parties will share the cost of this microarray experiment. Background: We have demonstrated that ethylene-insensitive mutants and wild type(col-0) Arabidopsis plants treated with an ethylene perception inhibitor have increased levels of expression of genes, such as GASA1 and g-TIP, that are thought to be regulated by GA (Vriezen et al, unpublished results). However, this observation was based on an RNA gel blot analysis and therefore limited to few genes. Aim: To investigate whether plants with decreased ethylene perception are generally hypersensitive to GA or whether this effect is restricted to specific genes. We plan to undertake a complete transcriptome analysis of GA-treated wild type andetr1-1 plants. The aim is to identify genes that are induced directly as a result of the GA treatment, and we will therefore focus on the time window 0-3h. Tissues to be sampled: Plants will be grown in vitroon MS/2 containing 1% sucrose, pH 5.7, at 22 C,70% RH, under white light (54 PAR) and a photoperiod of 16h light/8h dark. Plants will be treated at 14 days and harvested entirely, i.e. roots and shoots are extracted together. Experimental set-up: Col-0 and the ethylene-insensitive mutant etr1-1 will be sprayed with 50 microM GA4 in water. GA4 is the major bio-active GA in Arabidopsis. Samples will be taken after 0, 30 min, 1h, and 3h. In order to correct for touch-induced genes a control, which is sprayed with water only and harvested at 1h, will be included for both genotypes. The total number of chips to be hybridized is 10. The time course with 4 data points is preferred to a single time point with 3 repeats, because it will allow us to follow the induction kinetics and identify early response genes. For each timepoint, RNA will be extracted from at least 40 individuals. Experiment Overall Design: 18 samples
2008-06-14 | E-GEOD-6150 | biostudies-arrayexpress
Project description:The proposal aims to characterise the pathways of DSB repair and recombination in Arabidopsis with the main focus of this research being the NHEJ pathway of illegitimate recombination. We will build on our expertise and resources in the field of DSB repair in plants, using the Arabidopsis NHEJ mutant atku80 which is an excellent model system for the study of DSB repair in higher eukaryotes (West et al., 2002 Plant J. 31, 517-28). Comparison of the transcriptome in NHEJ mutant and wild type plants under different experimental conditions will identify novel candidate genes involved in DNA DSB repair or damage signalling pathways.We will conduct 4 separate experiments on Arabidopsis seedlings grown on 0.5 MS media: the first will be a control consisting of Wassilewskija (WS-2) plants grown under standard conditions. In the second experiment WS plants will be exposed to the chemotherapeutic agent bleomycin (1 microgram per ml). This agent has been shown to cause both single and double strand breaks in the genome of Arabidopsis seedlings (Menke et al., 2001 Mut. Res. 493, 87-93). This agent is used in preference to gamma irradiation, which causes high levels of oxidative damage to cellular components. These experiments will characterise for the first time the transcriptional responses of Arabidopsis cells to the specific induction of DNA strand breaks. The transcript profile will also be determined in untreated atku80 mutants. This experiment will identify the components of novel and previously characterised DNA repair pathways up regulated in the mutant background. Finally, transcript analysis of bleomycin treated atku80 mutants and comparison with untreated mutant plants and both untreated and treated WS plants will identify novel putative DSB repair genes up regulated in response to genotoxic stress in the absence of a Ku80 mediated DSB repair pathway.The results of these studies will provide new and important information which will be instrumental in identifying novel genes and pathways involved in DNA repair and genome stability in plants and help elucidate the fundamental differences that exist between animal and plant DSB repair processes. Experiment Overall Design: Number of plants pooled:20
2008-06-14 | E-GEOD-6178 | biostudies-arrayexpress
Project description:This application is the second part of a BBSRC-funded grant to compare and contrast the plastid-signalling pathways disrupted by Norflurazon and far-red light treatment of Arabidopsis seedlings. The first application of this laboratory to GARNet's Affymetrix service (2002-08-25-17.41.49_McCormac) addressed the Norflurazon pathway; this application addresses the far-red pathway. The assembly of photosynthetic complexes in developing chloroplasts is critical to the establishment of the autotrophic plant. This requires light-mediated upregulation of both nuclear- and chloroplast-encoded genes. The expression of such photosynthetically-associated nuclear genes is also often dependant on a retrograde plastid signal which emanates from chloroplasts to modulate nuclear transcription. Extensive studies using the herbicide Norflurazon to knock-out the plastid signal (including this lab's previous Affymetrix application to GARNet) are identifying the affected gene sets. However, genetic studies have indicated the existence of more than one plastid signalling pathway. We have recently investigated a phytochrome A-mediated, far-red (FR) input pathway which blocks subsequent chloroplast development under white light (WL). This has also been found to inhibit the transcription of a small group of known nuclear-encoded plastidic proteins. Here we wish to establish how wide-reaching this FR-effect is on nuclear transcription, and will directly compare the affected gene groups with those identified from our earlier (and other's) studies with a Norflurazon treatment. In this array experiment we will compare RNA from seedlings grown in complete darkness (D) before transfer to WL, with that of seedlings preconditioned under a restricted wavelength FR source before exposure to WL. This comparison of FR- and Norflurazon-affected gene groupings will indicate whether the plastid signalling pathways are likely to be the same, overlapping or highly divergent. As well as wild-type seedlings, the gun1,gun5 mutant line is to be used as both these alleles are well established as alleviating the Norflurazon-inhibited pathway, but their affect on the FR-pathway is less clear. A single replicate of a phyA-null mutant line will also be included in order to differentiate between specific phytochromeA-mediated responses and other FR effects. It is envisaged that, in general, D- and FR-treated samples of the phyA mutant line will respond in the same way as each other and as the wild-type D-treated samples and, thus, the lack of a biological repeat in this case is not a major short-fall. The proposed experiment will consist of: wild-type: D-pretreated (x2 biological replicates) wild-type: FR-preconditioned (x2) gun1,gun5: D-pretreated (x2) gun1,gun5: FR-preconditioned (x2) phyA: D-pretreated (x1) phyA: FR-preconditioned (x1) Experiment Overall Design: Number of plants pooled:300 seedlings
2008-06-14 | E-GEOD-6169 | biostudies-arrayexpress
Project description:Arabidopsis acetate non-utilizing mutants were isolated based on fluoroacetate resistant germination. Interestingly, a number of these mutants exhibited altered developmental characteristics in response to exogenous sucrose supply, such as bleaching of the cotyledons. A preliminary microarray experiment has already been conducted on one of the mutants, acn1-2. The gene expression analysis was done using 3 day-old seedlings of acn1-2 and the parent, Col-7, which were germinated on agar plates with and without exogenous sucrose. A cross-comparison of acn1-2 and Col-7 revealed that the expression of a number of carbohydrate responsive genes was altered in the mutant. The request for further microarray analysis is to confirm this result. Experiment Overall Design: Number of plants pooled:3 x 1000 seedlings
2008-06-14 | E-GEOD-6158 | biostudies-arrayexpress
Project description:Our goals are to discover the basis of the stress-sensitive phenotypes of the sfr2, sfr3 and sfr6 mutants, and to distinguish damage-repair from damage-prevention-related transcription in the wild type. The effects of sfr2 and sfr3 on cold-induced gene expression will be observed. Since sfr6 causes sensitivity to drought as well as freezing, the effects of sfr6 on the transcriptional response to drought is studied; an observation of cold-induced sfr6 expression is needed for direct comparison to the effect of drought. Unstressed mutants, and equivalently-stressed wild types, are necessary controls. The above experiments are conducted on tissue-culture-grown plants grown under 24 hr illumination for maximum reproducibility and comparability to other transcriptomic experiments.Freezing causes physiological changes even in a hardy, cold-acclimated wild type. During the recovery period, gene expression will reflect the induction of damage-repair processes distinct from the damage-prevention associated with cold acclimation. This will be detected by observing the wild-type transcriptome at two time points during recovery from a freezing episode. The appropriate controls is the unfrozen, cold-acclimated wild type. Plants for this experiment will be soil-grown in an 9/15 day/night cycle to the rosette stage, and this regime will be maintained during acclimation and freezing treatments.Cold-induction will be 10 days at 4°C; drought will be imposed by placing excised leaves in a desiccator for 6 h. The youngest fully-expanded rosette leaves will be harvested for RNA extraction. Experiment Overall Design: Number of plants pooled:18
2008-06-14 | E-GEOD-6177 | biostudies-arrayexpress
Project description:Aim To identify genes specifically involved in the storage reserve mobilisation programme in Arabidopsis. Background During germination and early post-germinative growth in Arabidopsis seed storage reserves are broken down to provide energy and nutrients for the developing seedling. Genes encoding enzymes involved in the mobilisation of both storage lipid and protein are expressed strongly 1-2 days following imbibition and then fall to very low levels. The regulatory mechanisms controlling expression of these genes are poorly understood. Although germination and reserve mobilisation occur at the same time we have obtained evidence using Abscisic Acid (ABA) treated seeds that the events are regulated by two separate programmes. Arabidopsis seeds treated with 10mM ABA still express genes involved in the mobilisation of storage reserves and break down storage lipid even though germination is blocked. ABA treated seeds therefore provide a powerful system for the identification of genes involved specifically in the reserve mobilisation programme. Microarray analysis will allow us to gain a global undertanding of the processes involved in storage reserve mobilisation and should also result in the identification of regulatory genes involved in this process. Experimental Set-up All seeds are Col-4 imbibed on plates containing 1/2 MS media for 4 days in the dark. All plant material will be grown in controlled environment growth rooms under defined light and temperature regimes. There are two parts to the experimental design. 1. Time course to identify genes involved in both seed storage reserve and germination programmes Comparison of mRNAs from seeds immediately after imbibition (storage reserve and germination programme genes being induced) with 2 day (storage reserve genes maximally expressed) and 7 day old seedlings (storage reserve and germination programme genes off, photoautotrophic genes on) will allow the identification of genes exclusively presentor present at enhanced levels at the peak of reserve mobilisation (day 2). 2. ABA treatment experiment to identify genes involved in the storage reserve programme ABA treatment blocks germination but does not block reserve mobilisation. Microarray analysis will be performed on RNA isolated from 2 day old seed imbibed in the presence of 10mM ABA. Comparison of the results of this experiment with those of the time course experiment should allow us to distinguish between genes involved in the two major programmes that we have uncovered. Experiment Overall Design: 4 samples
2008-06-14 | E-GEOD-6173 | biostudies-arrayexpress
Project description:Our interest lies in how plants respond to bacterial pathogens. Over the past three years we have identified and documented reproducible, landmark biochemical and molecular events following the challenge of Arabidopsis with the phytopathogenic enterobacteria P. syringae. Significantly, our studies revealed 60% of cDNA-AFLP differentials not present on the 8,200 feature GeneChips and 20% absent from public EST databases (de Torres in press). We now seek to exploit this background using carefully defined time-points to analyse global changes in the Arabidopsis transcriptome using challenges selected to define gene targets implicated in (i) expression of basal immunity (ii) the establishment of successful parasitism (resistance) by a virulent pathogen (host). The results will provide a rationale for future functional assays of the identified pathways using transgenic knockouts and mutant analyses. Additionally, data will provide underpinning support for comparative proteomics of the defense response currently in progress with GARNet support using the same experimental parameters (BBSRC 32/P14635). We propose the following treatments: (i) Mock vs. DC3000hrpA @ 60 min: 60 minutes is subsequent to host immediate-early stress responses and will catalogue the innate responses induced by pathogen associated molecular patterns. The hrpA lesion will ensure no type III effectors influence transcriptional responses. Gene products induced at this time are predicted to potentiate latter host responses (2 treatments X 3 biological replicates = 6 chips). (ii) Mock vs. DC3000 vs. DC3000hrpA vs. DC3000::avrRpm1 @ 4 hours: A key time point previously defined where no macroscopic symptoms are visible but significant differences exist between compatible and incompatible interactions at the molecular and physiological levels. These treatments will serve to define the earliest genes induced by the complement of DC3000 type III effector and will specifically define genes/pathways suppressed by virulence factors in addition to those implicated in orchestration of the hypersensitive cell death. We will also include an incompatible interaction on a transgenic line expressing an RPM1 interacting protein, which fails to mount an HR but exhibits hyper-resistance. We predict this challenge will separate the resistance response (pathogen restriction) from that associated with hypersensitive cell death (5 treatments X 3 biological replicates = 15 chips). (iii) Mock vs. DC3000 vs. DC3000hrpA @ 14 hours: At 10 h before phenotypes are apparent in the DC3000 background, Type III effector delivery is well advanced and impact on host transcription maximal (3 treatments X 3 biological replicates = 9 chips). Experiment Overall Design: Number of plants pooled:4 leaves/plant; 18 plants/time point
2008-06-14 | E-GEOD-6176 | biostudies-arrayexpress
Project description:Nitric oxide (NO.) is a well-established signal in mammalian cells regulating e.g. smooth muscle tone, neurotransmission and apoptosis. NO interacts with superoxide (O2-) to derive the highly reactive peroxynitrite (ONOO-) radical leading to the generation of lipid hydroxy-peroxides (ROO.) and cell death. Thus the recent reports implicating of .NO in the Hypersensitive Response (HR) a form of programmed cell death elicited by pathogens in plantsis suggestive of parallel roles in animals and plants. As part of BBSRC funded programmes which are investigating oxidative signaling and cell death in Arabidopsis we have collaborated with the Trace Gas Detection facility at the University of Nijmegen to be the first to measure NO in planta from a developing HR (Mur et al.paper in prep). The challenge remains to understand the spatio-temporal role(s) of .NO during the HR and disease development. In line with other groups e.g. Klessig et al.(2000) PNAS 978849-55 we have observed that .NO mediated event are both SA- dependent and independent. We propose a two-stage programme to investigate NO events which will lead to subsequent BBSRC grant bids. Firstly to exploit the GARNET Affymetrix transcriptomic service to identify genes which are upregulated by .NO (see programme below). These will be compared with similar data generated by other members of the consortium; Dr. Steve Neill for oxidative stress (Desikan et al. (2001). Plant Physiol 127(1): 159-72; Clarke et al.2000 Plant J.; 24:667-77); Dr. Paul Kenton who is mainly interested in signaling by the oxylipid Jasmonic acid (Kentonet al. (1999). MPMI 12(1): 74-78) as well as from other sources. Though these data in themselves will suggest modes of NO action. However as a second approach we will clone the promoter of a strongly NO-responsive gene which will be fused to positive and negative selectable markers as well as reporter genes e.g. LUC. to identify Arabidopsis EMS mutants which are perturbed in NO-mediated events. Programme. Our in planta measurement show that from a baseline production of 1nl.g fwt-1h-1 NO levels rise to 6nl. g fwt-h-1 (_plus/- 1.1 SE) prior to cell death and to 25nl g fwt-h-1 (_plus/- 4.2 SE) at cell death following which the concentration falls. At this juncture we will intend to gas Arabidopsis to ~75ppb (the head-space concentration when NO production was at 6nl. g fwt-h-1). Prior to using the DNA RNA will establish that this does not elicit cell death over the proposed treatment period and that both PR1 (SA-dependent) and PAL1 (SA-independent) genes are induced. We will compare this plant with sealed but non-treated Arabidopsis. Future targets for DNA RNAs analysis induce plant treated with both NO (Sodium Nitro Prusside) and O2- (Xanthine oxidase) generators and depending on their effectiveness (to be assessed by NO measurement) HR lesions treated with Nitric Oxide Synthase inhibitors. Experiment Overall Design: Number of plants pooled:8
2008-06-14 | E-GEOD-6170 | biostudies-arrayexpress