Project description:Metabolites of cold hardy versus cold susceptible flies were compared using N less than R-based metabolomics. We used 8 replicates per line (2 hardy lines, two susceptible lines), and sampled each line at three time points (before, during and after cold), giving rise to 96 samples total.
Project description:Two groups of mixtures with 5 replicates each were each made using 20 synthetic metabolites. Some metabolites were at equal concentrations in both groups, and 10 metabolites differed between groups with half higher in group A, and half higher in group B.
Project description:‘Pulsechip’, a boutique cDNA microarray, generated from a set of chickpea (Cicer arietinum L.) unigenes, grasspea (Lathyrus sativus L.) ESTs and lentil (Lens culinaris Med.) resistance gene analogs, was employed to generate an expression profile of chickpea accessions tolerant and susceptible to cold stress. Two groups of a tolerant and susceptible accession were challenged with cold stress. The experiments were performed in three biological replications. The experiments were conducted in reference design where respective tissues from unstressed plants served as control. The leaves and flowers/buds/early pods tissues were collected and used for hybridization to measure changes in RNA abundance of treatment vs. control. The tissues from five experimental replicate plants per biological replication were pooled together (leaf and flower tissues separate) before RNA extraction. This RNA was used to prepare cDNA targets for expression analysis using microarray. The microarray had six technical replicate spots per EST. The transcript level for each EST/cDNA was firstly calculated as the average intensity of the six technical replicates and then the average intensity of three biological replicates. Data analysis included LOWESS normalization (LOcally WEighted polynomial regreSSion) to adjust for differences in quantity of initial RNA, labeling and detection efficiencies. A dye swap in one biological replicate adjusted dye bias, if any. The Differentially Expressed (DE) ESTs were identified as those with a 95% confidence interval for mean fold change (FC) that extended beyond the two-fold cut-off and also passed the Students t test (P<0.05) and FDR correction. These cut-offs translate into induced ESTs having a log2 ratio > 1 and repressed ESTs a ratio of < -1. The analysis consisted of three fold comparison. Firstly, the ESTs that were differentially expressed between treatment and control plants of each accession were detected. Then the ESTs that were similarly expressed by tolerant and susceptible accessions were then eliminated by comparison. This included a two-way comparison, where tolerant and susceptible genotypes were compared within and between groups. Lastly, ESTs that were consensually differentially expressed between tolerant and susceptible accessions of the two batches were identified. The hypothesis was that if a putative gene was consistently expressed only in tolerant or susceptible genotype for a particular stress, it might be a candidate for tolerance/susceptibility for that stress. Globally, the level of 221 transcripts was affected in response to cold stress in all the genotypes and tissue types studied. The DE transcripts in response to cold stress fell into various functional categories, indicating a broad response. Sixteen out of the 221 DE transcripts were consistently expressed in cold tolerant/susceptible genotypes. All these transcripts were repressed and none was found to be consistently induced in response to cold-stress. Most of the putative genes were identified in leaves of tolerant genotypes, and included a beta-galactosidase (DY475141) transcript that was possibly indicative of disaccharide (e. g. sucrose) retention with the effect of protecting cell membranes during cold stress. Several protein synthesis/modification and energy/metabolism transcripts were also repressed (e.g. DY475282, DY396371 and DY475555), which was likely due to the impairment of photosynthesis and respiration at low temperature. Other consistently repressed transcripts in tolerant genotypes included putative signalling (DY396262, DY475384 and DY396307) and defence-related proteins (CV793589 and DY396343), which may be involved in the repression of cell death mechanisms that are absent in tolerant genotypes. In susceptible genotypes, a putative superoxide dismutase precursor protein (DY475397) and sorting nexin protein (DY475523) were the only known transcripts to be consistently repressed. Keywords: Chickpea, Cold stress, Tolerant, Susceptible, cDNA microarray
Project description:In this study, hepatopancreas tissues of cold-tolerant and common families of Litopenaeus vannamei were selected by the Guangxi Academy of Fishery Sciences for proteomic study. Hepatopancreas were treated at 28℃, 18℃ and 10℃ respectively based on DIA technology. There were three replicates of cold-tolerant families and common families at 28℃, 18℃ and 10℃ respectively, and each replicate contained hepatopancreas mixed samples of 6 shrimp at random. A total of 18 samples were analyzed. The original data of common families at 28℃, 18℃ and 10℃ were named Lv-C-28、Lv-C-18 and Lv-C-10 respectively, while the original data of cold-tolerant families at 28℃, 18℃ and 10℃ were named Lv-T-28、Lv-T-18 and Lv-T-10 respectively.
Project description:Profiling of differential gene expression of flies constitutively expressing NtFT4, a phosphatidylethanolamine-binding protein from tobacco. Flies expressing the tobacco PEBP were long lived compared to control flies. Differential expression was tested on pools of whole, female flies of 1d, 5d and 10d age. Three independent replicates of flies with the genotype da-Gal4 (control) and UAS-NtFT4 were collected.
Project description:With the growing limitations on arable land, alfalfa (a widely cultivated, low-input forage) is now being selected to extend cultivation into saline lands for low-cost biofeedstock purposes. Here, minerals and transcriptome profiles were compared between two new salinity-tolerant North American alfalfa breeding populations and a more salinity-sensitive Western Canadian alfalfa population grown under hydroponic saline conditions. All three populations accumulated two-fold higher sodium in roots than shoots as a function of increased electrical conductivity. At least 50% of differentially expressed genes (p < 0.05) were down-regulated in the salt-sensitive population growing under high salinity, while remaining unchanged in the saline-tolerant populations. In particular, most reduction in transcript levels in the salt-sensitive population were observed in genes specifying cell wall structural components, lipids, secondary metabolism, auxin and ethylene hormones, development, transport, signalling, heat shock, proteolysis, pathogenesis-response, abiotic stress, RNA processing, and protein metabolism. Transcript diversity for transcription factors, protein modification, and protein degradation genes was also more strongly affected in salt-tolerant CW064027 than in salt-tolerant Bridgeview and salt-sensitive Rangelander, while both saline-tolerant populations showed more substantial up-regulation in redox-related genes and B-ZIP transcripts. The report highlights the first use of bulked genotypes as replicated samples to compare the transcriptomes of obligate out-cross breeding populations in alfalfa. Three lines of Alfalfa (salt-tolerant CW064027, salt-tolerant Bridgeview, salt-sensitive Rangelander) were grown on 3 different concentrations of salt. For each cultivar-salt condition, 3 biological replicates were collected for a total of 27 samples.
Project description:Cold exposure leads to alteration in the structure of the male sex chromosome of the mutant strain In(1)BM2(reinverted). Genome wide expression profiling was used to identify candidate genes involved in the expression of this phenotype. Adult male flies were exposed to cold shock at 12±1°C for 4 hours and the differentially expressed genes in the strain was compared to similarly exposed wild type Oregon R males. The microarray data was further validated using real time PCR. Two-condition experiment, RT vs. CS flies. Biological replicates: 2 control replicates, 2 replicates exposed to cold shock.
Project description:Rice seedlings at 3-leaf stage were used for expression analysis in control and cold stressed (incloudling cold treatment for 3, 24hrs and recovery from cold stress for 24hrs) samples. Samples of shoots and roots from biological replicates of both genotypes were generated and the expression profiles were determined using Phalanx Rice OneArrayM-oM-<M- v1. Control and treated biological replicates of cold-tolerant cultivar TNG67 (japonica) and cold-sensitive cultivar TCN1 (indica) were analyzed