Determination of genes expressed in response to drought in root and shoot of Leucaena leucocephala
ABSTRACT: Leucaena leucocephala seedlings were treated with PEG6000 and the shoot and root tissues were collected after 48 hours following the treatment. The gene expressions were compared between treated and untreated in root and shoot separately. The differentially expressed genes may be related to drought resistance. RNA from shoot and root from treated and untreated L. leucocephala seedlings were extracted. Two biological replicates were made for each sample (each replicate represents about 10 individual seedlings).
Project description:The genes induced by mechanical stimuli may be also involved in disease resistance and wood formation and development in Acacia koa. If so, mechanically stressed A. koa may be used as a model to study disease resistance and wood formation and development. Microarray analysis was performed to determine expression levels of 4,000 genes related to disease resistance and wood development in Acacia koa in response to mechanical stimuli (touch). RNA was extracted from two groups of A. koa seedlings, (1) mechanically stressed and (2) unstressed koa seedlings. Each group had two biological replicates (n=2), where n represents pools of approcimately 20 individuals.
Project description:A dataset of ~600 RIL crosses using RILs from the Drosophila Synthetic Population Resource to be used for genomewide eQTL mapping. All samples are from female heads. 54 arrays with 12 samples per array resulting in data for 596 RIL crosses.
Project description:Analysis of changes in gene expression in Enterococcus faecalis OG1 delta-EF2638 mutant compared to wild-type OG1 strain. The deletion mutant has a growth defect when grown with aeration The mutant presented in this study is described and characterized in Vesic, D. and Kristich, C.J. 2012. A Rex-family transcriptional repressor influnces H2O2 accumulation by Enterococcus faecalis. (submitted for publication) Microarray analysis was done using RNA isolated from two independent cultures of wild-type Enterococcus faecalis OG1 and two independent cultres of Enterococcus faecalis OG1 delta-EF2638 mutant; each RNA sample was subjected to triplicate hybridization (technical replicates) . Microarrays were custom designed to investigate expression of ORFs in Enterococcus faecalis OG1RF genome. The arrays were designed based on the OG1RF annotation generated with the Rapid Annotation Using Subsystem Technology (RAST) server (Aziz et. al. 2008. BMC Genomics 9:75), as described in Frank et al (2012) Infect. Immun. 80:539. The aim was eighteen probe pairs per ORF, each of which is present in triplicate.
Project description:Comparison of gene expression between shoots of root-wounded seedlings and shoots of control seedlings in Arabidopsis. We identified wounding-induced early (30 min) and late (360 min) root to shoot responsive genes (RtS). Two-condition experiment, shoots of root-wounded seedlings vs. shoots of control seedlings. Biological replicates: 2 control replicates, 2 treated replicates. Technical replicate: Dyeswap
Project description:MPK6 shows transient increase in activity under hypoxia with maximal activity at 2 hrs. To study the role of MPK6 in hypoxia in Arabidopsis, 10 do seedlings of WT, mpk6 and MPK6 plants were exposed to 2 hrs hypoxia and 2hr air (mock). Because there are no major phenotypic differences between the genotypes, microarray was used to determine if there were transcript level differences between the genotypes. Wild type Col-0, MPK6 overexpression and mpk6 knockout mutants were exposed to 2 hr hypoxia and air and separated into root and shoot in order to determine the role of MPK6 in hypoxia in both root and shoot.
Project description:Genetic changes involved in the juvenile-to-adult transition in the shoot apex of Olea europaea L. occurs years before the first flowering. For the study of the genetic-expression pattern over development, 21 seedlings originating from open pollination of olive cultivar ‘Arbequina’ were grown in a greenhouse in Centro IFAPA “Churriana” Málaga, Spain. At the sixth month the apical shoot was removed and kept for genomic analysis. Any lateral shoot was removed to force the growth along just one axis. Every three months a new (1 cm long) apical-shoot tip was taken, which included the meristem down to two very small young leaves. When the apical-shoot tip is removed the two lateral buds immediately below are activated, one of them is removed, and the other one becomes the new apical-shoot tip. Seedlings reaching 50 nodes or 1 m high were allowed to form a top canopy. From then, the samples were taken from apical shoots of higher branches. We analyzed samples taken from the seedling/tree No 11, in a dense time-course study by microarray analysis. According to the nature of the samples, i.e. the main apical shoots, we had to use single samples during the first 6 to 15 months of growth. This limits the use of the statistics for this period but is compensated for by providing a series of consecutive data that make it possible to ascertain the time course of gene expression over plant development.
Project description:While CEP5 has been shown to play a role in shoot and root growth, possibly through interaction with the CEPR1/XIP1 and/or CEPR2 receptor kinase, very little is known about the downstream molecular effects. To gain insight in the changes downstream of CEP5, we quantified differences in phosphoproteomes of peptide treatment seedlings using label-free mass spectrometry-based proteomics
Project description:Genome-wide and organ-specific landscapes of epigenetic modifications and their relationships to mRNA and smRNA transcriptomes in maize We report an integrated genome-wide analysis of DNA methylation, histone modifications, smRNAs and mRNA transcriptional activity, using maize as a model. We surveyed the epigenomes of the maize inbred line B73 in shoot and root tissue by Illumina/Solexa 1G parallel sequencing after digesting genomic DNA with a methylation-sensitive restriction enzyme and after conducting chromatin immunoprecipitations (ChIP) using antibodies that target specific histone modifications (H3K4me3, H3K9ac, H3K27me3, H3K36me3, respectively). Additionally, we profiled RNA pools (micro RNA (miRNA), siRNA and mRNA) using the same sequencing strategy. Keywords: Epigenetics, mRNA transcription and small RNAs H3K4me3, H3K9ac, H3K27me3, H3K36me3, DNA methylation and mRNA, small RNA profiled from shoots and roots of 14 day-old maize B73 seedlings
Project description:In this research, an array of 27,448 rice genes was used to elucidate gene expression in air-dried rice seedlings (lead and root) at various periods of treatment times. The analyses show that rice responds to drought stress mainly by down-regulating many biological processes including gene expression and regulation, protein phosphorylation, and cellular metabolism. Among strategies to actively adapt to drought, most significant are inducing protective molecules, which may be differentially regulated based on plant organs. A total of 20 chips was used for the microarray analysis. Total RNAs were extracted from leaf and root of rice seedlings that had undergone 0-12 hrs acute drought. Experiments were duplicated. The profiling was conducted with the Rice 3'-Tiling Microarray designed from 27,448 genes deposited at IRGSP, RAP1 database (http://rapdb.dna.affrc.go.jp/).
Project description:Aerenchyma is a specialized tissue consisting of longitudinal gas spaces, which enables internal movement of gases (e.g., O2, CO2, ethylene and methane), in plant roots, petioles and stems. Especially, internal transport of oxygen via aerenchyma from shoots to roots is very important for adaptation or survival of plants under waterlogged condition. To identify aerenchyma formation-associated genes expressed in maize root, we used LM combined with a microarray for monitoring genes expressed in root cortical cells under three conditions: under aerobic condition and under waterlogged condition with and without pretreatment with 1-MCP, an inhibitor of ethylene perception. For the waterlogging treatments, the primary root (but not the shoots) was waterlogged. Two and half day-old-seedlings were pre-treated with an inhibitor of ethylene perception 1-methylcyclopropene (1-MCP; 1 ppm) for 12 hours before the waterlogging treatment. Three-day-old seedlings were growing under aerated condition at the same time with other treatments as a control. Total RNA was extracted from root cortex cells from the segment of the primary root, 0.5 cm long: from 1.5 to 2 cm from the junction shoot-root derived from 3-days-old maize seedlings, and subjected to 44k oligo-DNA microarray (1. Aerated vs Hypoxia, 2. Hypoxia+MCP vs Hypoxia) with 3 biological replicates and color swaps.