Project description:Adenocarcinoma in situ (AIS) of the lung has an extremely favorable prognosis, with a 5-year survival rate of 100%. However, early invasive adenocarcinoma (EIA) often has a fatal outcome. In this study, we compared the expression profiles of AIS with those of EIA showing a fatal outcome, and screened the differentially expressed genes by cDNA microarray.
Project description:The investigation contains two sets of experiment. Set I. Transcriptional profiling of salt treated WT A. thaliana (WS ecotype) (100mM NaCl WT/0mM NaCl WT): Set II. Transcriptional profiling of salt treated ABR17- A. thaliana lines (100mM NaCl ABR17/0mM NaCl ABR17). <br>Tissue for microarray analysis was obtained by placing surface sterilized seeds of A. thaliana (line 6.9) and the WT on half strength Murashige & Skoog (MS)(Murashige and Skoog, 1962) medium (1.5% sucrose, 0.8% agar with pH 5.7) medium in Petri dishes with or without 100mM NaCl at RT (21 ± 2 °C) after surface sterilization. The seeds were surface sterilized by rinsing with 70% ethanol for one minute, incubation in 20% bleach for 15 min and subsequent washes (four times for 5min each) to remove the bleach. MS plates with the seeds were placed at RT (21 ± 2 °C) under continuous fluorescent light 30 ?mol m-2 s-1 for 14 days. Seedlings (14 day-old) from three independently grown biological replicates in two set of experiments were removed from the MS plates, flash frozen in liquid nitrogen and stored at 80 °C until used for RNA extraction.<br>Technical protocols for preparing the hybridization extract:<br><br>1. RNA was isolated using the QIAGEN RNeasy Plant Mini Kit (Qiagen Inc., Mississauga, ON, Canada) from two-week-old WT (grown on 0 and 100mMNaCl) and ABR17 (grown on 0 and 100mMNaCl) seedling tissue grown at three independent times (biological replicates). The integrity of all RNA samples assessed by agarose gel (1.2 percent) electrophoresis. <br><br>2. 6 ?g (Six micrograms) of total RNA was used to synthesize cDNAs using SuperScript® II RT (Invitrogen Inc., Burlington, ON, Canada) with RT polyA-capture primers in 3D Array 900TM (Genisphere Inc., Hatfield, PA, USA). Each pair of treated (100mM NaCl) and untreated (0mM NaCl) samples within each of the three biological replicates from two sets of experiments (100mM NaCl WT/0mM NaCl WT ; 100mM NaCl ABR17/0mM NaCl ABR17) was labelled in a reciprocal dye-swap design, for a total of 12 hybridizations. <br><br><br>Note: In the transgenic plant production, the pea cDNA encoding for ABR17 was constitutively expressed under the control of Cauliflower mosaic virus 35S promoter. <br>Reference: Srivastava S., Rahman H., Shah S. and Kav N.N.V. Constitutive<br>expression of pea ABA-responsive 17 (ABR17) cDNA confers multiple<br>stress tolerance in Arabidopsis thaliana. Plant Biotechnology Journal<br>(2006) 4, 529-549.<br><br><br>
Project description:Loop-design (triangle design with the comparison of each triplet: hybrid + parent 1 and parent 2) and pairwise design (hybrid + parent 1, hybrid + parent 2) were used in the experiment.<br> Four inbred lines and their four inter-pool hybrids were hybridized respectively in two-colour chips experiments. <br> The objective of our study was to:(i) identify differentially expressed genes in relation to heterosis for plant height, (ii) relate gene expression patterns to the dominance and overdominance hypothesis, (iii) determine the consistency of expression patterns between inbred parent - hybrid triplets also in view of differing degrees of relatedness of triplets, and to (iv) validate consistently differentially expressed genes between hybrids and their parental inbreds by real-time (qRT) PCR.
Project description:We studied transcriptional regulations under drought stress of wheat roots in genotype "Opata" over two biological replicates. We imposed severe drought stress down to nearly permanent wilting point and flash frozen the roots of opata.
Project description:A transcriptomic time-course study was performed on the senescence process in flag leaves of the spring wheat cultivar Bobwhite grown in the green-house. Leaf samples were harvested at eight time-points from the time of ear emergence until 50% yellowing of the harvested leaf sample.
Project description:Genome-wide in planta determination of the quorum sensing regulon in Pectobacterium atrosepticum, through gene expression analysis of ExpI mutants using Agilent custom microarrays.
Project description:Plant material consisted of synthetic hexaploid wheat germplasm into the Opata background (Altar 84/ Aegilops squarrosa (TAUS)//Opata) . Plants were grown at a density of 9-11 individuals per 20cm x 10cm (diameter x height) plastic pot containing 1500g well-rinsed Turface MVP® medium (Profile Products LLC, Buffalo, IL), in controlled environment chambers at 23°C, 70% relative humidity, and 16h photoperiod with a photosynthetic photon flux (PPF) of 330±10 µmolem-2s-1 when measured at the top of the canopy at growth stage 22 to 24 in the Zadoks scale (Zadoks et al., 1974). Plants were watered daily until 21 days after seeding (DAS) by flooding trays with water for 5 minutes, then draining the trays. Drought stress was applied by water withholding, beginning on 21 DAS. Watering was withheld from plants belonging to drought treatment, while the control group received water above field capacity. Water content of the growth medium was gravimetrically monitored. Root tissues were collected from control and treated plants when the water content of the treatment group growth medium fell below the permanent wilting point. Three biological replicates were conducted in three separate time-span courses. Total RNA was isolated using a LiCl3 precipitation method following Moore et al., (2005). Dye swap desin microarray analyses of well-watered and water-stressed root tissues were conducted across three biological replicates totaling six hybridizations.
Project description:Gene level analysis of lactating day 10-11 16h Sprague-Dawley dams compared against age matched virgins. Lactation is a time of significantly increased energy demands imposed by the suckling young that requires a proportional adjustment in the ability of the lactating dam to absorb nutrients and to synthesize critical biomolecules to meet the dietary needs of both the offspring and the dam. We have shown an increase in the size and hydrophobicity of the bile acid pool during lactation [1], implying an increased absorption and disposition of lipids, sterols, nutrients, and xenobiotics. In order to investigate changes at the level of mRNA, we utilized an exon array and calculated gene level summaries to investigate changes in gene expression in the liver, duodenum, jejunum, and ileum of lactating dams when compared against age-matched virgin controls. Affymetrix Rat Exon 1.0ST arrays were used to determine expression of genes in the livers and small intestines of day 10-11 lactating Sprague Dawley rats and compared against virgins of comparable age.