Differential gene expression of candidate genes for growth in rainbow trout
ABSTRACT: This SuperSeries is composed of the SubSeries listed below. Growth in fishes is a complex trait, controlled by both genetic and environmental factors, that impacts many components of fitness. Gene expression studies may lead to the identification of candidate genes for growth and microarrays offer the opportunity to examine the expression of thousands of genes simultaneously. Gene expression differences in the liver and white muscle were examined in normally growing, 15 month-old, large and small size-selected rainbow trout (Oncorhynchus mykiss) derived from two different seasonal spawning groups (Sept. and Dec.). Examination of the gene expression differences in both liver and white muscle tissue allowed us to assess the seasonal influences upon gene expression patterns that occur in this species, and facilitated the identification of genes that may possess similar expression patterns regardless of seasonal effects. The analysis of global gene expression in large and small fish reared under standard conditions provides an understanding of typical growth patterns that may be observed in this species. The identification of candidate genes by this study may provide insight into the mechanisms of growth in fishes and may help to identify candidate genes for growth.
Project description:Transcriptional profiling of rainbow trout liver and muscle cells comparing small fish with large fish within a population of neomale offspring. Small vs. large-fish liver and muscle cells from neomale offspring. Biological replicates: 4 small replicates, 4 large replicates.
Project description:Transcriptional profiling of rainbow trout liver cells comparing liver cells from small fish with liver cells from large fish at two time periods. Two-condition experiment, small vs. large-fish liver cells. Sept. and Dec. spawning fish. Biological replicates: 4 small replicates, 4 large replicates for each time period.
Project description:Transcriptional profiling of rainbow trout muscle cells comparing muscle cells from small fish with muscle cells from large fish at two time periods. Two-condition experiment, small vs. large-fish muscle cells. Sept. and Dec. spawning fish. Biological replicates: 4 small replicates, 4 large replicates for each time period.
Project description:Atlantic salmon at their 2nd year in sea were fed with a low, medium or high histidine diet (L, M, and H, respectively) for several months. Samples were taken at three time points, after the first, second and third period, and a number of fishes were assigned to a new feed group following a crossover experimental design. The feeding experiment was carried out in duplicates in cages in sea water. A number of 6 fishes of each nutritional group and from each replicate were sampled at each time point, and weight, length and cataract development were monitored of the sampled fish and an additional number of fishes (18-34). Fish developed cataracts with different severity in response to dietary histidine levels. Lens N-acetylhistidine contents reflected the dietary histidine levels and were negatively correlated to cataract scores. This experiment contains four dietary groups of fish, named LM, HM, LLL and MMM. <br>LM: Low histidine diet in the first period, Medium histidine diet in the second period<br>HM: High first, Medium second period<br>LLL: Low diet in all three periods<br>MMM: Medium diet in all three periods<br>In the analysis LM and HM is compared for early effects, while LLL vs MMM is compared for stable long time effects. Each feeding period is roughly a month each. Each dietary group contains 11 biological replicates. The RNA samples were labelled and hybridised to two channel 16K cGRASP salmonid arrays using a common reference design. The common reference was made from a pool of all samples.
Project description:The angio-suppressive effect of 20(R)-ginsenoside Rg3 (Rg3-R) has been previously demonstrated, and microRNAs (miRNAs) are a vital group of small non-coding RNAs that function as post-transcriptional modulator of gene expression. Thus, using human umbilical vein endothelial cells (HUVEC) as model, we compared the microRNA (miRNA) expression profile of vascular endothelial growth factor (VEGF)-induced cells with the profile of the cell co-treated with VEGF and Rg3-R. Among the screened 553 human miRNAs, 6 up-regulated (miR-520h, miR-487b, miR-197, miR-524*, miR-342 and miR-219) and 3 down-regulated (miR-23a, miR-489 and miR-377) miRNAs were detected in Rg3-R treated vascular endothelial growth factor (VEGF)-induced HUVECs compared to VEGF alone. Real time RT-PCR was subsequently performed to verify the miRNA microarray result. Two condition experiment: VEGF-induced HUVEC and VEGF-induced HUVEC treated with Rg3-R. Three independent microarray experiments, with triplicate per microarray.
Project description:This study was designed to identify changes in gene expression when corn was placed under various related stresses including being grown with a competing weed (canola) to the V4 or V8 stage, or when 40% shade cloth was present to the V4 or V8 stage, or under low nitrogen (no added nitrogen fertilizer), or under weed/shade free fertilized control conditions. In all 5 treatments and the control, samples were harvested at V8. Mechanisms underlying early season weed stress on crop growth are not well described. Corn vegetative growth and development, yield, and gene expression response to nitrogen (N), light (40% shade), and weed stresses were compared with the response of nonstressed plants. Vegetative parameters, including leaf area and biomass, were measured from V2 toV12 corn stages. Transcriptome (2008) or quantitative Polymerase Chain Reaction (q PCR) (2008/09) analyses examined differential gene expression in stressed versus nonstressed corn at V8. Vegetative parameters were impacted minimally by N stress although grain yield was 40% lower. Shade, present until V2, reduced biomass and leaf area > 50% at V2 and, at V12, recovering plants remained smaller than nonstressed plants. Grain yields of shade-stressed plants were similar to nonstressed controls, unless shade remained until V8. Growth and yield reductions due to weed stress in 2008 were observed when weeds remained until V6. In 2009, weed stress at V2 reduced vegetative growth, and weed stress until V4 or later reduced yield. Principle component analysis of differentially expressed genes indicated that shade and weed stress had more similar gene expression patterns to each other than to nonstressed or low N stressed tissues. Weed-stressed corn had 630 differentially expressed genes compared with the nonstressed control. Of these genes, 259 differed and 82 were shared with shade-stressed plants. Corn grown in N-stressed conditions shared 252 differentially expressed genes with weed-stressed plants. Ontologies associated with light/photosynthesis, energy conversion, and signaling were down-regulated in response to all three stresses. Although shade and weed stress clustered most tightly together, only three ontologies were shared by these stresses, O-methyltransferase activity (lignification processes), Poly U binding activity (post-transcriptional gene regulation), and stomatal movement. Based on both morphologic and genomic observations, results suggest that shade, N, and weed stresses to corn are regulated by both different and overlapping mechanisms. three biological replicates for each treatment and the control were collected and the resulting labeled cDNA was hybridized to the 46,000-element maize microarray chip developed by the University of Arizona using their protocol (International Microarray Workshop Handbook, 2009Gardiner et al. 2005). The hybridization scheme was a dual hybridization using a rolling circle balanced dye swap design. Thus we had thre biological replicates for each growth condition amd two technical replicates for each biological sample.
Project description:Identification of a stable gene expression signature with high classifying potential to discriminate post-radiotherapy-induced thyroid tumors (follicular adenomas and papillary carcinomas) from their sporadic counterparts.
Project description:Seasonal wood development results in two distinct wood types: earlywood (EW) and latewood (LW), which is the major cause of wood qaulity variation. We investigate transcriptome reorganization during seasonal wood development in radiata pine using a newly developed 18k cDNA microarrays. Three sampling trees each at juvenile (5 yrs), transition (9 yrs) and mature (14 yrs) ages (based on the wood rings at breast height) were selected from a plantation forest of radiata pine at Bondo, NSW , Australia (35º 16' 44.04 S, 148º 26' 54.66 E). The sampling trees at juvenile and mature ages were grown within 50 m distance and under similar environment. Two sampling trees at rotation age (30 yrs) were chosen at Yarralumla, ACT, Australia (35° 18' 27'' S, 149° 7' 27.9'' E).
Project description:Bud formation is an adaptive trait that temperate forest trees have acquired to facilitate seasonal synchronization. We have characterized transcriptome-level changes that occur during bud formation of white spruce (Picea glauca [Moench] Voss.), a primarily determinate species in which preformed stem units contained within the apical bud constitute most of next season's growth. Microarray analysis identified 4460 differentially expressed sequences in shoot tips during short day-induced bud formation. Cluster analysis revealed distinct temporal patterns of expression, and functional classification of genes in these clusters implied molecular processes that coincide with anatomical changes occurring in the developing bud. Comparing expression profiles in developing buds under long day and short day conditions identified possible photoperiod-responsive genes that may not be essential for bud development. Several genes putatively associated with hormone signalling were identified, and hormone quantification revealed distinct profiles for ABA, cytokinins, auxin and their metabolites that can be related to morphological changes to the bud. Comparison of gene expression profiles during bud formation in different tissues revealed 108 genes that are differentially expressed only in developing buds and show greater transcript abundance in developing buds than other tissues. These findings provide a temporal roadmap of bud formation in white spruce. Shoot tips (terminal buds), needles, and secondary stems were collected from two-year-old white spruce plants over a 10-week time course of 0, 1, 3, 7, 14, 28, and 70 days after switching from 6 to 8 weeks of long daylight photoperiods (LD; 16 hours of light and 8 hours of dark) to short daylight photoperiods (SD; 8 hours of daylight and 16 hours of dark). Remaining plants were kept in short days for an additional 8-15 weeks, and then transferred to low temperature (LT; 2°C to 4°C) for 3 to 4 weeks with continuing SD prior to harvest. Another set of plants was grown and harvested under the same conditions as described above, but remained in LD at all times. Four sets of dye-swap design microarray experiments were conducted. The first set of experiments (samples 1-7) studied the SD time course of buds development. Terminal buds from each time point (1d, 3d, 7d, 14d, 28d, and 70d) and LT were co-hybridized with actively growing shoot tips (0d). The same time point comparison (without LT) of shoot tips from LD-treated trees was carried out as the second set of experiments (samples 8-13). The third experiment (samples 14-20) denoted a separate LD/SD comparison at seven different time points (0d, 1d, 3d, 7d, 14d, 28d, and 70d), and the last experiment (samples 21-26) compared SD shoot tips, needles, and secondary stems with each of the other tissues at 14d and 70d. In each experiment, four biological replicates were used, with two replicates representing the dye-swaps.
Project description:This SuperSeries is composed of the following subset Series: GSE29985: Identification by ChIP-on-Chip of ARX target genes, a transcription factor implicated in mental retardation and epilepsy GSE30190: Comparison of gene expression between Arx-transfected N2a cells and cells transfected by the corresponding empty vector Refer to individual Series