Gene expression patterns in the head horns, thoracic horns, and legs of the horned beetles Onthophagus taurus
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ABSTRACT: This series examines gene expression patterns in the head horns, thoracic horns, and legs of the horned beetles Onthophagus taurus. Expression in each of these tissues was compared to that in common non-appendage reference - abdominal epithelium. The series consists of three pair-wise comparisons: head horn versus abdominal epithelium, thoracic horn versus abdominal epithelium and legs versus abdominal epithelium. Each tissue sample was obtained by pooling tissue dissected from four pupae. Samples compared on the same array were derived from tissues dissected from the same four animals. Five independent biological replicates were performed for each comparison with dye flips (three in one direction and two in the opposite direction).
Project description:Developmental mechanisms play an important role in determining the costs, limits, and evolutionary consequences of phenotypic plasticity. One issue central to these claims is the metaphor of developmental “decoupling,” where alternate morphs result from evolutionarily independent developmental pathways. We test this assumption through a microarray study that explores differences in gene expression between alternate morphs relative to differences between sexes, a classic example of developmental decoupling. We then examine whether morph-biased genes are less conserved, relative to morph-shared genes, as predicted if developmental decoupling relaxes pleiotropic constraints on divergence. We focus on the developing horns and brains of two species of horned beetles with spectacular sexual- and morph-dimorphism in the expression of horns and fighting behavior. We find that patterns of gene expression were as divergent between morphs as they were between sexes. However, overall patterns of gene expression were also highly correlated across morphs and sexes. Morph-biased genes were more evolutionarily divergent, suggesting a role of relaxed pleiotropic constraints or relaxed selection. Together these results suggest that alternate morphs are somewhat developmentally decoupled, and that this decoupling has significant evolutionary consequences. However, alternative morphs may not be as developmentally decoupled as sometimes assumed and such hypotheses of development should be revisited and refined. We compared gene expression in three focal epidermal tissues (head, prothorax, legs) relative to a "control" tissue (dorsal abdominal epidermis) without any outgrowths. We also surveyed gene expression in the brain, relative to ganglionic neural tissue. We compared such patterns of gene expression between two male morphs (horned, fighter and hornless, sneaker males) and between males and females. We focused our array analyses (N = 48 arrays) on Onthophagus taurus (the species for which the array was designed), but also ran 19 arrays on thoracic tissue of Onthophagus nigriventris, a species which expresses thoracic horns as adults (O. taurus expresses head horns). Finally, we included a small subset of arrays (N = 4) directly hybridizing head epidermis tissue of O. taurus male morphs to validate our overall estimates of morph-biased expression. For more detail, refer to Snell-Rood et al. 2010, Evolution.
Project description:Abstract Background: Bone marrow stromal cells (BMSCs) are being used for immune modulatory, anti-inflammatory and tissue engineering applications, but the properties responsible for these effects are not completely understood. Human BMSCs were characterized to identify factors that might be responsible for their clinical effects and biomarkers for assessing their quality. Methods: Early passage BMSCs prepared from marrow aspirates of 4 healthy subjects were compared to 3 human embryonic stem cell (hESC) samples, CD34+ cells from 3 healthy subjects and 3 fibroblast cell lines. The cells were analyzed with oligonucleotide expression microarrays with more than 35,000 probes. Results: BMSC gene expression signatures of BMSCs differed from those of hematopoietic stem cells (HSCs), hESCs and fibroblasts. Genes up-regulated in BMSCs were involved with cell movement, cell-to-cell signaling and interaction and proliferation. The BMSC up-regulated genes were most likely to belong to integrin signaling, integrin linked kinase (ILK) signaling, NFR2-mediated oxidative stress response, regulation of actin-based motility by Rho, actin cytoskeletal signaling, caveolar-mediated endocytosis, clathrin-mediated endocytosis and Wnt/beta catenin signaling pathways. Among the most highly up-regulated genes were structural extracellular (ECM) proteins: alpha1 and beta1 integrin chains, fibronectin, collagen type IIIalpha1, and collagen type Valpha1 and functional EMC proteins: connective tissue growth factor (CTGF) and transforming growth factor beta induced protein (TGFBI) and ADAM12. Conclusions: Global analysis of human BMSCs suggests that they are mobile, metabolically active, proliferative and interactive cells that make use of integrins and integrin signaling. They produce abundant ECM proteins; some of which may contribute to their clinical immune modulatory and anti-inflammatory effects. Seven samples from early passage BMSCs were prepared from marrow aspirates of healthy subjects and compared to 3 human embryonic stem cell (hESC) samples, CD34+ cells from 3 healthy subjects and 3 fibroblast cell lines. Total RNA from a pool of PBMCs from six healthy subjects was extracted and amplified into aRNA to serve as a reference.
Project description:Transcriptional profiling of eight normal adult chicken tissues in 10-week old brown (lohmann brown) hens, the eight tissues include brain, bursa of Fabricius, jejunum, kidney, liver, lung, spleen, thymus. Keywords: normal chicken tissues, transcriptional profiling. eight different normal chicken adult tissue types, five biological replicates per tissue, each individual sample was hybridized with a common reference pool (pool of RNA samples from all individual samples). All individual samples were labeled with Cy3, common reference was labeled with Cy5.
Project description:To identify key genes in the regulation of salt tolerance in the mangrove plant Bruguiera gymnorhiza, the transcriptome profiling under salt stress was carried out. Main roots and lateral roots were collected from the mangrove plants at 0, 1, 3, 6, 12 and 24 h, 3 6 and 12 days after NaCl-treatment. Samples were collected from each set of three trees at 0, 1, 3, 6, 12 and 24 h, 3 6 and 12 days after NaCl-treatment, that is 27 trees were used in total. RNA was extracted from mixture of the samples from 3 trees to average genotypes of 3 trees.
Project description:The transcriptional and metabolic profiles of rosettes of three independent Arabidopsis thaliana ecotype Wassiliewska lines overexpressing the soybean early noduline GmENOD40 gene were compared to those of wt, and a biomarker analysis was performed. ENOD40 overexpression resulted in 382 modulated genes, 142 of which upregulated and 165 downregulated in all the three transformed lines. Cell wall, membrane, hydrolase activity on glycosidic bonds, defense response and response to stimulus gene categories were overrepresented in the modulated genes compared to TAIR complete database. Metabolomics analysis (through liquid chromatography-mass spectrometry) allowed to putatively identify 13 different glucosinolates, some flavonoids, sinapic and ferulic acid derivatives, hydroxybenzoic acid derivatives, non aromatic organic acids, amino acids. Positive genes biomarkers of the transformed plants were mainly involved in cell wall turnover, whereas positive metabolite biomarkers were the methylthioalkyl-glucosinolates. The transcriptional profile of rosettes of three independent Arabidopsis thaliana ecotype Wassiliewska lines overexpressing the soybean early noduline GmENOD40 gene were compared to those of wt, and a biomarker analysis was performed.
Project description:Treatment of oocytes derived from large (4-6 mm; LG) or small (>3 mm; SM) follicles with glial cell line-derived neurotrophic factor (GDNF) during in vitro maturation. Four-condition experiment, SM and LG oocytes, each with and without GDNF. Biological replicates: 9 per condition, independently collected. Pools of three replicates per array.
Project description:Cumulus cells, surrounding the oocyte, play a key role in the acquisition of oocyte competence to be fertilized and to sustain early embryo development. Cumulus cells contribute to oocyte development by metabolizing energy substrates such as glutathione that may protect the oocyte from oxidative stress damages. The aim of our study was to compare transcriptomics profiles of cumulus enclosed (CEO) and cumulus denuded (CDO) oocytes after in vitro maturation. Global transcriptional profiling was performed using cumulus enclosed and cumulus denuded oocytes after in vitro maturation. Matured oocytes were obtained after 22h of maturation with (CEO) or without (CDO) cumulus cells and four replicates of 25 oocytes were collected for RNA extraction. Gene expression analysis was performed by comparing CDO versus CEO oocytes that represents a total of 8 slides using a dye swap hybridisation protocol.
Project description:Assisted reproduction technologies (ART) and high selection pressure observed in the dairy industry are leading towards the use of younger females for reproduction purpose, reducing the interval between generations. This situation might have an impact on 10 young Holstein cows were used 3 times each at different ages for ovarian stimulation protocols and oocyte collections (at 8, 11 and 14 months). These oocytes were then fertilized in vitro with adult bull semen, generating 3 lots of embryos per animal.
Project description:In dairy ruminants transcriptome profiling has enabled the identification of genes, pathways and regulatory networks activated in mammary tissues during experimental infection by various pathogens, including E. coli, S. aureus and S. uberis. Information in goats are still low and many host-pathogen interaction mechanisms have to be explained. The objectives of the present study were (1) to identify the network of genes that becomes activated in caprine blood and milk somatic cells in early response towards a S. aureus challenge in order to better understand the local and sistemic response and (2) to search any difference in this immune response by using two animal groups belonging to a caprine reference family established based on founders with adverse SCC breeding values. Udders from ten healthy French Alpine goats were infected with S. aureus and samples of blood and milk cells were collected at 0, 24 and 30 hours after infection. Alterations in the transcriptome profile were investigated using a custom bovine DNA microarray containing 43.822 unique gene probes.
Project description:Comparative transcriptomic analyses were performed at both the immature and at the mature stages between oocytes collected from cows with a high or low embryo development potential (HOP, LOP) as characterized by in vitro fertilization and embryo development. 1 biological replicate each from 3 HOP animals and 3 LOP animals, both at the immature stage and mature stage