Project description:Correlative controls (influences of one organ over another organ) of seeds over maternal growth are one of the most obvious phenotypic expressions of the trade-off between growth and reproduction. However, the underlying molecular mechanisms are largely unknown. Here, we characterize the physiological and molecular effects of correlative inhibition by seeds on Arabidopsis thaliana inflorescences, i.e. global proliferative arrest (GPA) during which all maternal growth ceases upon the production of a given number of seeds. We use laser-assisted microdissection and RNA-seq or Affymetrix GeneChip hybridizations to compare sterile growing, fertile growing and fertile arrested meristems or whole inflorescences. In shoot tissues, we detected the induction of stress- and senescence-related gene expression upon fruit production and GPA, and a drop in chlorophyll levels - suggestive of altered source-sink relationships between vegetative shoot and reproductive tissues. Levels of shoot reactive oxygen species, however, strongly decreased upon GPA - a phenomenon that is associated with bud dormancy in some perennials. Indeed, gene expression changes in arrested apical inflorescences after fruit removal resembled changes observed in axillary buds following release from apical dominance. This suggests that GPA represents a form of bud dormancy, and that dominance is gradually transferred from growing inflorescences to maturing seeds - allowing offspring control over maternal resources, simultaneously restricting offspring number. Examination of transcriptomes of four reproductive stages: i) sterile growing plants, ii) fertile growing plants, iii) fertile arrested plants, iv) arrested plants after removal of all fruits from the plant
Project description:Correlative controls (influences of one organ over another organ) of seeds over maternal growth are one of the most obvious phenotypic expressions of the trade-off between growth and reproduction. However, the underlying molecular mechanisms are largely unknown. Here, we characterize the physiological and molecular effects of correlative inhibition by seeds on Arabidopsis thaliana inflorescences, i.e. global proliferative arrest (GPA) during which all maternal growth ceases upon the production of a given number of seeds. We use laser-assisted microdissection and RNA-seq or Affymetrix GeneChip hybridizations to compare sterile growing, fertile growing and fertile arrested meristems or whole inflorescences. In shoot tissues, we detected the induction of stress- and senescence-related gene expression upon fruit production and GPA, and a drop in chlorophyll levels - suggestive of altered source-sink relationships between vegetative shoot and reproductive tissues. Levels of shoot reactive oxygen species, however, strongly decreased upon GPA - a phenomenon that is associated with bud dormancy in some perennials. Indeed, gene expression changes in arrested apical inflorescences after fruit removal resembled changes observed in axillary buds following release from apical dominance. This suggests that GPA represents a form of bud dormancy, and that dominance is gradually transferred from growing inflorescences to maturing seeds - allowing offspring control over maternal resources, simultaneously restricting offspring number. Examination of transcriptomes of four reproductive stages: i) sterile growing plants, ii) fertile growing plants, iii) fertile arrested plants, iv) arrested plants after removal of all fruits from the plant; includes whole inflorescences and laser-dissected shoot apices (meristematic regions)
Project description:This SuperSeries is composed of the following subset Series: GSE33335: Expression data from gastric tissues: Cancer Samples vs. Matched Adjacent Noncancerous Samples GSE33428: Copy number variation profiling of gastric tissues: Cancer Samples vs. Matched Adjacent Noncancerous Samples Refer to individual Series
Project description:Breast cancer (BC) is the leading cause of women's cancer death worldwide. Here, in the BC – Anti Progestin Prevention Study 1 (BC-APPS1; NCT02408770), we assess whether progesterone receptor antagonism with ulipristal acetate (UA) for 12 weeks reduces surrogate markers of BC risk in 24 premenopausal women. We employ a multi-layered OMICs and live-cell approach as readouts for molecular features alongside clinical imaging and tissue micro-mechanics correlates. UA reduced epithelial proliferation (Ki67) and the proportion, proliferation, and colony formation capacity of luminal progenitor (LP) cells, the precursors of aggressive BCs. MRI scans showed reduction in fibroglandular volume with treatment, while single-cell RNAseq, proteomics, histology and atomic force microscopy identified extracellular matrix remodelling with reduced collagen organisation and tissue stiffness. Laser capture targeted mass spectrometry revealed Ccollagen VI as the most significantly down-regulated protein after UA treatment and we uncovered an unanticipated spatial association between Collagen VI and Sox9hi LP cell localization, establishing a link between collagen organization and LP activity. This study offers a template for molecularly informed early phase prevention trials and demonstrates the potential for premenopausal BC prevention with progesterone receptor antagonists through stromal remodelling and LP suppression.
Project description:To elucidate gene expression associated with copy number changes, we performed a genome-wide copy number and expression microarray analysis of 25 pairs of gastric tissues. 25 pairs of gastric tissues: gastric cancer tissues vs. matched adjacent noncancerous tissues.
Project description:Copy number variation profiling of gastric tissues comparing gastric cancer tissues with matched adjacent noncancerous tissues. Goal was to determine the effects of chromosomal imbalances on gene expression and carcinogenesis or progression. 27 pairs of gastric tissues: gastric cancer tissues vs. matched adjacent noncancerous tissues.
Project description:In order to provide a better understanding of molecular interactions/responses of snail host hemocyte and early-developing schistosome larvae (sporocyst stage) we perfomed comparative proteomic analyses on hemocytes during active encapsulation of sporocysts under in vitro conditions
Project description:Tissue-specific transcriptional profiling of the abscission layer (AL) at the base of young flower in rice using laser micro-dissection: NIL(qSH1) vs. Nipponbare. We used two rice varieties, NIL(qSH1) and Nipponbare. NIL(qSH1) is a nearly isogenic line containing the seed shattering gene qSH1. Seed shattering is easy in NIL(qSH1), but it is not in Nipponbare. So, we used some stages of young flower in NIL(qSH1) and some in Nipponbare. Four regions: 1. abscission layer region of NIL(qSH1), 2. upper abscission region of NIL(qSH1), 3. lower abscission layer region of NIL(qSH1), and 4. abscission layer region of Nipponbare. Sample experiments: NIL(qSH1) AL vs. Nipponbare AL, NIL(qSH1) AL vs. NIL(qSH1) upper region of AL, and NIL(qSH1) AL vs. NIL(qSH1) lower region of AL.