Similar Datasets
Project description:Plants align flowering with optimal seasonal conditions to increase reproductive success. This process depends on modulating signalling pathways that respond to diverse environmental and hormonal inputs, thereby regulating the transition to flowering at the shoot apical meristem. In Arabidopsis, long-day photoperiods (LDs) stimulate the transcription of FLOWERING LOCUS T (FT), encoding the main florigenic signal. FT activation is mediated by the transcriptional regulator CONSTANS (CO), which binds to the CO responsive elements (COREs) located in the proximal FT promoter region. The phytohormone abscisic acid also (ABA) contributes to FT activation together with GIGANTEA (GI) to regulate drought escape (DE). Whether CO is a target of ABA and GI actions for the regulation of FT is, however, unknown. Here we report that ABA and its signalling components promote CO recruitment to the COREs, without causing clear effects on the diel pattern of CO protein accumulation. We also found that GI promotes CO recruitment to the COREs region, and that CO recruitment is required for the accumulation of RNAPol II at the TRANSCRIPTION START SITE of FT. Finally, we show that GI and ABA signalling pathways are largely epistatic in the control of flowering time, suggesting their involvement in the same molecular process. Taken together, these observations suggest that varying water deficit conditions modulate CO recruitment and FT expression, thus dictating DE strategies in Arabidopsis.
2025-05-13 | GSE291256 | GEO
Project description:Flowering of Arabidopsis thaliana is accelerated by several environmental cues, including exposure to long days. The photoperiod-dependent promotion of flowering involves the transcriptional induction of FLOWERING LOCUS T (FT) in the phloem of the leaf. FT encodes a mobile protein that is transported from the leaves to the shoot apical meristem, where it forms part of a regulatory complex that induces flowering. Whether FT also has biological functions in leaves of wild-type plants remains unclear. In order to address this issue, we first studied the leaf transcriptomic changes associated with its over expression in the companion cells of the phloem. To this end, transgenic A. thaliana plants that misexpress FT from the pGAS1 promoter in a ft-10 tsf-1 double mutant background were employed (pGAS1:FT ft-10 tsf-1). In these transgenic plants, the use of the pGAS1 promoter ensures that the FT transgene is expressed in phloem companion cells of the minor veins, recreating the spatial pattern of expression described for the native gene. In this studuy, the transcriptome of leaves of pGAS1:FT ft-10 tsf-1 transgenic plants was compared to that of ft-10 tsf-1 and Col-0 plants using Tiling Arrays.
2020-02-05 | GSE125054 | GEO
Project description:Despite its significance to reproduction, fertility, sexually transmitted infections and various pathologies, the fallopian tube (FT) is relatively understudied. Strong evidence points to the FT as the tissue-of-origin of high grade serous ovarian cancer (HGSOC), the most fatal gynaecological malignancy. HGSOC precursor lesions arise specifically in the distal FT (fimbria) which is reported to be enriched in stem-like cells. Investigation of the role of FT stem cells in health and disease has been hampered by a lack of characterization of FT stem cells and lack of models that recapitulate stem cell renewal and differentiation in vitro. Using optimized organoid culture conditions to address these limitations, we found that FT stem cell renewal is highly dependent on WNT/β-catenin signaling and engineered endogenous WNT/β-catenin signaling reporter organoids to biomark, isolate and characterize putative FT stem cells. Using functional approaches as well as bulk and single cell transcriptomic analyses, we show that an endogenous hormonally-regulated WNT7A-FZD5 signaling axis is critical for self-renewal of human FT stem cells, and that WNT/β-catenin pathway-activated cells form a distinct transcriptomic cluster of FT cells enriched in ECM remodelling and integrin signaling pathways. In addition, we find that the WNT7A-FZD5 signaling axis is dispensable for mouse oviduct regeneration. Overall, we provide a deep characterization of FT stem cells and their molecular requirements for self-renewal, paving the way for mechanistic work investigating the role of stem cells in FT health and disease.
2023-11-01 | GSE239582 | GEO
Project description:Despite its significance to reproduction, fertility, sexually transmitted infections and various pathologies, the fallopian tube (FT) is relatively understudied. Strong evidence points to the FT as the tissue-of-origin of high grade serous ovarian cancer (HGSOC), the most fatal gynaecological malignancy. HGSOC precursor lesions arise specifically in the distal FT (fimbria) which is reported to be enriched in stem-like cells. Investigation of the role of FT stem cells in health and disease has been hampered by a lack of characterization of FT stem cells and lack of models that recapitulate stem cell renewal and differentiation in vitro. Using optimized organoid culture conditions to address these limitations, we found that FT stem cell renewal is highly dependent on WNT/β-catenin signaling and engineered endogenous WNT/β-catenin signaling reporter organoids to biomark, isolate and characterize putative FT stem cells. Using functional approaches as well as bulk and single cell transcriptomic analyses, we show that an endogenous hormonally-regulated WNT7A-FZD5 signaling axis is critical for self-renewal of human FT stem cells, and that WNT/β-catenin pathway-activated cells form a distinct transcriptomic cluster of FT cells enriched in ECM remodelling and integrin signaling pathways. In addition, we find that the WNT7A-FZD5 signaling axis is dispensable for mouse oviduct regeneration. Overall, we provide a deep characterization of FT stem cells and their molecular requirements for self-renewal, paving the way for mechanistic work investigating the role of stem cells in FT health and disease.
2023-11-01 | GSE239581 | GEO
Project description:Background: It has been shown previously that administration of Francisella tularensis (Ft) LVS lipopolysaccharide (LPS) protects mice against subsequent challenge with Ft LVS and blunts the pro-inflammatory cytokine response. Methods: To investigate further the molecular mechanisms that underlie Ft LVS LPS-mediated protection, we profiled global hepatic gene expression following Ft LVS LPS or saline pretreatment and subsequent Ft LVS challenge using Affymetrix arrays. Results: A large number of genes (> 3000) were differentially expressed at 48 hours post-infection. The degree of modulation of inflammatory genes by infection was clearly attenuated by LPS-pretreatment in the surviving mice. However, LPS alone had a subtle but significant effect on the gene expression profile of the uninfected mice. By employing gene set enrichment analysis, we discovered significant up-regulation of peroxisome proliferator activated receptors (PPARs) and their target genes in LPS-treated liver. Conclusions: We hypothesize that the LPS-induced blunting of pro-inflammatory response in mouse is, in part, mediated by PPARs (alpha and gamma). Experiment Overall Design: Two groups of 9 mice each were used for this experiment. 48 hours prior to Ft LVS challenge, mice were injected i.p. with either 100 ng of Ft LVS LPS or an equivalent volume of saline. On the day of challenge, 3 saline- and 3 Ft LVS LPS-pretreated animals were sacrificed (uninfected controls), while all remaining mice were challenged i.p. with ~4-5 X 105 Ft LVS. Ft LVS-challenged mice were sacrificed (in groups of 3) at 24 and 48 hours post-infection.
2010-02-21 | E-GEOD-16207 | biostudies-arrayexpress
Project description:The variability of the marine intertidal environment poses unique challenges for sessile species. Diurnal, tidal, and seasonal cycles introduce drastic variations in temperature, salinity, availability of nutrients and water. The California ribbed mussel Mytilus californianus is a filter feeder that dominates a middle range of the intertidal of many wave-swept rocky shores. The bivalve attaches to the substrate by several byssal threads. This sessile lifestyle allows us to accurately document the thermal history of an individual. We have profiled gene expression in M. californianus during a natural tidal cycle using a cDNA microarray composed of genes from mussels exposed to various stressors. Over three days, mussels were sampled from two sites differing in emersion exposure and average temperature. At each time point, three mussels were cut open in the field and frozen immediately on dry ice and stored at -80 degrees C until the gill, hepatopancreas, and adductor muscle were excised and processed for RNA extraction, reverse transcription, and hybridization to our microarrays. The resulting expression profile showed that genes involved in the cell cycle were diurnally regulated, heat shock proteins increased with temperature, and expression of several hundred other genes varied across the tidal cycle. Tide series (times and tide height): 26th July, low tide 0052, 0.8 ft; high tide 0705, 3.1 ft; low tide 1113, 2.4 ft; high tide 1810, 5.9ft. 27th July, low tide 0154, 0.1 ft; high tide 0837, 3.3 ft; low tide 1216, 2.7ft; high tide 1903, 6.2 ft. 28th July, low tide 0249, -0.6ft; high tide 0943, 3.5 ft; low tide 1323, 2.8ft; high tide 1903, 6.2ft. 15th Aug, low tide 0530, 0.26 ft; high tide 1200, 4.08 ft, low tide 0432, 2.65 ft; high tide 1036, 5.84 ft.
2007-07-30 | E-TABM-287 | biostudies-arrayexpress
Project description:Molecular Features of the Serological IgG Repertoire Elicited by Egg-based, Cell-based, or Recombinant HA Seasonal Influenza Vaccines. __sample information__ Donorname day0S1 or day28S2 Elu or FT Pf number A1 S1 FT 7649_JL_5a.raw A1 S1 FT 7649_JL_5b.raw A1 S1 FT 7649_JL_5c.raw A1 S2 FT 7649_JL_7a.raw A1 S2 FT 7649_JL_7b.raw A1 S2 FT 7649_JL_7c.raw A1 S1 Elu 7649_JL_6a.raw A1 S1 Elu 7649_JL_6b.raw A1 S1 Elu 7649_JL_6c.raw A1 S2 Elu 7649_JL_8a.raw A1 S2 Elu 7649_JL_8b.raw A1 S2 Elu 7649_JL_8c.raw A2 S1 FT 8078_JP_1a.raw A2 S1 FT 8078_JP_1b.raw A2 S1 FT 8078_JP_1c.raw A2 S2 FT 8078_JP_2a.raw A2 S2 FT 8078_JP_2b.raw A2 S2 FT 8078_JP_2c.raw A2 S1 Elu 8078_JP_3a.raw A2 S1 Elu 8078_JP_3b.raw A2 S1 Elu 8078_JP_3c.raw A2 S2 Elu 8078_JP_4a.raw A2 S2 Elu 8078_JP_4b.raw A2 S2 Elu 8078_JP_4c.raw A3 S1 FT 8116_JP_1a.raw A3 S1 FT 8116_JP_1b.raw A3 S1 FT 8116_JP_1c.raw A3 S2 FT 8116_JP_2a.raw A3 S2 FT 8116_JP_2b.raw A3 S2 FT 8116_JP_2c.raw A3 S1 Elu 8116_JP_3a.raw A3 S1 Elu 8116_JP_3b.raw A3 S1 Elu 8116_JP_3c.raw A3 S2 Elu 8116_JP_4a.raw A3 S2 Elu 8116_JP_4b.raw A3 S2 Elu 8116_JP_4c.raw A4 S1 FT 8149_JP_1a.raw A4 S1 FT 8149_JP_1b.raw A4 S1 FT 8149_JP_1c.raw A4 S2 FT 8149_JP_2a.raw A4 S2 FT 8149_JP_2b.raw A4 S2 FT 8149_JP_2c.raw A4 S1 Elu 8149_JP_3a.raw A4 S1 Elu 8149_JP_3b.raw A4 S1 Elu 8149_JP_3c.raw A4 S2 Elu 8149_JP_4a.raw A4 S2 Elu 8149_JP_4b.raw A4 S2 Elu 8149_JP_4c.raw A5 S1 FT 8209_JP_1a.raw A5 S1 FT 8209_JP_1b.raw A5 S1 FT 8209_JP_1c.raw A5 S2 FT 8209_JP_2a.raw A5 S2 FT 8209_JP_2b.raw A5 S2 FT 8209_JP_2c.raw A5 S1 Elu 8209_JP_3a.raw A5 S1 Elu 8209_JP_3b.raw A5 S1 Elu 8209_JP_3c.raw A5 S2 Elu 8209_JP_4a.raw A5 S2 Elu 8209_JP_4b.raw A5 S2 Elu 8209_JP_4c.raw B1 S1 FT 7924_JL_1a.raw B1 S1 FT 7924_JL_1b.raw B1 S1 FT 7924_JL_1c.raw B1 S2 FT 7924_JL_2a.raw B1 S2 FT 7924_JL_2b.raw B1 S2 FT 7924_JL_2c.raw B1 S1 Elu 7924_JL_4a.raw B1 S1 Elu 7924_JL_4b.raw B1 S1 Elu 7924_JL_4c.raw B1 S2 Elu 7924_JL_5a.raw B1 S2 Elu 7924_JL_5b.raw B1 S2 Elu 7924_JL_5c.raw B2 S1 FT 7947_JL_1a.raw B2 S1 FT 7947_JL_1b.raw B2 S1 FT 7947_JL_1c.raw B2 S2 FT 7947_JL_2a.raw B2 S2 FT 7947_JL_2b.raw B2 S2 FT 7947_JL_2c.raw B2 S1 Elu 7947_JL_3a.raw B2 S1 Elu 7947_JL_3b.raw B2 S1 Elu 7947_JL_3c.raw B2 S2 Elu 7947_JL_4a.raw B2 S2 Elu 7947_JL_4b.raw B2 S2 Elu 7947_JL_4c.raw B3 S1 FT 8129_JL_1a.raw B3 S1 FT 8129_JL_1b.raw B3 S1 FT 8129_JL_1c.raw B3 S2 FT 8129_JL_2a.raw B3 S2 FT 8129_JL_2b.raw B3 S2 FT 8129_JL_2c.raw B3 S1 Elu 8129_JL_3a.raw B3 S1 Elu 8129_JL_3b.raw B3 S1 Elu 8129_JL_3c.raw B3 S2 Elu 8129_JL_4a.raw B3 S2 Elu 8129_JL_4b.raw B3 S2 Elu 8129_JL_4c.raw B4 S1 FT 8164_JP_1a.raw B4 S1 FT 8164_JP_1b.raw B4 S1 FT 8164_JP_1c.raw B4 S2 FT 8164_JP_2a.raw B4 S2 FT 8164_JP_2b.raw B4 S2 FT 8164_JP_2c.raw B4 S1 Elu 8164_JP_3a.raw B4 S1 Elu 8164_JP_3b.raw B4 S1 Elu 8164_JP_3c.raw B4 S2 Elu 8164_JP_4a.raw B4 S2 Elu 8164_JP_4b.raw B4 S2 Elu 8164_JP_4c.raw B5 S1 FT 8237_JP_1a.raw B5 S1 FT 8237_JP_1b.raw B5 S1 FT 8237_JP_1c.raw B5 S2 FT 8237_JP_2a.raw B5 S2 FT 8237_JP_2b.raw B5 S2 FT 8237_JP_2c.raw B5 S1 Elu 8237_JP_3a.raw B5 S1 Elu 8237_JP_3b.raw B5 S1 Elu 8237_JP_3c.raw B5 S2 Elu 8237_JP_4a.raw B5 S2 Elu 8237_JP_4b.raw B5 S2 Elu 8237_JP_4c.raw C1 S1 FT 8108_JP_1a.raw C1 S1 FT 8108_JP_1b.raw C1 S1 FT 8108_JP_1c.raw C1 S2 FT 8108_JP_2a.raw C1 S2 FT 8108_JP_2b.raw C1 S2 FT 8108_JP_2c.raw C1 S1 Elu 8108_JP_3a.raw C1 S1 Elu 8108_JP_3b.raw C1 S1 Elu 8108_JP_3c.raw C1 S2 Elu 8108_JP_4a.raw C1 S2 Elu 8108_JP_4b.raw C1 S2 Elu 8108_JP_4c.raw C2 S1 FT 8048_JL_1a.raw C2 S1 FT 8048_JL_1b.raw C2 S1 FT 8048_JL_1c.raw C2 S2 FT 8048_JL_2a.raw C2 S2 FT 8048_JL_2b.raw C2 S2 FT 8048_JL_2c.raw C2 S1 Elu 8048_JL_3a.raw C2 S1 Elu 8048_JL_3b.raw C2 S1 Elu 8048_JL_3c.raw C2 S2 Elu 8048_JL_4a.raw C2 S2 Elu 8048_JL_4b.raw C2 S2 Elu 8048_JL_4c.raw C3 S1 FT 8068_JP_1a.raw C3 S1 FT 8068_JP_1b.raw C3 S1 FT 8068_JP_1c.raw C3 S2 FT 8068_JP_2a.raw C3 S2 FT 8068_JP_2b.raw C3 S2 FT 8068_JP_2c.raw C3 S1 Elu 8068_JP_3a.raw C3 S1 Elu 8068_JP_3b.raw C3 S1 Elu 8068_JP_3c.raw C3 S2 Elu 8108_JP_5a.raw C3 S2 Elu 8108_JP_5b.raw C3 S2 Elu 8108_JP_5c.raw C4 S1 FT 8203_JP_1a.raw C4 S1 FT 8203_JP_1b.raw C4 S1 FT 8203_JP_1c.raw C4 S2 FT 8203_JP_2a.raw C4 S2 FT 8203_JP_2b.raw C4 S2 FT 8203_JP_2c.raw C4 S1 Elu 8203_JP_3a.raw C4 S1 Elu 8203_JP_3b.raw C4 S1 Elu 8203_JP_3c.raw C4 S2 Elu 8203_JP_4a.raw C4 S2 Elu 8203_JP_4b.raw C4 S2 Elu 8203_JP_4c.raw C5 S1 FT 8258_JP_1a.raw C5 S1 FT 8258_JP_1b.raw C5 S1 FT 8258_JP_1c.raw C5 S2 FT 8258_JP_2a.raw C5 S2 FT 8258_JP_2b.raw C5 S2 FT 8258_JP_2c.raw C5 S1 Elu 8258_JP_3a.raw C5 S1 Elu 8258_JP_3b.raw C5 S1 Elu 8258_JP_3c.raw C5 S2 Elu 8258_JP_4a.raw C5 S2 Elu 8258_JP_4b.raw C5 S2 Elu 8258_JP_4c.raw
2025-01-15 | PXD046473 | Pride
Project description:Camelina sativa is an important polyploid oilseed crop with multiple favorable agronomic traits. Capturing the leaf transcriptome of 48 accessions of C. sativa suggests allelic variation for gene expression levels and notably sub-genome dominance, both of which could provide opportunities for crop improvement. Flowering time (FT) is a crucial factor affecting the overall yield of crops. However, our understanding of the molecular mechanisms underlying FT regulation in C. sativa are still limited, partly due to its complex allohexaploid genome. In this study, weighted gene co-expression network analysis (WGCNA), expression quantitative trait loci (eQTL) analysis and transcriptome-wide association study (TWAS) were employed to explore the FT diversity among 48 C. sativa accessions and dissect the underlying molecular basis. Our results revealed a FT-related co-expressed gene module highly enriched with SOC1s and SOC1-like genes, and identified 10 significant FT-associated single nucleotide polymorphisms (SNPs), thus providing a molecular basis for future genetic improvements in C. sativa breeding
2025-03-25 | GSE253393 | GEO
Project description:Background: It has been shown previously that administration of Francisella tularensis (Ft) LVS lipopolysaccharide (LPS) protects mice against subsequent challenge with Ft LVS and blunts the pro-inflammatory cytokine response. Methods: To investigate further the molecular mechanisms that underlie Ft LVS LPS-mediated protection, we profiled global hepatic gene expression following Ft LVS LPS or saline pretreatment and subsequent Ft LVS challenge using Affymetrix arrays. Results: A large number of genes (> 3000) were differentially expressed at 48 hours post-infection. The degree of modulation of inflammatory genes by infection was clearly attenuated by LPS-pretreatment in the surviving mice. However, LPS alone had a subtle but significant effect on the gene expression profile of the uninfected mice. By employing gene set enrichment analysis, we discovered significant up-regulation of peroxisome proliferator activated receptors (PPARs) and their target genes in LPS-treated liver. Conclusions: We hypothesize that the LPS-induced blunting of pro-inflammatory response in mouse is, in part, mediated by PPARs (alpha and gamma).
2010-01-31 | GSE16207 | GEO