Metabolomics,Unknown,Transcriptomics,Genomics,Proteomics

Dataset Information

Seasonal bud dormancy progression

ABSTRACT: This study investigated changes in the transcriptome of outdoor grown leafy spurge crown buds as they progress from paradormancy in August and September into endo dormancy in October through to ecodormancy in November and December. Keywords: Dormancy leafy spurge adventitious-buds A series of balanced dyeswap rolling circle hybiridizations were used with each year representing s seperate circle and with direction of the circles reversing on alternate years. Note, the Aug-Sep 04 hybridization failed and is missing from the dataset

ORGANISM(S): Euphorbia esula

SUBMITTER: David Horvath

PROVIDER: E-GEOD-8849 | biostudies-arrayexpress |

REPOSITORIES: biostudies-arrayexpress

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Publications

Transcriptome analysis identifies novel responses and potential regulatory genes involved in seasonal dormancy transitions of leafy spurge (Euphorbia esula L.).

Horvath David P DP Chao Wun S WS Suttle Jeffrey C JC Thimmapuram Jyothi J Anderson James V JV

BMC genomics 20081112

<h4>Background</h4>Dormancy of buds is a critical developmental process that allows perennial plants to survive extreme seasonal variations in climate. Dormancy transitions in underground crown buds of the model herbaceous perennial weed leafy spurge were investigated using a 23 K element cDNA microarray. These data represent the first large-scale transcriptome analysis of dormancy in underground buds of an herbaceous perennial species. Crown buds collected monthly from August through December, ...[more]

PMID: 19014493

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Project description:OBJECTIVE: MEIS1, a HOX cofactor, collaborates with multiple HOX and NUP98-HOX fusion proteins to accelerate the onset of acute myeloid leukemia (AML) through largely unknown molecular mechanisms. MATERIALS AND METHODS: To further resolve these mechanisms, we conducted a structure-function analysis of MEIS1 and gene-expression profiling, in the context of NUP98-HOXD13 (ND13) leukemogenesis. RESULTS: We show, in a murine bone marrow transplantation model, that the PBX-interaction domain, the homeodomain, and the C-terminal domain of MEIS1, are all required for leukemogenic collaboration with ND13. In contrast, the N-terminal domain of MEIS1 is dispensable for collaboration with ND13, but is required for Flt3 upregulation, indicating additional roles for MEIS1 in induction of leukemia independent of alterations in Flt3 expression. Gene-expression profiling of a cloned ND13 preleukemic cell line transduced with wild-type or Meis1 mutant forms revealed deregulation of multiple genes, including a set not previously implicated as MEIS1 targets. Chromatin immunoprecipitation revealed the in vivo occupancy of MEIS1 on regulatory sequences of Trib2, Flt3, Dlk1, Ccl3, Ccl4, Pf4, and Rgs1. Furthermore, engineered overexpression of Trib2 complements ND13 to induce AML while Ccl3 potentiates the repopulating ability of ND13. CONCLUSION: This study shows that Meis1-induced leukemogenesis with ND13 can occur in the absence of Flt3 upregulation and reveals the existence of other pathways activated by MEIS1 to promote leukemia. Establishment of pre-leukemic bone marrow cell lines following transduction with ND13 have been previously described (Pineault, Abramovich et al. 2005). In brief, lines were established from BM cells previously treated with 5-fluorouracil (5-FU) from (C57Bl/6Ly-Pep3b x C3H/HeJ) F1 (PepC3) (Ly5.1+/Ly5.2+) mice freshly transduced with the ND13-GFP or ND13pac virus and maintained in liquid culture. To generate ND13+Meis1 or ND13+Meis1 mutant BM cell lines, the ND13 BM cells were transduced by co-cultivation on irradiated (4,000 cGy) E86 producers for Meis1-YFP (or Meis1 mutant forms), respectively, for a period of 2 days in the presence of 5 µg/ml of protamine sulfate. Three independent experiments were performed for each of the four different conditions included in the study.

Project description:Enteric pathogens have developed several resistance mechanisms to survive the antimicrobial action of bile. We investigated the transcriptional profile of Vibrio cholerae O1 El Tor strain C6706 under virulence gene inducing conditions, in the presence and absence of bile. Microarray analysis revealed that the expression of 119 genes was affected by bile. The mRNA levels of genes encoding proteins involved in transport was increased in the presence of bile, whereas mRNA levels of genes encoding proteins involved in pathogenesis and chemotaxis was decreased. This study identified genes encoding transcriptional regulators from the TetR family (vexR and breR) and multidrug efflux pumps from the RND superfamily (vexB and vexD [here renamed breB]) that were induced in response to bile. Further analysis regarding vexAB and breAB expression in the presence of various antimicrobial compounds established that vexAB was induced in the presence of bile, SDS or novobiocin, whereas induction of breAB was specific to bile. BreR is a direct repressor of the breAB promoter and is able to autoregulate its own expression, as demonstrated by transcriptional and electrophoretic mobility shift assays (EMSA). Expression of breR and breAB is induced in the presence of the bile salts cholate, deoxycholate or chenodeoxycholate and EMSA showed that deoxycholate is able to abolish formation of BreR-PbreR complexes. We propose that deoxycholate is able to interact with BreR and induce a conformational change that will interfere with its DNA binding ability resulting in breAB and breR expression. These results provide new insight into a transcriptional regulator and a transport system that likely play an essential role in the ability of Vibrio cholerae to resist the action of bile in the host. Keywords: Vibrio cholerae response to bile Three independent experiments were performed for the microarray analysis. From each experiment, RNA was obtained from four different time points and was prepared for hybridization, therefore, a total of 3 slides were analyzed per time point. The growth conditions were as follows; C6706 str2 was grown 15 h in LB medium at 30 degrees C with aeration. The cultures were then diluted 100-fold into AKI medium with, or without, 0.4% crude bile (high bile concentration) and were grown at 37degrees C for 3.5 h stationary followed by 2 h with aeration to induce virulence gene expression. Then the cultures were diluted 100-fold into AKI medium with, or without, 0.02% crude bile (low bile concentration) and were grown at 37 degrees C for 2 h stationary. Samples were obtained from 4 different time points: 2, 4, and 5.5 h from the high bile cultures, and at 2 h from the low bile cultures.

Dataset Information

Seasonal bud dormancy progression

Publications

Transcriptome analysis identifies novel responses and potential regulatory genes involved in seasonal dormancy transitions of leafy spurge (Euphorbia esula L.).

Similar Datasets

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