Source: https://www.omicsdi.org/dataset/arrayexpress-repository/E-GEOD-13717
Timestamp: 2019-04-18 20:57:17+00:00

Document:
ABSTRACT: Partial genome microarray and plankton cells RNA was isolated from biofilms and from planktonic cells grown in SD media. Samples were labeled with either Cy5 or Cy3. Four independent biological replicates were compared, including dye swaps.
Correlation between biofilm formation and the hypoxic response in Candida parapsilosis.
Project description:We used the results of a genome sequence survey to design and manufacture partial genomic microarrays that were applied to determining the transcriptional response of C. parapsilosis to the presence of exogenous farnesol. Keywords: drug response, farnesol, Transcriptional profiling was performed following exposure to 50 microM of farnesol compare to the control experiment (no treatment). Six independent experiment comparisons (including 3 dye swaps) were performed.
Project description:Intracellular pH affects many cellular systems but its mechanisms of regulation and perception are mostly unknown. Weak organic acids such as acetate are potent fungistatic agents used in food preservation, but their intracellular targets are poorly understood. We thus searched for transcriptional response in Saccharomyces cerevisiae to intracellular acidification caused by two hours 30mM acetic acid treatment. Two independent experiments were performed for both acid-treated/non-treated cells. The experimental design for both cases was a Balanced Block Design with four biological replicates, two of them dye swaps.
Project description:Effect of the vegetal hormone ethylene in Arabidopsis thaliana plants grown on agar.
Project description:Metabolic pathways are largely conserved in eukaryotes, but the transcriptional regulation of these pathways can sometimes vary between species; this has been termed rewiring. Recently it has been established that in the Saccharomyces lineage starting from Saccharomyces castelli, genes involved in allantoin breakdown have been genomically relocated to form the DAL cluster. The formation of the DAL cluster occurred along with the loss of urate permease (UAP) and urate oxidase (UOX), reducing the requirement for oxygen and bypassing the candidate Ppr1 inducer, uric acid. In Saccharomyces cerevisiae this allantoin catabolism cluster is regulated by the transcription factor Dal82, which is not present in many of the pre-rearrangement fungal species. We have used ChIP-Chip analysis, transcriptional profiling of an activated Ppr1 protein, bioinformatics, and nitrogen utilization studies, to establish that in Candida albicans the zinc cluster transcription factor Ppr1 controls this allantoin catabolism regulon. Intriguingly, in S. cerevisiae the Ppr1 ortholog binds the same DNA motif (CGG(N6)CCG) as in C. albicans, but serves as a regulator of pyrimidine biosynthesis. This transcription factor rewiring appears to have taken place at the same phylogenetic step as the formation of the rearranged DAL cluster. This transfer of the control of allantoin degradation from Ppr1 to Dal82, together with the repositioning of Ppr1 to the regulation of pyrimidine biosynthesis, may have resulted from a switch to a metabolism that could exploit hypoxic conditions in the lineage leading to S. castellii and S. cerevisiae. 2 samples were analyzed. Cells were grown in YPD media at 30 degrees celcius to OD 0.8. Ppr1 gain of function mutant strain (SCPPR1GAD1A) vs wild type (SC5314) were hybridized, dye swap was done. One replica per array.
Project description:Transcription profiling of post-anthesis unfertilized pistil development and senescence in Arabidopsis, in a serie including samples from seven different stages according to pistil age in days post-anthesis (dpa). The time course started at anthesis and ended at 12-14 dpa, several days later of the loss of fruit set capacity. Keywords: Developmental time course Unfertilized pistils were obtained growing under low humidity cer6-2 conditional male sterile mutant of Arabidopsis in Ler background. The seven stages considered were: 0-1 dpa, 2-3 dpa, 4-5 dpa, 6-7 dpa, 8-9 dpa 10-11 dpa and 12-14 dpa. Two biological replicas with two technical replicas each were performed for each stage. The biological replicas were grown independently, and all the samples of each one were harvested simultaneously. Amplified RNA from each sample was hibridized together with a global reference over the DNA microarray. The reference was generated from an equimolar mix of amplified RNAs from each of the seven samples of the corresponding biological replica. Amplified RNA from each sample was labelled separately with Cy5 and with Cy3, and each labelling was compared in the DNA microarray with Cy3-labelled and with Cy5-labelled RNA from the reference mix, respectively.
Project description:Quorum sensing (QS) is a cell density regulated communication system that bacteria use to coordinate activities, including biofilm formation, involved in colonization and pathogenesis. We have previously shown that inactivation of the QS master regulator LitR attenuates the Vibrio (Allivibrio) salmonicida strain LFI1238 in a fish model. In this work we show that LFI1238 as well as a panel of naturally occurring V. salmonicidia strains are poor biofilm producers. Inactivation of litR strongly enhances medium and temperature dependent adhesion, rugose colony morphology and biofilm formation. Chemical treatment and scanning electron microscopy of the biofilm identified an extracellular matrix consisting mainly of protein filaments and polysaccharides. Further, microarray analysis of planktonic and biofilm cells identified a number of genes regulated by LitR, and among these were homologues of the Vibrio fischeri symbiosis polysaccharide (syp) genes. Disruption of syp alleviated the different phenotypes regulated by LitR in V. salmonicida. Hence, LitR is a repressor of syp expression that is necessary for rugose colony morphology, adhesion and biofilm formation, three phenotypes of the DlitR mutant that are expressed at temperatures below 12ºC. The DlitR mutant mimics low cell density behavior suggesting that these phenotypes are important during the initial steps of colonization. Although the syp operon in V. salmonicida shows identical gene synteny to the one in the squid symbiont V. fischeri, its regulation is probably more related to vibrio polysaccharide (vps) expression in the human pathogenic Vibrio cholera which is controlled by the LitR homologue HapR. V. salmonicida wild type strain LFI1238 (control) and the isogenic DlitR deletion mutant were grown in suspension in SWT medium at 8°C with 200 rpm and harvested at OD=0.8. Biological replicates for each sample: 4 wild type, 4 DlitR mutant (including one dye swap), independently grown and harvested. One replicate per array.
Project description:Quorum sensing (QS) is a cell density regulated communication system that bacteria use to coordinate activities, including biofilm formation, involved in colonization and pathogenesis. We have previously shown that inactivation of the QS master regulator LitR attenuates the Vibrio (Allivibrio) salmonicida strain LFI1238 in a fish model. In this work we show that LFI1238 as well as a panel of naturally occurring V. salmonicidia strains are poor biofilm producers. Inactivation of litR strongly enhances medium and temperature dependent adhesion, rugose colony morphology and biofilm formation. Chemical treatment and scanning electron microscopy of the biofilm identified an extracellular matrix consisting mainly of protein filaments and polysaccharides. Further, microarray analysis of planktonic and biofilm cells identified a number of genes regulated by LitR, and among these were homologues of the Vibrio fischeri symbiosis polysaccharide (syp) genes. Disruption of syp alleviated the different phenotypes regulated by LitR in V. salmonicida. Hence, LitR is a repressor of syp expression that is necessary for rugose colony morphology, adhesion and biofilm formation, three phenotypes of the DlitR mutant that are expressed at temperatures below 12ºC. The DlitR mutant mimics low cell density behavior suggesting that these phenotypes are important during the initial steps of colonization. Although the syp operon in V. salmonicida shows identical gene synteny to the one in the squid symbiont V. fischeri, its regulation is probably more related to vibrio polysaccharide (vps) expression in the human pathogenic Vibrio cholera which is controlled by the LitR homologue HapR. V. salmonicida wild type strain LFI1238 (control) and the isogenic DlitR mutant were grown as statical biofilm in SWT medium, at 4°C and harvested after 72 hours. Biological replicates for each sample: 4 wild type, 4 DlitR mutant (including one dye swap), independently grown and harvested. One replicate per array.

References: V. 
 V. 
 V. 
 V. 
 V. 
 V. 
 V. 
 V. 
 V. 
 V.