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Displaying 20 of 124 results for "OXR1"
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  1. Transcriptomics analysis of biopolymer (medium chain length polyhydroxyalkanoate) producing strain P.putida LS46 cultured with biodiesel derived waste... OmicsDI

    ID: E-GEOD-65029

    Date Released: 05-09-2015

    Description: es of copAB, which are usually involved in copper resistance and tolerance to other monovalent heavy metals. A local gene relocation was observed in cluster 1 consisting cusABC and copAB relative to the KT2440 type strain according to the phylogenetic and gene neighbourhood analyses on various P. putida strains. P. putida LS46 also contains 11 putative MerR family regulators, which sense various environmental stimuli including heavy metals. MerR-1 is an ortholog of the copper response regulator of other gram-negative bacteria, and was highly up-regulated in waste glycerol cultures. Finally, a number of genes involved in cell responses to high extra-cellular Na+ concentrations, and genes of the fatty acid beta-oxidation pathway were up-regulated in waste glycerol cultures Major results from objective b): Regardless to the type of substrates, up-regulation of two mcl-PHA synthase (PhaC1 and PhaC2), and two phasin proteins (PhaF and PhaI) are the most common genotype under mcl-PHA production conditions. PhaG and possible PhaJ4 connect fatty acid de novo synthesis to mcl-PHA in waste glycerol culture. Interestingly, expression of gene, fabZ, in production of unsaturated fatty acid from fatty acid de novo synthesis was only observed in waste glycerol culture. On the other hand, PhaJ1 and PhaJ4 derived mcl-PHA production via fatty acid beta-oxidation was observed under waste fatty acid culture. These results would help to explain observed different production kinetics and monomer distribution of the polymer. Although under active mcl-PHA produc...

  2. Paralogous MarR/DUF24-family repressors YodB and CatR control expression of the catechol dioxygenase CatE in Bacillus subtilis ArrayExpress

    ID: E-GEOD-22603

    Description: -2,3-dioxygenase that also contributes to quinone resistance. Inactivation of both paralogs, CatR and YodB, results in full derepression of catDE transcription. DNA-binding assays and promoter mutagenesis studies showed that CatR protects two inverted repeats with the consensus sequence TTAC-N5-GTAA overlapping the -35 promoter region (BS1) and the transcriptional start site (BS2). The BS1 operator was required for binding of YodB in vitro. CatR and YodB share the conserved N-terminal Cys residue that is essent...

  3. Transcriptional Regulation of the GPX1 Gene by TFAP2C and Aberrant CpG Methylation in Human Breast Cancer ArrayExpress

    ID: E-GEOD-36351

    Description: induced GPX activity and significantly increased resistance to tert-butyl hydroperoxide. Methylation of the CpG island encompassing the AP-2 regulatory region was identified in cell lines where TFAP2C failed to bind the GPX1 promoter and GPX1 expression was unresponsive to TFAP2C. Furthermore, in cell lines where GPX1 promoter methylation was associated with gene silencing, treatment with 5-aza-dC (an inhibitor of DNA methylation) resulted in activation of GPX1 RNA and protein expression. Methylation of the GPX1 promoter was identified in approximately 20% of primary breast cancers and a highly significant correlation between TFAP2C and GPX1 expression was confirmed when considering only those tumors with an unmethylated promoter, whereas the related factor, TFAP2A, failed to demonstrate a correlation. The results demonstrate that TFAP2C regulates the expression of GPX1, which influences the redox state and sensitivity to oxidative stress induced by peroxides. Given the established role of GPX1 in breast cancer, the results provide an important mechanism for TFAP2C to furth...

  4. Transcription profiling of a rat resistant model - Dioxin lethality: aryl hydrocarbon receptor (AHR)-mediated gene expression ArrayExpress

    ID: E-GEOD-10083

    Description: to a major deletion in the AHR's transactivation domain (TAD). The total number of TCDD-responsive genes was smaller in rats with the AHRH/W genotype than in rats with wildtype AHR. However, genes in the classic AH gene battery such as CYP1A1, CYP1A2 and CYP1B1 remained fully responsive to TCDD in AHRH/W rats; thus the TAD deletion selectively interferes with expression of a subset of hepatic genes rather than abolishing global AHR-mediated responses. Genes in the following functional categories differ in response to TCDD between dioxin-sensitive rats and dioxin-resistant rats: fatty acid oxidation, metabolism (xenobiotic, alcohol, amino acid, and fatty acid), phosphate transport, regulation of steroid biosynthesis, nitrogen compound catabolism, and generation of precursor metabolites and energy. M...

  5. PRDM14 promotes active DNA demethylation through the Ten-eleven translocation (TET)–mediated base excision repair pathway in embryonic stem cells ArrayExpress

    ID: E-GEOD-52598

    Description: se excision repair (BER) pathway, implicating 5mC oxidation in active DNA demethylation. Genome-wide DNA methylation is erased in the transition from metastable states to ground state of embryonic stem cells (ESCs) and in migrating primordial germ cells (PGCs), while some resistant regions become demethylated only in gonadal PGCs. Understanding the mechanisms underlying global hypomethy...

  6. Gene expression response to the antifungal compound 6-Nonadecynoic acid (6-NDA) in Saccharomyces cerevisiae and Candida albicans ArrayExpress

    ID: E-GEOD-35604

    Description: ranscription factors that regulate fatty acid -oxidation showed increased sensitivity to 6-NDA. Fatty acid profile analysis indicated that 6-NDA inhibited the formation of fatty acids longer than 14 carbons in length. In addition, the growth inhibitory effect of 6-NDA was rescued in the presence of exogenously supplied oleate. To investigate the response of a pathogenic fungal species to 6-NDA, transcriptional profiling and biochemical analyses were also conducted in C. albicans. The transcriptional response and fatty acid profile of C. albicans were comparable to those obtained in S. cerevisiae, and the rescue of growth inhibition with exogenous oleate was also observed in C. albicans. In addition, 6-NDA enhanced the potency of the antifungal drug fluconazole in a fluconazole-resistant clinical isola...

  7. Salmonid host response to Hematopoietic Necrosis virus: cellular receptors, viral control and novel pathways of defence OmicsDI

    ID: E-GEOD-6924

    Date Released: 05-02-2014

    Description: samples from five fish sampled on each of days 0, 1, 5 and 9 were analysed in the microarray study. Validation of nine of the significant genes was conducted on fish sampled on alternate days from 1 to 13 and compared to the unchallenged control sampled on day 0. The key pathways up-regulated in response to the virus included endosomal transport, type I and II interferon responses, the alternative comple...

  8. gainst Diet and Age-Induced Adiposity and Insulin Resistance... OmicsDI

    ID: E-GEOD-29984

    Date Released: 06-27-2012

    Description: increased mitochondrial biogenesis, hepatic lipid oxidation, and energy expenditure, but decreased hepatic de novo lipogenesis. Loss of mIndy activates hepatic AMPK, which induces PGC-1?, inhibits ACC-2, and reduces SREBP-1c levels. In contrast to wild- type mice, mINDY-/- mice have reduced body weight and are protected from insulin resistance that evolves with high-fat feeding and aging. These studies demonstrate that mIndy functions as a novel regulator of mammalian energy metabolism and suggest that mIndy might be a novel therapeutic target for the treatment of obesity and type 2 diabetes. An SLC13A5 knockout mouse model (mINDY-/-) was generated. The litters produced when heterozygous (KO/+) mINDY mice (mINDY+...

  9. Leveraging natural variation in the Saccharomyces cerevisiae stress response to understand lignocellulosic hydrolysate toxicity ArrayExpress

    ID: E-GEOD-77505

    Description: Here, we explored natural variation in stress tolerance and in transcriptomic responses to synthetic hydrolysate, mimicking chemically pretreated plan...

    datasetDistributions.accessURL: https://www.ebi.ac.uk/arrayexpress/files/E-GEOD-77505/E-GEOD-77505.raw.1.zip
  10. Metabolic reprogramming of triple-negative breast cancer and melanoma cell lines by the Let-7a microRNA ArrayExpress

    ID: E-GEOD-60326

    Description: cell growth, proliferation, invasiveness and drug resistance. In this study we identified a new metabolic role of let-7a in triple-negative breast cancer and metastatic melanoma cell lines. We show that let-7a down-regulates key anabolic enzymes, promotes oxidative phosphorylation and mitochondrial ROS formation accompanied by the up-regulation of the oxidative stress responsive genes. To assess if we could exploit these increased ROS levels for therapeutic purposes, we combined let-7a transfection with the antitumor drug doxorubicin. In both cancer types we observed a stronger response to the doxorubicin treatment in let-7a transfected cells. Pre-treatment wi...

  11. Next generation sequencing of Desulfovibrio vulgaris Hildenborough in the presence of Free Nitrous Acid stress OmicsDI

    ID: E-GEOD-78834

    Date Released: 07-01-2016

    Description: detected by sequencing. Transcripts exhibiting ≥1 or ≤-1 fold abundance change in the presence of FNA were designated as differentially expressed. Results:The results imply that FNA exerted multiple antimicrobial effects. Growth of the culture was inhibited by FNA and significant proportions of the cells were killed during the exposure. Respiration by sulfate reduction and lactate oxidation was shut down along with ATP production when exposed to FNA. Correspondingly, decreased transcript levels of genes involved in these metabolic pathways were detected. Detoxification of FNA was evident by nitrite reduction and the genes coding both nitrite reductase (NrfA) and hydroxylamine reduct...

  12. Transcription profiling by array of Arabidopsis Columbia and Wassilewskija ecotypes and gl1-1 after salt stress treatment ArrayExpress

    ID: E-GEOD-16765

    Description: (Col), and a single gene mutation (glabrous, gl1-1) in the Col background (Col(gl)), in relation to genetic, phenotypic, and fitness differences. Growth analyses were performed with seedlings germinated on culture media and growth chamber-grown plants carried through the full life cycle. Transcriptome analyses were performed with salt treated and control growth-chamber grown plants six days post initiation of salt stress. Ws plants had the least salt injury and highest dry matter accumulation and seed production in salt stressed conditions. ELPs among genoytypes and in response to 100 mM NaCl were enriched for genes associated with response to stress, including stress-associated transcription factors, heat shock and redox metabolism genes, and R genes. Application of salt resulted in many more transcripts up- or down-regulated in Col and Ws than in Col(gl). Many of the transcripts influenced by salt i...

  13. Genome-wide transcriptional response of the archaeon Thermococcus gammatolerans to cadmium ArrayExpress

    ID: E-GEOD-13546

    Description: ed. We showed that T. gammatolerans exhibits high resistance to cadmium (Cd), cobalt (Co) and zinc (Zn), a weaker tolerance to nickel (Ni), copper (Cu) and arsenate (AsO4) and that cells exposed to 1mM Cd exhibit a cellular Cd concentration of 66µM. A time-dependent transcriptomic analysis using microarrays was performed at a non-toxic (100μM) and a toxic (1mM) Cd dose. The reliability of microarray data was strengthened by real time RT-PCR validations. Altogether, ...

  14. Pathways leading to phosphorylation of p450c17 and to the post-translational regulation of androgen biosynthesis BioProject

    ID: PRJNA189440

    Keywords: Transcriptome or Gene expression

    Access Type: download

    dataset.description: components of the ERK1/2 and MAPK/ERK kinase (MEK)1/2 pathways, which have been implicated in the insulin resistance of PCOS, were not found in NCI-H295A cells, implying that these pathways do not participate in P450c17 phosphorylation. Treatment with various kinase inhibitors that probe the protein kinase A/phosphatidylinositol 3-kinase/Akt pathway and the calcium/calmodulin/MAPK kinase pathway had no effect on the ratio of 17,20 lyase activity to 17alpha-hydroxylase activity, appearing to eliminate these pathways as candidates leading to the phosphorylation of P450c17. Two inhibitors that target the Rho-associated, coiled-coil containing protein kinase (ROCK)/Rho pathway suppressed 17,20 lyase activity and P450c17 phosphorylation, both in NCI-H295A cells and in COS-1 cells transfected with a P450c17 expression vector. ROCK1 phosphorylated P450c17 in vitro, but that phosphorylation did not affect 17,20 lyase ...
  15. Physiological and transcriptome responses to elevated CO2 and magnesium in Arabidopsis thaliana BioProject

    ID: PRJNA271131

    Keywords: Transcriptome or Gene expression

    Access Type: download

    dataset.description: igated the influence of elevated CO2 (800 μL L−1) on physiological and transcriptomic profiles in Arabidopsis cultured in hydroponic media treated with 1 μM (low), 1000 μM (normal) and 10000 μM (high) Mg2+. Following 7-d treatment, elevated CO2 increased the shoot growth and chlorophyll content under both low and normal Mg supply, whereas root growth was improved exclusively under normal Mg nutrition. Notably, the effect of elevated CO2 on mineral homeostasis in both shoots and roots was less than that of Mg supply. Irrespective of CO2 treatment, high Mg increased leaf number but decreased root growth and absorption of P, K, Ca, Fe...
  16. Transcriptomic and phenotypic variation for salt stress response in Arabidopsis BioProject

    ID: PRJNA117417

    Keywords: Transcriptome or Gene expression

    Access Type: download

    dataset.description: (Col), and a single gene mutation (glabrous, gl1-1) in the Col background (Col(gl)), in relation to genetic, phenotypic, and fitness differences. Growth analyses were performed with seedlings germinated on culture media and growth chamber-grown plants carried through the full life cycle. Transcriptome analyses were performed with salt treated and control growth-chamber grown plants six days post initiation of salt stress. Ws plants had the least salt injury and highest dry matter accumulation and seed production in salt stressed conditions. ELPs among genoytypes and in response to 100 mM NaCl were enriched for genes associated with response to stress, including stress-associated transcription factors, heat shock and redox metabolism genes, and R genes. Application of salt resulted in many more transcripts up- or down-regulated in Col and Ws than in Col(gl). Many of the transcripts influenced by salt i...
  17. Temporal gene expression of the cyanobacterium Arthrospira in response to gamma rays BioProject

    ID: PRJNA267105

    Keywords: Transcriptome or Gene expression

    Access Type: download

    dataset.description: after irradiation. The dynamic transcriptome and associated physiological traits showed clearly two events: (1) an intense global emergency response with general reprogramming of carbon and energy metabolism and (2) a recovery period. Genes expressed during early response indicated a reduction of photosynthesis and reduced tricarboxilic acid (TCA) and Calvin Benson Cycles, while a likely activation of pentose phosphate pathway. Activation of biosynthesis of additional carbon storage molecules, compatible solutes, vitamins and sugars transport occurred after irradiation. In addition the cells enhance t...
  18. Beta vulgaris (sugarbeet) infected with BNYVV (beet necrotic yellow vein virus) OmicsDI

    ID: PXD000237

    Date Released: 05-20-2014

    Description: o enable detection of a broad range of proteins associated with compatible interactions, two sources of BNYVV were used; standard BNYVV pathotype A, originally collected from Spence Field at the USDA-ARS in Salinas, CA, and resistance-breaking BNYVV-IV originating from the field, Rockwood 158, Imperial County, CA. Pooled leaf tissue from each cup was ground in liquid nitrogen and lyophilized. Total protein was extracted from 100 mg (dry weight) of lyophilized leaf tissue of each sample using the Plant Total Protein Extraction Kit (Sigma, St. Louis, MO) according to manufacturer’s recommendations. Protease i...

  19. e and secretome modulates the adherence and drug resistance of the fungal pathogen Candida albicans... OmicsDI

    ID: PXD000008

    Date Released: 02-20-2013

    Description: ection. The pellet was washed several times with 1 M NaCl and stored overnight at 4°C. The following day, the pellet was washed several times with MilliQ-water and then boiled four times for 10 min in SDS extraction buffer (150 mM NaCl, 2% (w/v) SDS, 100 mM Na-EDTA, 100 mM β-mercaptoethanol, 50 mM Tris-HCl, pH 7.8), washed with MilliQ-water and lyophilized overnight. The resulting purified wall pellets were either stored at -80°C or directly reduced and S-alkylated [37]. 2.4 Mass spectrometric analyses of cell wall proteomes and secretomes. Lyophilized cell walls were reduced with 10 mM dithiothreitol in 100 mM NH4HCO3 (1 h at 55C). After cooling to room temperature and centrifugation, the supernatant was discarded. The reduced proteins were alkylated with 65 mM iodoacetamide in 100 mM NH4HCO3 for 45 min at room temperature in the dark. The samples were quenched with 55 mM dithiothreitol in 100 mM NH4HCO3 for 5 min. Subsequently, the samples were washed six ti...

  20. Gsr1 in Arabidopsis thaliana: A locus inferred to regulate gene expression in response to exogenous glutamine ArrayExpress

    ID: E-GEOD-37220

    Description: segregation and map location so one mutant, gsr1-1, was selected for intensive analysis. Co-segregation of gsr1 with DNA markers showed the gene was on chromosome 5 between markers CA72 and nga151, an interval of about 0.42 Mbp. The co-segregating mutant phenotypes associated with gsr1 included; yellow color caused by a reduction in chloroplast number; reduced chlorophyll content; decreased nitrate reductase (EC 1.7.1.3) activity in the root; and increased glutamate dehydrogenase (EC 1.4.1.2) activity in root and shoot. Decreased transcripts included those encoding several nitrogen metabolism enzymes. In contrast, the mutation increased only 4 and 7 transcript abundances by more than two fold. RT-PCR showed that in the dark, regula...


Displaying 20 of 124 results for "OXR1"