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GSE104862
Pseudomonas aeruginosa pao1
6 Downloadable Samples
Affymetrix Pseudomonas aeruginosa Array (paeg1a)
Description
P. aeruginosa possesses the ability to utilize a wild range of compounds as the sole source of carbon and nitrogen, including proteogenic amino acids. In particular, utilization of L-Asp and L-Asn is insensitive to carbon catabolite repression as strong growth retains in the cbrAB mutants devoid of the essential regulators for the activation of most catabolic genes. Transcriptome analysis and functional characterization were conducted to identify genes that participate in the catabolism, uptake, and regulation of these two amino acids. Through gene knockout and growth phenotype analysis, degradation of L-Asn to L-Asp was shown to be mediated by two asparaginases AsnA and AsnB, whereas only AnsB is required for the deamidation of D-Asn to D-Asp. While D-Asp is a dead-end product, conversion of L-Asp to fumurate is catalyzed by an aspartase AspA as further evidenced by enzyme kinetics. The results from the measurements of promoter-lacZ expression in vivo and mobility shift assays in vitro demonstrated that the asnR and aspR genes encode two transcriptional regulators in response to L-Asn and L-Asp, respectively, for the induction of the ansPA operon and the aspA gene. In addition, exogenous L-Glu also cause induction of the aspA gene, most likely due to its conversion to L-Asp by the aspartate transaminase AspC. Expression of several transporters were also found inducible by L-Asn and/or L-Asp, including AatJQMP for acid amino acids, DctA and DctPQM for C4-dicarboxylates, and PA5530 for C5-dicarboxylates. In summary, a complete pathway and regulation for L-Asn and L-Asp catabolism was established in this study. Cross induction of three transport systems for dicarboxylic acids may provide a physiological explanation for the insensitivity of L-Asn and L-Asp utilization to carbon catabolite repression.
Publication Title
No associated publication
Sample Metadata Fields
No sample metadata fields
View Samples- Pseudomonas aeruginosa pao1
- 4 Downloadable Samples
- Affymetrix Pseudomonas aeruginosa Array (paeg1a)
Description
MvaT and MvaU are two redundant xenogeneic silencing proteins of the H-NS family in Pseudomonas aeruginosa. Previous studies to investigate the physiological consequences of mvaT and mvaU depletion were hampered by activation of Pf4 prophage in the resulting mutants. In this study, an mvaT mvaU double knockout mutant (PAO△TU) was constructed in a strain of PAO1 (Δpf4) devoid of the Pf4 prophage on the chromosome.Transcriptome analysis by GeneChip (Affymetrix) revealed that over 227 genes were found up-regulated in PAO△TU, including several multi-gene loci for type III and type VI protein secretion systems, O-antigen, exopolysaccharide, pili assembly, and many others of unknown functions.
Publication Title
No associated publication
Sample Metadata Fields
No sample metadata fields
View Samples- Homo sapiens
- 35 Downloadable Samples
- Affymetrix Human Genome U133 Plus 2.0 Array (hgu133plus2)
Description
Obesity is a risk factor for numerous metabolic disorders; however, not all obese individuals are prone to insulin resistance. The central aim of this study was to identify molecular pathways directly related to insulin resistance independent of BMI in obesity.
Publication Title
Body mass index-independent inflammation in omental adipose tissue associated with insulin resistance in morbid obesity.
Sample Metadata Fields
Sex, Specimen part
View Samples- Homo sapiens
- 17 Downloadable Samples
- Affymetrix Human Genome U133 Plus 2.0 Array (hgu133plus2)
Description
Obesity is a risk factor for numerous metabolic disorders; however, not all obese individuals are prone to insulin resistance. The central aim of this study was to identify molecular pathways directly related to insulin resistance independent of BMI in obesity.
Publication Title
Body mass index-independent inflammation in omental adipose tissue associated with insulin resistance in morbid obesity.
Sample Metadata Fields
Sex, Specimen part
View Samples- Arabidopsis thaliana
- 18 Downloadable Samples
- Affymetrix Arabidopsis ATH1 Genome Array (ath1121501)
Description
When iron is withdrawn from the growth medium of plants, large changes in gene expression have been observed. A double mutant with T-DNA insertions in the Arabidopsis yellow stripe1-like1 (At4g24120) and yellow stripe3-like (At5g53550) genes shows strong iron-related phenotypes. This study is intended to uncover the gene expression changes that occur in leaves and roots of the double mutant compared to wild type plants.
Publication Title
No associated publication
Sample Metadata Fields
Specimen part, Treatment
View Samples- Xenopus laevis
- 9 Downloadable Samples
- Affymetrix Xenopus laevis Genome Array (xenopuslaevis)
Description
ADAMs are transmembrane metalloproteases that control cell behavior by cleaving both cell adhesion and signaling molecules. The cytoplasmic domain of ADAMs can regulate the proteolytic activity by controlling the subcellular localization and/or the activation of the protease domain. Here we show that the cytoplasmic domain of ADAM13 is cleaved and translocates into the nucleus. Preventing this translocation renders the protein incapable of promoting cranial neural crest (CNC) cell migration in vivo, without affecting its proteolytic activity. In addition, the cytoplasmic domain of ADAM13 regulates the expression of multiple genes in the CNC. This study shows that the cytoplasmic domain of ADAM metalloproteases can perform essential functions in the nucleus of cells and may contribute substantially to the overall function of the protein.
Publication Title
Translocation of the cytoplasmic domain of ADAM13 to the nucleus is essential for Calpain8-a expression and cranial neural crest cell migration.
Sample Metadata Fields
Specimen part
View Samples- Mus musculus
- 4 Downloadable Samples
- Affymetrix Mouse Genome 430A 2.0 Array (mouse430a2)
Description
Analysis of CPEB translational regulator target mRNAs
Publication Title
Cytoplasmic polyadenylation element binding protein deficiency stimulates PTEN and Stat3 mRNA translation and induces hepatic insulin resistance.
Sample Metadata Fields
Age
View Samples- Escherichia coli
- 18 Downloadable Samples
- Affymetrix E. coli Genome 2.0 Array (ecoli2)
Description
SoxR and SoxS constitute an intracellular signal response system that rapidly detects changes in superoxide levels and modulates gene expression in E. coli.
Publication Title
Rapid changes in gene expression dynamics in response to superoxide reveal SoxRS-dependent and independent transcriptional networks.
Sample Metadata Fields
No sample metadata fields
View Samples- Danio rerio
- 16 Downloadable Samples
- Affymetrix Zebrafish Genome Array (zebrafish)
Description
Domesticated animal populations often show profound reductions in predator avoidance and fear-related behavior compared to wild populations. These reductions are remarkably consistent and have been observed in a diverse array of taxa including fish, birds, and mammals. Experiments conducted in common environments indicate that these behavioral differences have a genetic basis. In this study, we quantified differences in fear-related behavior between wild and domesticated zebrafish strains and used microarray analysis to identify genes that may be associated with this variation.
Publication Title
Brain transcriptome variation among behaviorally distinct strains of zebrafish (Danio rerio).
Sample Metadata Fields
Sex, Specimen part
View Samples- Arabidopsis thaliana
- 5 Downloadable Samples
- Affymetrix Arabidopsis ATH1 Genome Array (ath1121501)
Description
Background:
Publication Title
Transcriptional responses to polycyclic aromatic hydrocarbon-induced stress in Arabidopsis thaliana reveal the involvement of hormone and defense signaling pathways.
Sample Metadata Fields
Age, Specimen part, Treatment
View Samples