We conducted a set of lab-evolution experiments in yeast and followed the long-term dynamics of aneuploidy under diverse conditions including heat shock and high PH.
Chromosomal duplication is a transient evolutionary solution to stress.
No sample metadata fields
View SamplesThe eukaryotic cytoplasmic chaperonin-containing TCP-1 (CCT) is a complex formed by two back-to-back stacked hetero-octameric rings that assists the folding of actins, tubulins and other proteins in an ATP-dependent manner. Here, we decided to test the significance of the hetero-oligomeric nature of CCT for its function by introducing, in each of the eight subunits in turn, an identical mutation at a position involved in ATP binding and conserved in all the subunits, in order to establish the extent of individuality of the various subunits. Our results show that these identical mutations lead to dramatically different phenotypes. For example, cells with the mutation in CCT2 have an excess of actin patches and are the only pseudo-diploid strain. By contrast, cells with the mutation in CCT7 are the only ones to accumulate juxta-nuclear protein aggregates that may reflect the absence of stress response in this strain. System-level analysis of the strains using RNA microarrays reveals connections between CCT and several cellular networks including ribosome biogenesis and TOR2 that help to explain the phenotypic variability observed
Equivalent mutations in the eight subunits of the chaperonin CCT produce dramatically different cellular and gene expression phenotypes.
No sample metadata fields
View SamplesTumor formation constitutes a major obstacle to the clinical application of embryonic stem cells (ESCs). As P-RPCs could successfully integrate into host eyes without development of teratomas or NOG, we sought to identify differentially expressed genes between P-RPCs and ESC-RPCs through genome-wide transcript profiling. Inhibition of Wnt signaling by DKK1 promotes the commitment of ESC-RPCs to more mature retinal cells and reduces the occurrence of NOG to 3%. DKK1-treated ESC-RPCs efficiently integrate to the host retina, form synaptic connections and restore visual function.
WNT signaling determines tumorigenicity and function of ESC-derived retinal progenitors.
Specimen part, Treatment
View SamplesBoth leukemia inhibitory factor (LIF) and interleukin-6 (IL-6) increase the invasiveness of JEG-3 and HTR-8/SVneo cells. This study examines the effect of LIF and IL-6 on gene expression in trophoblastic cell models viz. JEG-3 and HTR-8/SVneo cells to decipher the molecular basis of the increase in invasiveness.
No associated publication
Cell line, Treatment
View SamplesThis SuperSeries is composed of the SubSeries listed below.
A fine balance: epigenetic control of cellular quiescence by the tumor suppressor PRDM2/RIZ at a bivalent domain in the cyclin a gene.
Cell line
View SamplesKnockdown of PRDM2 led to precocious differentiation. To understand the molecular basis for this phenotype, we performed microaary analysis of 28hr differentiated myoblasts.
A fine balance: epigenetic control of cellular quiescence by the tumor suppressor PRDM2/RIZ at a bivalent domain in the cyclin a gene.
Cell line
View SamplesKnockdown of PRDM2 led to precocious differentiation. To understand the molecular basis for this phenotype, we performed microaary analysis of quiescent myoblasts.
A fine balance: epigenetic control of cellular quiescence by the tumor suppressor PRDM2/RIZ at a bivalent domain in the cyclin a gene.
Cell line
View SamplesDespite their importance, plant MAP kinase targets are still poorly elucidated. Here, the specific in vivo interaction of an ethylene response factor (ERF104) with the Arabidopsis MAP kinase, MPK6, is shown by fluorescence resonance energy transfer. The interaction, which is lost within minutes after treatment with the flagellin-derived flg22 peptide, is dependent on both MPK6 kinase activity and rapid ethylene signaling initiated downstream of MPK6 activation. ERF104 is an MPK6 substrate and phosphorylation site mutations affected its stability. ERF104 activates promoters with GCC elements. This was evident from microarray data of overexpressing transgenic plants, where promoters of up regulated genes contain GCC motifs and chromatin immunoprecipitation showing ERF104 association with PDF1.2 promoter. The ERF104 overexpressor did not affect biotrophic bacteria proliferation but was more susceptible to necrotrophic Botrytis cinerea. Microarray performed with erf104 or mpk6 revealed only a limited number of flg22-induced genes that require these elements - possibly as a
Flg22 regulates the release of an ethylene response factor substrate from MAP kinase 6 in Arabidopsis thaliana via ethylene signaling.
No sample metadata fields
View SamplesMany of the genes coding for secreted protein effectors are arranged in gene clusters in the genome of the biotrophic plant pathogen Ustilago maydis. The largest of these gene clusters, cluster 19A, encodes 24 secreted effectors. Deletion of the entire cluster results in severe attenuation of virulence. The generation and analysis strains carrying sub-deletions identified 9 genes significantly contributing to tumor formation after seedling infection. As the individual contributions of these genes to tumor formation were small, we studied the response of maize plants to the whole cluster mutant as well as to several individual mutants by array analysis. This revealed distinct plant responses, demonstrating that the respective effectors have discrete plant targets. Many of the genes coding for secreted protein effectors are arranged in gene clusters in the genome of the biotrophic plant pathogen Ustilago maydis. The largest of these gene clusters, cluster 19A, encodes 24 secreted effectors. Deletion of the entire cluster results in severe attenuation of virulence. The generation and analysis strains carrying sub-deletions identified 9 genes significantly contributing to tumor formation after seedling infection. As the individual contributions of these genes to tumor formation were small, we studied the response of maize plants to the whole cluster mutant as well as to several individual mutants by array analysis. This revealed distinct plant responses, demonstrating that the respective effectors have discrete plant targets.
Characterization of the largest effector gene cluster of Ustilago maydis.
Specimen part, Treatment
View SamplesThe basidiomycete Ustilago maydis causes smut disease in maize. Colonization of the host plant is initiated by direct penetration of cuticle and cell wall of maize epidermis cells. The invading hyphae are surrounded by the plant plasma membrane and proliferate within the plant tissue. We identified a novel secreted protein, termed Pep1. Disruption mutants of pep1 are not affected in saprophytic growth and develop normal infection structures. However, pep1 mutants fail to penetrate the epidermal cell wall and elicit a strong plant defense response. Using Affymetrix maize arrays we identified about 110 plant genes which are differentially regulated in pep1 and wild type infections during the penetration stage.
Pep1, a secreted effector protein of Ustilago maydis, is required for successful invasion of plant cells.
No sample metadata fields
View Samples