Ontology highlight
ABSTRACT:
PROVIDER: PRJNA1045277 | ENA |
REPOSITORIES: ENA
Similar Datasets
Project description:Isolation of novel species of prokaryotes from aquatic environments
| PRJDB17504 | ENA
Project description:Colorectal cancer (CRC) is characterized by extensive intra-tumor heterogeneity. The cancer stem cell (CSC) theory may explain the mechanisms underlying the non-genetic heterogeneity and their characteristics of prominent plasticity are emerging to be elucidated. By tracking the spheroid formation and growth capacity of CRC CSCs with a single-cell resolution using an organoid culture, we revealed CSCs consisted of subpopulations with a dual (fast and slow)-growing pattern. When isolated, the slow-growing CSCs remained slow-growing and converted into dual-growing CSCs under certain conditions. The slow-growing cells showed low levels of MAP kinase activity and were resistant to a MEK1/2 inhibitor as well as chemo-drugs. The MSI1 gene was down-regulated in the slow-growing CSCs and played a key role in the transition between slow- and dual-growing CSCs. Isolation of slow-growing CSCs will provide a platform to elucidate the role of the plasticity of CSCs in drug resistance and tumor recurrence. To disclose the molecular characteristics of the CSC subclones with the distinct growth features, we analyzed the differentially expressed genes between the subgroups.
2021-10-01 | GSE185012 | GEO
Project description:Chemostats have been used for decades in studying cell growth under controlled environments. Whole transcriptome sequencing by RNA-seq is a relatively new method for gene expression analysis. We utilized both tools for expression analysis of Pseudomonas aeruginosa growing slowly in synthetic cystic fibrosis medium under growth-limiting nitrate and oxygen levels. We established steady-state cultures under two divergent growth rates and found that during slower growth at a doubling time of 9.8 h, 76 known quorum genes were up-expressed while just 11 were down-expressed. Quorum-controlled genes were also more expressed in response to oxygen limitation. 21% of up-expressed genes under slow, oxygen-limited growth are quorum controlled while just 6% are up-expressed under slow, nitrate-limited growth. We found that the autoinducer for regulator RhlR, C4-HSL, is ~3.4 times higher when cells are growing slowly under oxygen limitation while the concentration of the autoinducer for LasR remained unchanged. Experiments with deletion mutants show the importance of rhlR for expression of quorum-controlled genes under slow, oxygen-limited conditions. This is an intriguing observation since P. aeruginosa is likely growing in similar environments in the cystic fibrosis lung, and lasR mutations are known to arise during chronic infection.
2016-12-01 | GSE71880 | GEO
Project description:Background: The Dobzhansky-Muller (D-M) model of speciation by genic incompatibility is widely accepted as the primary cause of interspecific postzygotic isolation. Since the introduction of this model, there have been theoretical and experimental data supporting the existence of such incompatibilities. However, speciation genes have been largely elusive, with only a handful of candidate genes identified in a few organisms. The Saccharomyces sensu stricto yeasts have small genomes, can be easily cultured, and can mate interspecifically to produce sterile hybrids, are thus an ideal model for studying postzygotic isolation. Among them, only a single D-M pair has been found, between S. bayanus and S. cerevisiae, comprising the mitochondrially targeted product of a nuclear gene, AEP2, and a mitochondrially encoded locus, OLI1, the 5' region of whose transcript is bound by Aep2. Thus far, no D-M pair of nuclear genes has been identified between any sensu stricto yeasts. Methods: We report here the first detailed genome-wide analysis of rare F2 progeny from an otherwise sterile hybrid, and show that no classic D-M pairs of speciation genes exist between the nuclear genomes of the closely related yeasts S. cerevisiae and S. paradoxus. Instead, our analyses suggest that more complex interactions may be responsible for their post-zygotic separation. These interactions most likely involve multiple loci having weak effects, as there were multiple significant pairwise combinations of loci, with no single combination being completely excluded from the viable F2s. Conclusions: The lack of a nuclear encoded classic D-M pair between these two yeasts, yet the existence of multiple loci that may each exert a small effect through complex interactions, suggests that initial speciation events might not always be mediated by D-M pairs. An alternative explanation may be that "death by a thousand cuts" leads to speciation, whereby an accumulation of polymorphisms can lead to an incompatibility between the species "transcriptional and metabolic networks, with no single pair at least initially being responsible for the incompatibility. After such a speciation event, it is possible that one or more D-M pairs might subsequently arise following isolation. Genotypes for hybrids between S. cerevisiae and S. paradoxus. A genotyping experiment design type classifies an individual or group of individuals on the basis of alleles, haplotypes, SNP's.
2010-06-08 | GSE19683 | GEO
Project description:Understanding the conditions that promote the evolution of reproductive isolation, and thus speciation. Here we empirically test some of the key predictions of speciation theory (Coyne 2004; Kohn 2005) by experimentally evolving the initial stages of speciation in yeast. After allowing replicate populations to adapt to two divergent environments, we observed the consistent, de novo evolution of two forms of postzygotic isolation: reduced rate of mitotic reproduction and reduced efficiency of meiotic reproduction. In general, divergent selection resulted in greater reproductive isolation than parallel selection, as predicted by ecological speciation theory. Our experimental system allowed for the first controlled comparison of the relative importance of ecological and genetic mechanisms of isolation, and the novel ability to quantify the effects of antagonistic epistasis. For mitotic reproduction, hybrid inferiority was conditional upon the selective environments and was both ecological and genetic in basis. In contrast, isolation associated with meiotic reproduction was unconditional and was caused solely by genetic mechanisms. Overall, our results show that adaption to divergent environments promotes the evolution of isolation through antagonistic epistasis, providing evidence of a plausible common avenue to speciation and adaptive radiation in nature (Schluter 2000,2001: Funk 2006) Keywords: Speciation, antagonistic epistasis, divergent adaptation
2007-06-21 | GSE6870 | GEO
Project description:Aquatic environments microbiome an metagenome Metagenome
| PRJNA991127 | ENA
Project description:Gill transcriptome of fast- and slow-growing mussels reared under continuous food supply was recently analysed in order to ascertain the differential gene expression underlying interindividual differences in growth rate. The present study aims to analyse the gene expression differences between fast- and slow-growing mussels submitted to an air exposure of 8 hours a day during the rearing period. Transcriptome will be also compared with their continuously submerged counterparts in order to analyse the effect of air exposure on the gene expression of fast- and slow-growing individuals.
2019-09-15 | GSE131910 | GEO