Synthetic organism
Ontology highlight
ABSTRACT:
PROVIDER: PRJNA587523 | ENA |
REPOSITORIES: ENA
Similar Datasets
Project description:Circular permutation profiling with DNA sequencing (CPP-seq)
| PRJNA418341 | ENA
Project description:Hypothalamic hamartomas (HHs) are congenital lesions of the neuroendocrine brain composed of neurons and astroglia. Frequently, HHs are associated with central precocious puberty (CPP) and/or gelastic seizures. Because HHs might express genes similar to those required for the initiation of normal puberty we used cDNA arrays to compare the gene expression profile of a HH associated with CPP with three HHs not accompanied by sexual precocity. Our aim was to identify genes whose expression may be selectively altered in the HH with CPP and hence, involved in the onset of puberty. Keywords: comparison between HH with and without CPP
2007-02-27 | GSE7142 | GEO
Project description:Reward-related memory is an important factor in cocaine seeking. One necessary signaling mechanism for long-term memory formation is the activation of poly(ADP-ribose) polymerase-1 (PARP-1), via poly(ADP-ribosyl)ation. We demonstrate herein that auto-poly(ADP-ribosyl)ation of activated PARP-1 was significantly pronounced during retrieval of cocaine-associated contextual memory, in the central amygdala (CeA) of rats expressing cocaine-conditioned place preference (CPP). Intra-CeA pharmacological and shRNA depletion of PARP-1 activity during cocaine-associated memory retrieval abolished CPP. In contrast, PARP-1 inhibition after memory retrieval did not affect CPP reconsolidation process and subsequent retrievals. Chromatin Immuoprecipitation (ChIP) sequencing revealed that PARP-1 binding in the CeA is highly enriched in genes involved in neuronal signaling. We identified amongst PARP targets in CeA a single gene, yet uncharacterized and encoding a putative transposase inhibitor, at which PARP-1 enrichment dramatically increases during cocaine-associated memory retrieval and positively correlates with CPP. Our findings have important implications for understanding drug-related behaviors, and suggest possible future therapeutic targets for drug abuse. 4 samples, each is pooled central amygdalae tissues collected from 2 rats. Rats were trained for cocaine-conditioned place-preference (CPP), tissues were harvested immediately following cocaine-CPP retrieval. Three groups of rats were used: high cocaine CPP, low cocaine CPP and control saline only trained rats.
2016-06-25 | E-GEOD-83718 | biostudies-arrayexpress
Project description:Organisms are defined by the information encoded in their genomes, and since the origin of life this information has been encoded using a two-base-pair genetic alphabet (A-T and G-C). In vitro, the alphabet has been expanded to include several unnatural base pairs (UBPs). We have developed a class of UBPs formed between nucleotides bearing hydrophobic nucleobases, exemplified by the pair formed between d5SICS and dNaM (d5SICS-dNaM), which is efficiently PCR-amplified and transcribed in vitro, and whose unique mechanism of replication has been characterized. However, expansion of an organism's genetic alphabet presents new and unprecedented challenges: the unnatural nucleoside triphosphates must be available inside the cell; endogenous polymerases must be able to use the unnatural triphosphates to faithfully replicate DNA containing the UBP within the complex cellular milieu; and finally, the UBP must be stable in the presence of pathways that maintain the integrity of DNA. Here we show that an exogenously expressed algal nucleotide triphosphate transporter efficiently imports the triphosphates of both d5SICS and dNaM (d5SICSTP and dNaMTP) into Escherichia coli, and that the endogenous replication machinery uses them to accurately replicate a plasmid containing d5SICS-dNaM. Neither the presence of the unnatural triphosphates nor the replication of the UBP introduces a notable growth burden. Lastly, we find that the UBP is not efficiently excised by DNA repair pathways. Thus, the resulting bacterium is the first organism to propagate stably an expanded genetic alphabet.
| S-EPMC4058825 | biostudies-literature
Project description:In order to screen for molecules contributing to the effects of FGF1/CPP-C on radiation-induced intestinal damage, the total RNA expression profile of the irradiated jejunum was obtained using a DNA microarray analysis after Carbon-ion irradiation with the FGF1/CPP-C pretreatment.
2018-11-14 | GSE113641 | GEO
Project description:Toxoplasma gondii possesses three protein kinase A (PKA) orthologs. PKA C3 has been implicated as a negative regulator of transformation from the acute stage tachyzoites to the chronic stage bradyzoites. We performed immunoprecipitation of PKA C3 and identified interaction partners by mass spectrometry. The apicomplexan-specific AGC kinase SPARK emerged as a strong interaction partner of PKA C3.
2024-07-12 | PXD039896 | Pride
Project description:Circular DNAs have been reported for decades and have been linked to tumorigenesis in humans. Previous sequencing-based genomic approaches capture circular DNA and average their readout over millions of cells, thereby losing insight into intercellular variation. Here, we introduce single-cell Circle-seq and show that the occurrence of most circular DNA species is stochastic, with some oncogene-containing large circular DNAs observed relatively frequently among different single cells. Despite this stochasticity, circular DNA is cell type-specific, which is concordant with H3K9me3 and H3K4me3 chromatin modification specificity of the corresponding cell lines. Moreover, we identify a cell type-specific circular DNA signature in cancer cells, which, we believe holds potential for early cancer diagnosis. In sum, our novel method single-cell Circle-seq dissects the randomness and cell type-specificity of circular DNAs at the single-cell level and uncovers the potential clinical application of circular DNA.
2024-01-02 | GSE221884 | GEO