Tryptophan as a miR team organizer prevents colon cancer liver metastasis [small intestine]
Ontology highlight
ABSTRACT:
PROVIDER: PRJNA876251 | ENA |
REPOSITORIES: ENA
Similar Datasets
Project description:Tryptophan as a miR team organizer prevents colon cancer liver metastasis [colon]
| PRJNA876285 | ENA
Project description:Tryptophan treatment play a significant role in miR expression. We have characterized the miR expression network through miR-on-chip profiling of the mouse treated with or without tryptophan. In this dataset, we include the expression data from mouse small intestine and colon tissue treated with or without tryptophan.
2023-09-03 | GSE212607 | GEO
Project description:Tryptophan treatment play a significant role in miR expression. We have characterized the miR expression network through miR-on-chip profiling of the mouse treated with or without tryptophan. In this dataset, we include the expression data from mouse small intestine and colon tissue treated with or without tryptophan.
2023-09-03 | GSE212633 | GEO
Project description:Studies of the Xenopus organizer have laid the foundation for our understanding of the conserved signaling pathways that pattern vertebrate embryos during gastrulation. Here, we use this wealth of knowledge as leverage in the design and analysis of a genomic visualization of organizer-related gene transcription. Using ectopic expression of the two major activities of the organizer, BMP and Wnt inhibition, as well as endogenous tissues, we generate a focused set of samples that represent different aspects of organizer signaling. The genomic expression values of each sample are then measured with oligonucleotide arrays. From this data, genes regulated by organizer signaling are selected and then clustered by their patterns of regulation. A new GO biological process annotation of the Xenopus genome allows us to rapidly identify clusters that are highly enriched for known gastrula patterning genes. Within these clusters, we can predict the expression patterns of unknown genes with remarkable accuracy, leading to the discovery of new organizer-related gastrula stage expression patterns for 19 genes. Moreover, the patterns of gene response observed within these clusters allow us to parse apart the contributions of BMP and Wnt inhibition in organizer function. We find that the majority of gastrula patterning genes respond transcriptionally to these activities according to only a few stereotyped patterns, allowing us to describe suites of genes that are likely to share similar regulatory mechanisms. These suites of genes demonstrate a mechanism where BMP inhibition initiates the organizer program before gastrulation, and Wnt inhibition maintains and drives the organizer program during gastrulation. Keywords: development, organizer, noggin, dkk-1, xenopus, gastrulation
2006-06-30 | GSE3368 | GEO
Project description:Recapitulation of development in vitro relies primarily on treatment of progenitor cells with media-borne morphogens, without the complex spatial instructions normally presented by native developmental niches. Here we build simple spatially asymmetric developmental niches by engineering synthetic organizer cells that self-assemble around stem cells and provide spatially-defined morphogenic instructions. Using a toolkit of natural and engineered adhesion molecules we harness differential adhesion to program the formation of specific organizer cell geometries around the stem cells, allowing the generation of morphogen gradients with tunable position, amplitude, and signal types. Synthetic niches presenting the antagonistic morphogens WNT3A and DKK1 were used to guide development of pluripotent stem cells. These synthetic organizers generated distinct morphological outcomes, including formation of a beating heart-like chamber and embryoids containing a complement of diverse cell lineages derived from mesoderm, endoderm and ectoderm. The resulting morphologies were reproducible in high-throughput format. Spatially programmable synthetic organizer cells, which integrate the principles of differential adhesion and positional information, thus provide a systematic approach to guide, recapitulate, and modify development in a controlled fashion.
2024-12-09 | GSE244033 | GEO
Project description:Eosinophilia–myalgia syndrome (EMS) is characterized by subacute onset of myalgias and peripheral eosinophilia, followed by chronic neuropathy and skin induration. The EMS epidemic in 1989 was linked to L-tryptophan consumption originating from a single source. Following the Food and Drug Administration (FDA) ban on the sale of L-tryptophan, the incidence of EMS declined rapidly. Moreover, no new cases have been published since the FDA ban was lifted in 2005. We report the clinical, histopathological and immunogenetic features of a new case of L-tryptophan-associated EMS along with evidence of activated transforming growth factor-ß and interleukin-4 signaling in the lesional skin. 6 samples were analyzed to include EMS patient and two replicates along with three normal controls
2012-01-28 | E-GEOD-26934 | biostudies-arrayexpress
Project description:DNA microarray analysis of gene expression in response to physiological and genetic changes that affect tryptophan metabolism in Escherichia coli. We investigated the global changes in mRNA abundance in Escherichia coli elicited by various perturbations of tryptophan metabolism. To do so we printed DNA microarrays containing 95% of all annotated E. coli ORFs. We determined the expression profile that is predominantly dictated by the activity of the tryptophan repressor. Only three operons, trp, mtr, and aroH, exhibited appreciable expression changes consistent with this profile. The quantitative changes we observed in mRNA levels for the five genes of the trp operon were consistent within a factor of 2, with expectations based on established Trp protein levels. Several operons known to be regulated by the TyrR protein, aroF-tyrA, aroL, aroP, and aroG, were down-regulated on addition of tryptophan. TyrR can be activated by any one of the three aromatic amino acids. Only one operon, tnaAB, was significantly activated by the presence of tryptophan in the medium. We uncovered a plethora of likely indirect effects of changes in tryptophan metabolism on intracellular mRNA pools, most prominent of which was the sensitivity of arginine biosynthetic operons to tryptophan starvation. This study is detailed in Khodursky AB et al.(2000) Proc Natl Acad Sci U S A 97:12170-5 Keywords: other
2001-07-30 | GSE7 | GEO
Project description:Mice were fed a normal chow diet or a tryptophan depleted diet for two weeks under normal 12-hr light/dark cycles (LD) or in constant darkness (DD). Mice were sacrificed every 4th hour over the 24-hr circadian cycle. The suprachiasmatic nucleus (SCN) was harvested and RNA was isolated using a standard TRIZOL protocol. The data suggest that dietary tryptophan is an important component of the diet regulating circadian homeostsis.
2023-05-30 | GSE186242 | GEO
Project description:Isobutanol is considered a potential biofuel and can be produced by genetically modified microorganisms. Saccharomyces cerevisiae inherently produces isobutanol through valine intermediate(s), so it serves as a good host. However, isobutanol's toxicity remains a key obstacle for bioproduction. In our study, we first used image recognition to screen the colony growth of a yeast gene deletion library and inferred that genes involved in tryptophan biosynthesis, ubiquitination, and the pentose phosphate pathway (PPP) contribute to isobutanol tolerance. The importance of tryptophan in yeast's tolerance to isobutanol was confirmed by the recovery of isobutanol tolerance in a tryptophan biosynthesis defective strain by adding exogenous tryptophan. Transcriptomic analysis revealed that amino acid biosynthesis- and transportation-related genes in a tryptophan biosynthesis defective host were up regulated under conditions such as nitrogen starvation. This may explain why ubiquitination for protein degradation was involved for the protein turnover. PPP metabolites and vitamin B1/B6 may serve as precursors and cofactors in tryptophan biosynthesis to enhance isobutanol tolerance. Furthermore, the tolerance mechanism may also be linked to tryptophan metabolism, including the kynurenine pathway and nicotinamide adenine dinucleotide biosynthesis. Both pathways are responsible for cellular redox balance and antioxidative ability and figured out that tryptophan may play a crucial role on isobutanol tolerance. Our study highlights the central role of tryptophan in yeast's isobutanol tolerance and offers new clues for engineering a yeast host with strong isobutanol tolerance.
2021-10-20 | GSE175794 | GEO