Bacterium NHP-B
Ontology highlight
ABSTRACT:
PROVIDER: PRJNA507068 | ENA |
REPOSITORIES: ENA
Similar Datasets
Project description:Previous studies from our laboratory have shown that the resistance increase observed after biological systemic acquired resistance (SAR) induction in plants can be mimicked by exogenous plant treatment with N-hydroxypipecolic acid (NHP, Hartmann et al., 2018, Schnake et al., 2020). Moreover, exogenous application of the NHP biosynthetic precursor pipecolic acid (Pip) induced a transcriptional response that was overlapping with the SAR transcriptional response and fully depended on the NHP synthase FMO1 (Hartmann et al., 2018; E-MTAB-6243). In order to investigate whether elevations of NHP lead to a SAR-like transcriptional reprogramming, we supplied individual Arabidopsis wildtype Col-0 plants, as well as sid2-1 and npr1-3 mutant plants, with doses of 10 µmol NHP and determined the transcriptional response in leaves 24 hours later on the whole genome level by RNA-sequencing analyses in relation to control-treated (H2O) plants. Col-0 plants were additionally treated with doses of 10 µmol Pip in order to directly compare the transcriptional responses of the foliage between Pip and NHP. Arabidopsis thaliana plants were grown individually in pots containing a mixture of soil, vermiculite and sand (8:1:1) in a controlled cultivation chamber with a 10-h day (9 AM to 7 PM; photon flux density 100 mol m-2 s-1) / 14-h night cycle and a relative humidity of 70 %. Day and night temperatures were set to 21°C and 18°C, respectively. Experiments were performed with 5-week-old, naive plants exhibiting a uniform appearance. Treatments with NHP and Pip were essentially performed as detailed in Hartmann et al. (2018, Cell 173, 456–469). In brief, 10 ml of a 1 mM aqueous solution of NHP or Pip (equates to a dose of 10 µmol) were pipetted onto the soil of individually cultivated plants. 10 ml of water applied in the way served as control treatments. In total, three biologically independent, replicate experiments were performed. In each experiment, 18 full-grown leaves from 6 different plants were pooled 24 hours after the respective treatments for one biological replicate. In this way, 3 biologically independent, replicate samples per treatment and plant genotype were obtained.
2021-05-03 | E-MTAB-10230 | biostudies-arrayexpress
Project description:Normal human prostate (NHP) epithelial cells undergo senescence in vitro and in vivo, but the underlying molecular mechanisms remain incompletely understood. Here we first show that multiple primary strains of NHP cells are all immunophenotyped as CK5+/CK18+CD44+α2β1+p63+hTERT+ progenitor cells, which gradually lose progenitor markers as they lose proliferative capacity. NHP cell senescence involves loss of telomerase expression, upregulation of p16, and activation of p53. Using genetically defined manipulations of these three signaling pathways, we show that p16 is the primary determinant of the NHP cell proliferative capacity and hTERT is required for unlimited proliferative lifespan. Hence, suppression of 16 alone significantly extends NHP cell lifespan but both p16 inhibition and hTERT are required to immortalize NHP cells. Importantly, the immortalized NHP cells are normal progenitors that possess the ability to differentiate into functional prostatic glands containing both basal and luminal cells and, frequently, neuroendocrine cells. The immortalized NHP cells possess gene expression profiles characteristic of proliferating progenitor cells. Our studies shed light on the molecular mechanisms regulating the proliferative lifespan of NHP progenitor cells and provide direct evidence that basal-like progenitor cells can regenerate the entire prostatic glands in vivo. The availability of these cells should facilitate future studies of prostate cancer development. Further processed data linked below as Supplementary files. TestvsControl: corresponding GSM# 3vs1: GSM266720, 721, 722 4vs1: GSM266727, 730, 731 5vs1: GSM266732, 733, 734 7avs1: GSM266735, 736, 737 9vs1: GSM266772, 773, 812 11vs1: GSM266813, 816, 823 13vs1: GSM266824, 826, 828 Note: The 'TestvsControl' comparisons report the top 100 up- or down-regulated genes. The numeric designations (1 to 13) are used in the corresponding manuscript. The 'SignificantGenes' lists were used in clustering analysis. Keywords: Cell type comparison (senscent and immortalized NHP cells compared to young NHP progenitors)
2008-10-09 | GSE10570 | GEO
Project description:Proteomic analysis was performed on secreted proteins from non human primate (NHP) heart slices (from Macaca fascicularis) in presence or absence of Cardiac progenitors (CPs) 48 h after radiofrequency ablation (RFA) to mimic tissue damage.
2022-02-28 | PXD019521 | Pride
Project description:Nanostring ncounter NHP Immunology V2 panel
| PRJNA792145 | ENA
Project description:Graft versus host disease (GVHD) is the most common complication of hematopoietic stem cell transplant (HCT). However, our understanding of the molecular pathways that cause this disease remains incomplete, leading to inadequate treatment strategies. To address this, we measured the gene expression profile of non-human primate (NHP) T cells during acute GVHD. This transcriptome analysis enables an unsupervised approach to the identification of targets for disease control using a model with an immune system that closely overlaps with the human and has a high degree of cross-reactivity with human antibody-based therapeutics.
2015-11-29 | GSE73723 | GEO
Project description:Graft versus host disease (GVHD) is the most common complication of hematopoietic stem cell transplant (HCT). However, our understanding of the molecular pathways that cause this disease remains incomplete, leading to inadequate treatment strategies. To address this, we measured the gene expression profile of non-human primate (NHP) T cells during acute GVHD. In this study we specifically interrogated the transcriptional signatures of animals treated with FR104 monotherapy and FR104/Sirolimus combination therapy
2018-06-21 | GSE116070 | GEO
Project description:Graft versus host disease (GVHD) is the most common complication of hematopoietic stem cell transplant (HCT). However, our understanding of the molecular pathways that cause this disease remains incomplete, leading to inadequate treatment strategies. To address this, we measured the gene expression profile of non-human primate (NHP) T cells during acute GVHD. In this study we specifically interrogated the transcriptional signatures of animals treated with KY1005 monotherapy and KY1005/Sirolimus combination therapy
2017-08-01 | GSE99644 | GEO
Project description:We measured abundances of tRNAs by means of hydro-tRNA-seq (Gogakos et al., 2017), a method based on partial alkaline RNA hydrolysis that generates fragments suitable for sequencing, in the genome-reduced bacterium Mycoplasma pneumoniae.
2023-06-29 | E-MTAB-11930 | biostudies-arrayexpress
Project description:Transcriptome Profiling in KY1005-treated NHP HCT-recipients
| PRJNA476948 | ENA
Project description:Given the facilities for whole genome sequencing with next-generation sequencers, structural and functional gene annotation is now only based on automated prediction. However, errors in terms of gene structure are still frequently reported especially for the correct determination of initiation start codons. Here, we propose a strategy to enrich and detect protein N-termini by mass spectrometry in order to refine genome annotation. After selective protein N-termini derivatization using (N-Succinimidyloxycarbonylmethyl)tris(2,4,6-trimethoxyphenyl)phosphonium bromide (TMPPAc-OSu) as labeling reagent, protein digestion was performed with three proteases in parallel. TMPP-labeled N-terminal-most peptides were further resolved from internal peptides by the COmbined FRActional DIagonal Chromatography (COFRADIC) sorting methodology before analysis with tandem mass spectrometry. We refined the annotation of the genome of a model marine bacterium, Roseobacter denitrificans.
2014-02-19 | PXD000337 | Pride