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Metabolomics,Unknown,Transcriptomics,Genomics,Proteomics

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Transcription profiling of acid exposed H. pylori Two independent exposures (labeled T1 and T2) to pH 5.0. Samples were harvested at 30, 60, 90 and 120 minutes

ABSTRACT: Two independent exposures (labeled T1 and T2) to pH 5.0. Samples were harvested at 30, 60, 90 and 120 minutes and used to make cDNA. Arrays are set up such that each time point was hybridized to the individual T=0 starting culture.

ORGANISM(S): Helicobacter pylori

SUBMITTER: Janos Demeter

PROVIDER: E-SMDB-1998 | biostudies-arrayexpress |

REPOSITORIES: biostudies-arrayexpress

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pH-regulated gene expression of the gastric pathogen Helicobacter pylori.

Merrell D Scott DS Goodrich Maria L ML Otto Glen G Tompkins Lucy S LS Falkow Stanley S

Infection and immunity 20030601 6

Colonization by the gastric pathogen Helicobacter pylori has been shown to be intricately linked to the development of gastritis, ulcers, and gastric malignancy. Little is known about mechanisms employed by the bacterium that help it adapt to the hostile environment of the human stomach. In an effort to extend our knowledge of these mechanisms, we utilized spotted-DNA microarrays to characterize the response of H. pylori to low pH. Expression of approximately 7% of the bacterial genome was repro ...[more]

PMID: 12761138

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Yeast magnesium starvation, 90 minutes

Project description:To learn about the cellular processes involved in Mg2+ transport and the mechanisms allowing cells to cope with low Mg2+ availability, we performed RNA expression profiling experiments, and followed changes in gene activity upon Mg2+ depletion on a genome-wide scale. A striking portion of genes up-regulated under Mg2+ depletion is also induced by high Ca2+ and/or alkalinization. Among the genes significantly up-regulated by Mg2+ starvation, Ca2+ stress and alkalinization are ENA1 (encoding a P-type ATPase sodium pump) and PHO89 (encoding a sodium/phosphate cotransporter). We show that up-regulation of these genes is dependent on the calcineurin/Crz1p signaling pathway. Similarly to Ca2+ stress, Mg2+ starvation induces translocation of the transcription factor Crz1p from the cytoplasm into the nucleus. The up-regulation of ENA1 and PHO89 upon Mg2+ starvation depends on extracellular Ca2+. Using fluorescence resonance energy transfer microscopy we demonstrate that removal of Mg2+ results in an immediate increase in free cytoplasmic Ca2+. This effect is dependent on external Ca2+. Results presented indicate that Mg2+ depletion in yeast cells leads to enhanced cellular Ca2+ concentrations, which activate the Crz1p/calcineurin pathway. We provide evidence that calcineurin/Crz1p signaling is crucial for yeast cells to cope with Mg2+ depletion stress. Keywords: stress response (magnesium starvation)

2007-03-08 | GSE6687 | GEO

Free-breathing simultaneous T1 , T2 , and T2∗ quantification in the myocardium.

Project description:PurposeTo implement a free-breathing sequence for simultaneous quantification of T1 , T2 , and T2∗ for comprehensive tissue characterization of the myocardium in a single scan using a multi-gradient-echo readout with saturation and T2 preparation pulses.MethodsIn the proposed Saturation And T2 -prepared Relaxometry with Navigator-gating (SATURN) technique, a series of multi-gradient-echo (GRE) images with different magnetization preparations was acquired during free breathing. A total of 35 images were acquired in 26.5 ± 14.9 seconds using multiple saturation times and T2 preparation durations and with imaging at 5 echo times. Bloch simulations and phantom experiments were used to validate a 5-parameter fit model for accurate relaxometry. Free-breathing simultaneous T1 , T2 , and T2∗ measurements were performed in 10 healthy volunteers and 2 patients using SATURN at 3T and quantitatively compared to conventional single-parameter methods such as SASHA for T1 , T2 -prepared bSSFP, and multi-GRE for T2∗ .ResultsSimulations confirmed accurate fitting with the 5-parameter model. Phantom measurements showed good agreement with the reference methods in the relevant range for in vivo measurements. Compared to single-parameter methods comparable accuracy was achieved. SATURN produced in vivo parameter maps that were visually comparable to single-parameter methods. No significant difference between T1 , T2 , and T2∗ times acquired with SATURN and single-parameter methods was shown in quantitative measurements (SATURN T1=1573±86ms , T2=33.2±3.6ms , T2∗=25.3±6.1ms ; conventional methods: T1=1544±107ms , T2=33.2±3.6ms , T2∗=23.8±5.5ms ; P>.2 ) CONCLUSION: SATURN enables simultaneous quantification of T1 , T2 , and T2∗ in the myocardium for comprehensive tissue characterization with co-registered maps, in a single scan with good agreement to single-parameter methods.

| S-EPMC8252099 | biostudies-literature

Annotation of Fusarium graminearum (PH-1) Version 5.0.

Project description:Fusarium graminearum floral infections are a major risk to the global supply of safe cereal grains. We report updates to the PH-1 reference genome and significant improvements to the annotation. Changes include introduction of legacy annotation identifiers, new gene models, secretome and effectorP predictions, and inclusion of extensive untranslated region (UTR) annotations.

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Correlation of T1- to T2-weighted signal intensity ratio with T1- and T2-relaxation time and IDH mutation status in glioma.

Project description:The current study aimed to test whether the ratio of T1-weighted to T2-weighted signal intensity (T1W/T2W ratio: rT1/T2) derived from conventional MRI could act as a surrogate relaxation time predictive of IDH mutation status in histologically lower-grade gliomas. Strong exponential correlations were found between rT1/T2 and each of T1- and T2-relaxation times in eight subjects (rT1/T2 = 1.63exp-0.0005T1-relax + 0.30 and rT1/T2 = 1.27exp-0.0081T2-relax + 0.48; R2 = 0.64 and 0.59, respectively). In a test cohort of 25 patients, mean rT1/T2 (mrT1/T2) was significantly higher in IDHwt tumors than in IDHmt tumors (p < 0.05) and the optimal cut-off of mrT1/T2 for discriminating IDHmt was 0.666-0.677, (AUC = 0.75, p < 0.05), which was validated in an external domestic cohort of 29 patients (AUC = 0.75, p = 0.02). However, this result was not validated in an external international cohort derived from TCIA/TCGA (AUC = 0.63, p = 0.08). The t-Distributed Stochastic Neighbor Embedding analysis revealed a greater diversity in image characteristics within the TCIA/TCGA cohort than in the two domestic cohorts. The failure of external validation in the TCIA/TCGA cohort could be attributed to its wider variety of original imaging characteristics.

| S-EPMC9637175 | biostudies-literature

A. nidulans wild type and atmA null mutant strains transcriptome analysis in conidia grown for 60, 90 and 120 minutes

Project description:ATM is a phosphatidyl-3-kinase-related protein kinase that functions as a central regulator of the DNA damage response in eukaryotic cells. In humans, mutations in ATM cause the devastating neurodegenerative disease Ataxia Telangiectasia. Previously, we characterized the homologue of ATM (AtmA) in the filamentous fungus Aspergillus nidulans. In addition to its expected role in the DNA damage response, we found that AtmA is also required for polarized hyphal growth. In order to investigate which pathways are controlled by AtmA during proliferation and polar growth, we determined the transcriptional profile of A. nidulans wild type and delta atmA mutant strains in different growth conditions. Conidia from both wild type and delta atmA mutant were incubated with 50 mM of hydroxyurea to synchronize the germlings in the S-phase of cell cycle. After this time, the cultures were centrifuged, washed and pre-warmed drug-free fresh media was aseptically added to the cultures. They were allowed to grow for additional 60, 90 and 120 minutes after the HU-release. At each time point, the germlings were also harvested by centrifugation and used for competitive microarray hybridizations. Our results indicate several genes that have decreased mRNA expression in the delta atmA mutant which are involved in the formation of a polarized hyphae and control of polar growth; in the synthesis of phosphatidic acid; in the ergosterol biosynthesis; and intracellular trafficking, secretion, and vesicular transport. Keywords: gene expression array-based, log2 ratio

2007-07-25 | GSE8183 | GEO

Desulfobacillus biomass profiling grown at pH 3.9 and pH 5.0

Project description:Novel Desulfobacillus species biomass was grown in reactors at pH3.9 and pH5.0 with 2 biological replicated. Shotgun proteomics was performed to identify differentially expressed proteins.

2022-05-19 | PXD022508 | Pride

MR fingerprinting with simultaneous T1, T2, and fat signal fraction estimation with integrated B0 correction reduces bias in water T1 and T2 estimates.

Project description:PURPOSE:MR fingerprinting (MRF) sequences permit efficient T1 and T2 estimation in cranial and extracranial regions, but these areas may include substantial fat signals that bias T1 and T2 estimates. MRI fat signal fraction estimation is also a topic of active research in itself, but may be complicated by B0 heterogeneity and blurring during spiral k-space acquisitions, which are commonly used for MRF. An MRF method is proposed that separates fat and water signals, estimates water T1 and T2, and accounts for B0 effects with spiral blurring correction, in a single sequence. THEORY AND METHODS:A k-space-based fat-water separation method is further extended to unbalanced steady-state free precession MRF with swept echo time. Repeated application of this k-space fat-water separation to demodulated forms of the measured data allows a B0 map and correction to be approximated. The method is compared with MRF without fat separation across a broad range of fat signal fractions (FSFs), water T1s and T2s, and under heterogeneous static fields in simulations, phantoms, and in vivo. RESULTS:The proposed method's FSF estimates had a concordance correlation coefficient of 0.990 with conventional measurements, and reduced biases in the T1 and T2 estimates due to fat signal relative to other MRF sequences by several hundred ms. The B0 correction improved the FSF, T1, and T2 estimation compared to those estimates without correction. CONCLUSION:The proposed method improves MRF water T1 and T2 estimation in the presence of fat and provides accurate FSF estimation with inline B0 correction.

| S-EPMC6581466 | biostudies-literature

Expression data from placenta harvested from WT and Pth-null fetuses treated 90 minutes prior with saline or PTH (1-84)

Project description:Parathyroid hormone (PTH) plays an essential role in regulating calcium and bone homeostasis in the adult, but whether PTH is required at all for regulating fetal-placental mineral homeostasis is uncertain. To address this we treated Pth-null mice in utero with 1 nmol PTH (1-84) or saline and examined placental calcium transfer 90 minutes later. It was found that placental calcium transfer increased in Pth-null fetuses treated with PTH as compared to Pth-null fetuses treated with saline. Subsequently, to determine the effect of PTH treatment on placental gene expression, in a separate experiment, 90 minutes after the fetal injections the placentas were removed for subsequent RNA extraction and microarray analysis.

2010-03-01 | GSE16983 | GEO

Joint myocardial T1 and T2 mapping using a combination of saturation recovery and T2 -preparation.

Project description:PurposeTo develop a heart-rate independent breath-held joint T1 -T2 mapping sequence for accurate simultaneous estimation of coregistered myocardial T1 and T2 maps.MethodsA novel preparation scheme combining both a saturation pulse and T2 -preparation in a single R-R interval is introduced. The time between these two pulses, as well as the duration of the T2 -preparation is varied in each heartbeat, acquiring images with different T1 and T2 weightings, and no magnetization dependence on previous images. Inherently coregistered T1 and T2 maps are calculated from these images. Phantom imaging is performed to compare the proposed maps with spin echo references. In vivo imaging is performed in ten subjects, comparing the accuracy and precision of the proposed technique to existing myocardial T1 and T2 mapping sequences of the same duration.ResultsPhantom experiments show that the proposed technique provides accurate quantification of T1 and T2 values over a wide-range (T1 : 260 ms to 1460 ms, T2 : 40 ms to 200 ms). In vivo imaging shows that the proposed sequence quantifies T1 and T2 values similar to a saturation-based T1 mapping and a conventional breath-hold T2 mapping sequence, respectively.ConclusionThe proposed sequence allows joint estimation of accurate and coregistered quantitative myocardial T1 and T2 maps in a single breath-hold. Magn Reson Med 76:888-896, 2016. © 2015 Wiley Periodicals, Inc.

| S-EPMC4811754 | biostudies-literature

Myocardial T1, T2, T2*, and fat fraction quantification via low-rank motion-corrected cardiac MR fingerprinting.

Project description:PurposeDevelop a novel 2D cardiac MR fingerprinting (MRF) approach to enable simultaneous T1, T2, T2*, and fat fraction (FF) myocardial tissue characterization in a single breath-hold scan.MethodsSimultaneous, co-registered, multi-parametric mapping of T1, T2, and FF has been recently achieved with cardiac MRF. Here, we further incorporate T2* quantification within this approach, enabling simultaneous T1, T2, T2*, and FF myocardial tissue characterization in a single breath-hold scan. T2* quantification is achieved with an eight-echo readout that requires a long cardiac acquisition window. A novel low-rank motion-corrected (LRMC) reconstruction is exploited to correct for cardiac motion within the long acquisition window. The proposed T1/T2/T2*/FF cardiac MRF was evaluated in phantom and in 10 healthy subjects in comparison to conventional mapping techniques.ResultsThe proposed approach achieved high quality parametric mapping of T1, T2, T2*, and FF with corresponding normalized RMS error (RMSE) T1 = 5.9%, T2 = 9.6% (T2 values <100 ms), T2* = 3.3% (T2* values <100 ms), and FF = 0.8% observed in phantom scans. In vivo, the proposed approach produced higher left-ventricular myocardial T1 values than MOLLI (1148 vs 1056 ms), lower T2 values than T2-GraSE (42.8 vs 50.6 ms), lower T2* values than eight-echo gradient echo (GRE) (35.0 vs 39.4 ms), and higher FF values than six-echo GRE (0.8 vs 0.3 %) reference techniques. The proposed approach achieved considerable reduction in motion artifacts compared to cardiac MRF without motion correction, improved spatial uniformity, and statistically higher apparent precision relative to conventional mapping for all parameters.ConclusionThe proposed cardiac MRF approach enables simultaneous, co-registered mapping of T1, T2, T2*, and FF in a single breath-hold for comprehensive myocardial tissue characterization, achieving higher apparent precision than conventional methods.

| S-EPMC9306903 | biostudies-literature

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