NMR 1D and 2D DOSY analysis of protein-lipid complexes in Bacteroides fragilis toxin with outer membrane vesicles
Ontology highlight
ABSTRACT:
INSTRUMENT(S): Bruker 9 Advance III 500 MHz NMR spectrometer (Bruker, USA) equipped with a Prodigy TCI 10 cryogenic triple-channel probe.
ORGANISM(S): Bacteroides Fragilis 638r (ncbitaxon:862962)
SUBMITTER: Victor V. Podgorsky,Natalya B. Zakharzhevskaya
PROVIDER: MSV000080385 | MassIVE | Thu Dec 08 06:50:00 GMT 2016
REPOSITORIES: MassIVE
Similar Datasets
Project description:Different water suppression pulse sequences, namely 1D NOESY presat and optimized PURGE were compared for urine samples. The original PURGE sequence was also tested to show the postential for lineshape distortions with the pulse sequence.
2017-09-01 | ST000891 | MetabolomicsWorkbench
Project description:In this study we determined the target spectra of the MicV and VrrA sRNAs via pulse-expression followed by RNA-sequencing.
2019-01-22 | GSE125160 | GEO
Project description:Intervention1: Capecitabine Manufactured by Mylan Pharmaceutical Inc., USA: Each patient will receive a Capecitabine 1250 mg/m2 administered twice daily orally :BD (morning and evening; equivalent to 2500 mg/m2 total daily dose)for 14 days. The dose will be comprised of multiples of the 500 mg tablet
Control Intervention1: XELODAÂ (Capecitabine 500 mg) tablets: capecitabine tablets in the doses of 2500 mg/m2/day in two divided dose i.e. in morning and evening
Control Intervention2: XELODAÂ (Capecitabine 500 mg) tablets.: XELODAÂ 500 mg tablets, Manufactured by Genentech US Inc. USA).Each patient will receive a Capecitabine 1250 mg/m2 administered twice daily orally :BD (morning and evening; equivalent to 2500 mg/m2 total daily dose)for 14 days. The dose will be comprised of multiples of the 500 mg tablet.
Primary outcome(s): To characterize the pharmacokinetic profile of the sponsors test formulation (Capecitabine Tablets 500 mg, Manufactured by Mylan Pharmaceutical Inc., USA) relative to that of reference formulation (XELODAÂ 500 mg tablets, Manufactured by Genentech US Inc. USA) in patients of Metastatic Breast Cancer, Dukes C Colon Cancer or Metastatic Colorectal Cancer under fed condition and to assess the bioequivalence.Timepoint: NIL
Study Design: Randomized, Crossover Trial
Method of generating randomization sequence:Computer generated randomization Method of allocation concealment:An Open list of random numbers Blinding and masking:Open Label
| 2573271 | ecrin-mdr-crc
Project description:The aim of this study was to identify quantitative trait loci (QTL) associated with variation in circadian photosensitivity in Drosophila, by measuring the locomotor response to early night light pulse (Zt15). We used QTL mapping of recombinant inbred lines (RIL), which was followed by microarrays expression comparison of two RI lines which differed significantly in their light response (RIL 104 shows a strong long phase delay response while RIL 58 shows a weak light response). Each of the two strains was sampled after light pulse, and without a light pulse (control), totalling 8 samples: 2x lines (L) x treatments (T) x 2 replicates
2016-02-09 | E-GEOD-77116 | biostudies-arrayexpress
Project description:This data displays both known and unknown extra-cellular proteins from 13 species of Lactic Acid bacteria found in the honey-crop of the honeybee Apis. mellifera mellifera. The tryptic peptides from the secreted proteins were run on an Agilent HPLC on a C18 reverse phase column (75 µm x 150 mm, particle size 3 µm). Total run time was 90 min and flow rate 300 nl/min. Buffers used for gradient was 0.1% formic acid in water (buffer A) and 0.1% formic acid in acetonitrile (buffer B). The buffer mixing was 5 min 5% buffer B, followed by 5%-45% buffer B in a linear gradient for 50 min, followed by 45%-80% buffer B in a linear gradient for 5 min. The 80% of buffer B was then kept for 15 min and then rapidly back to 5% buffer B for the final 15 min. The fractions from HPLC were loaded on an LCQ Deca XP Plus Ion trap mass spectrometer (ThermoScientific). Genomic DNA were prepared from all 13 LAB strains depicted earlier and sequenced at MWG Eurofins Operon (Ebensburg, Germany) using Roche GS FLX Titanium technology from Roche (Basel, Switzerland). For each genome a shotgun library was constructed with up to 700,000 reads per segment and was generated by sequencing in 2x half segment of a full FLX+ run. Each genome had an 8 kpb long-paired end library constructed. Approximately 300,000 true paired end reads, sequence tags, and scaffolds with GS FLX+ chemistry using 2x half segment of a full run were generated. Clonal amplification was performed by emPCR in both library types. The sequencing was continued until 15-20 fold coverage was reached. The obtained reads were assembled by the software Newbler 2.6 from Roche (Basel, Switzerland). ORF prediction and automated annotation was performed at Integrated Genomics Assets Inc. (Mount Prospect, Illinois, USA). In ORF prediction three different software were used, GLIMMER, Critica, and Prokpeg. Automated annotation was performed with the ERGOTM algorithms (Integrated Genomics Assets Inc. Mount Prospect, Illinois, USA). The resulting mass spectra-files obtained from the mass spectrometry analysis were searched using MASCOT against a local database containing the predicted proteome of the 13 LAB. We used a cut off Ions score of 38 as a value for determining that the protein was identified. Individual ion scores that were greater than 38 indicated identity or extensive homology (p<0.05) of the protein. Protein sequence similarity searches were performed with software BLASTP in the software package BLAST 2.27+ against a non-redundant protein database at NCBI. Pfam (default database), and InterProScan (default databases). Expressed proteins identified by peptide mass fingerprinting were manually re-annotated.
2013-10-01 | PXD000187 | Pride
Project description:A pooled plasma sample obtained from Red Cross has been seperated into 20 samples. 10 of them were simply mixed with a D2O phosphate buffer, while the other 10 were centrifuged first, then dried and resuspended in a 90/10 H2O/D2O phosphate buffer. The 20 NMR samples were analysed by NMR (4 spectra per sample, but different pulse sequences and parameters were used for each group). Standard addition was used in order to measure the concentration of 5 metabolites: valine, lactate, glucose, phenylalanine and formate.
2017-09-01 | ST000892 | MetabolomicsWorkbench
Project description:Samples were analyzed using a Maxis II QTOF instrument (Bruker Daltonik GmbH, Bremen, Germany) equipped with CaptiveSpray nanoBooster ion source coupled to a Dionex UltiMate 3000 RSLCnano system (Sunnyvale, CA, USA). Peptides were separated on an Acquity M-Class BEH130 C18 analytical column using gradient elution (isocratic hold at 4% for 11 min, then elevating B solvent content to 25% in 75 min, and to 40% in 15 min) following trapping on an Acclaim PepMap100C18 trap column. Solvent A consisted of water + 0.1% formic acid, Solvent B was acetonitrile + 0.1% formic acid, and the sample loading buffer was 0.1% TFA and 0.01% HFBA in water.
The MS/MS measurements were carried out in DDA mode. The cycle time was set at 2.5 sec, with a dynamic MS/MS exclusion of the same precursor ion for 2 minutes, or if the intensity is at least 3 times larger. Preferred charge states were set between +2 and +5. MS spectra were acquired at 3 Hz in the 150-2200 m/z range, while MS/MS spectra at 4 or 16 Hz depending on the intensity of the precursor. For single stage MS measurements spectra were recorded over the mass range of 300-3000 m/z at 1 Hz.
2021-04-28 | MSV000087329 | MassIVE
Project description:Intervention1: XELODAÂ -Capecitabine 500 mg tablets: Capecitabine 1250 mg/m2 administered twice daily orally :BD (morning and evening; equivalent to 2500 mg/m2 total daily dose) for 14 days including of three study periods.
Control Intervention1: Capecitabine 500 mg tablets: Capecitabine 1250 mg/m2 administered twice daily orally; BD morning and evening; equivalent to 2500 mg/m2 total daily dose for 14 days including of three study periods.
Primary outcome(s): To characterize the pharmacokinetic profile of the sponsors test formulation (Capecitabine Tablets 500 mg, Manufactured by Cadila Heathcare Limited, India) relative to that of reference formulation (XELODAÂ 500 mg tablets, Manufactured by Genentech USA Inc. USA) in patients of Metastatic Breast Cancer, Dukes C Colon Cancer or Metastatic Colorectal Cancer under fed condition and to assess the bioequivalence.Timepoint: Time points are 30 minutes prior to drug dosing and at 0.25hr, 0.50hr, 1hr, 1.5hr, 2hr, 2.5hr, 3hr, 4hr, 5hr, 6hr, 8hr and 10 hours post-dose.
Study Design: Randomized, Crossover Trial
Method of generating randomization sequence:Computer generated randomization Method of allocation concealment:An Open list of random numbers Blinding and masking:Open Label
| 2573937 | ecrin-mdr-crc
Project description:Metabolic perturbations resulting from excessive hepatic fat accumulation are poorly understood. Thus, in this study, leptin-deficient ob/ob mice, a mouse model of fatty liver disease, were used to investigate metabolic alterations in more detail. Metabolites were quantified in intact liver tissues of ob/ob (n=8) and control (n=8) mice using high-resolution magic angle spinning (HR-MAS) 1H-NMR. In addition, after demonstrating that HR-MAS 1H-NMR does not affect RNA integrity, transcriptional changes were measured by quantitative real-time PCR on RNA extracted from the same specimens after HR-MAS 1H-NMR measurements. Importantly, the gene expression changes obtained agreed with those observed by Affymetrix microarray analysis performed on RNA isolated directly from fresh-frozen tissue. In total, 40 metabolites could be assigned in the spectra and subsequently quantified. Quantification of lactate was also possible after applying a lactate-editing pulse sequence that suppresses the lipid signal, which superimposes the lactate methyl resonance at 1.3 ppm. Significant differences were detected for creatinine, glutamate, glycine, glycolate, trimethylamine-N-oxide, dimethylglycine, ADP, AMP, betaine, phenylalanine, and uridine. Furthermore, alterations in one-carbon metabolism, supported by both metabolic and transcriptional changes, were observed. These included reduced demethylation of betaine to dimethylglycine and the reduced expression of genes coding for transsulfuration pathway enzymes, which appears to preserve methionine levels, but may limit glutathione synthesis. Overall, the combined approach is advantageous as it identifies changes not only at the single gene or metabolite level but also deregulated pathways, thus providing critical insight into changes accompanying fatty liver disease. Graphical abstract A Evaluation of RNA integrity before and after HR-MAS 1H-NMR of intact mouse liver tissue. B Metabolite concentrations and gene expression levels assessed in ob/ob (steatotic) and ob/+ (control) mice using HR-MAS 1H-NMR and qRT-PCR, respectively.
2018-01-31 | MTBLS400 | MetaboLights
Project description:2-cell (E1.5) stage embryos were cultured in normal KSOM+AA conditions until E3.5 +2h and thereafter 100 embryos each were moved to control or p38-MAPKi conditions and cultured for another 7 hours (E3.5 +9h). The embryos were then washed through pre-warmed (37˚C) Hank’s balanced salt solution (HBSS, Sigma-Aldrich; Cat. No. H9269) and lysed by moving to a 1.5ml centrifuge tube containing about 15µl of SDT-lysis buffer (4% (w/v) SDS, 100 mM Tris-HCl pH 7.6, 0.1 M DTT). Cell lysis was performed by incubating the tubes in a 95˚C thermoblock for 12 minutes, brief centrifugation at 750 rpm, cooling to room temperature and storage at -80˚C. Individual protein solutions were processed by filter-aided sample preparation (FASP) method with some modifications (see the associated publication for more details). Resulting peptides were cleaned by liquid-liquid extraction (3 iterations) using water saturated ethyl acetate. 1/10th of the FASP eluate was taken out for direct LC-MS measurements, evaporated completely in SpeedVac concentrator (Thermo Fisher Scientific). Peptides were further transferred into LC-MS vials using 50μL of 2.5% formic acid (FA) in 50% acetonitrile (ACN) and 100μL of pure ACN and with addition of polyethylene glycol (final concentration 0.001%) and concentrated in a SpeedVac concentrator. Phosphopeptides were enriched from the remaining 9/10th of the cleaned FASP eluate after complete solvent evaporation (SpeedVac concentrator) using High-Select™ TiO2 Phosphopeptide Enrichment Kit (Thermo Fisher Scientific) according to manufacturer protocol. Phosphopeptide standards (0.1 pmol of MS PhosphoMix 1, 2, 3 Light; Sigma-Aldrich, St. Louis, Missouri, USA) was added to suspended sample in binding/equilibration buffer. Flow-through fraction was dried and used for second enrichment step using High-Select™ Fe-NTA Phosphopeptide Enrichment Kit (Thermo Fisher Scientific, Waltham, Massachusetts, USA) according to manufacturer protocol. Resulting phosphopeptides were extracted into LC-MS vials by 2.5% FA in 50% ACN and 100% ACN with addition of polyethylene glycol (final concentration 0.001%) and concentrated in a SpeedVac concentrator). LC-MS/MS analyses of all peptide mixtures (2 peptide solutions for each sample – 1) not enriched; 2) enriched on phosphopeptides using TiO2 enrichment kit) were done using RSLCnano system connected to Orbitrap Fusion Lumos mass spectrometer (Thermo Fisher Scientific). Prior to LC separation, tryptic digests were online concentrated and desalted using trapping column (100 μm × 30 mm, column compartment temperature of 40˚C) filled with 3.5-μm X-Bridge BEH 130 C18 sorbent (Waters). After washing of trapping column with 0.1% FA, the peptides were eluted (flow rate - 300nl/min) from the trapping column onto an analytical column (Acclaim Pepmap100 C18, 3 µm particles, 75 μm × 500 mm; column compartment temperature of 40˚C, Thermo Fisher Scientific) by using 50 or 100 minutes long nonlinear gradient program (1-56% of mobile phase B; mobile phase A: 0.1% FA in water; mobile phase B: 0.1% FA in 80% ACN) for analysis of phosphopeptide enriched fractions or not enriched peptide mixtures, respectively. Equilibration of the trapping column and the analytical column was done prior to sample injection to sample loop. The analytical column outlet was directly connected to the Digital PicoView 550 (New Objective) ion source with sheath gas option and SilicaTip emitter (New Objective; FS360-20-15-N-20-C12) utilization. ABIRD (ESI Source Solutions) was installed. MS data were acquired in a data-dependent strategy with cycle time for 3 seconds and with survey scan (350-2000 m/z). The resolution of the survey scan was 60000 (200 m/z) with a target value of 4×105 ions and maximum injection time of 50ms. HCD MS/MS (30% relative fragmentation energy, normal mass range) spectra were acquired with a target value of 5.0x104. The MS/MS spectra were recorded in Orbitrap at resolving power of 30,000 or 15,000 (200 m/z) and the maximum injection time for MS/MS was 500 or 22 ms for analysis of phosphopeptides enriched fraction or non-enriched peptide mixture, respectively. Dynamic exclusion was enabled for 60 seconds after one MS/MS spectra acquisition. The isolation window for MS/MS fragmentation was set to 1.6 m/z.
2021-07-12 | PXD025754 | Pride