ABSTRACT: These data are from 17 strains of 11 Tolypocladium spp., derived from various substrata, with various ecologies. The fungi were grown in agar culture extracted and pre-fractioned. These were crude fractions were separated on C18 HPLC, and mass data obtained on an ABSciex 3200 QTrap (low-res)
Project description:Crude extracellular vesicles (EVs) from eight healthy volunteers were separated into 6 fractions based on their densities by using the iodixanol-based density gradient centrifugation method. To determine the distribution of miRNAs among these fractions, quantities of 93 miRNAs were quantified by the TaqMan real time PCR method using the BioMark HD system (Fluidigm) equipped with 96.96 dynamic array (Fluidigm). Six samples were fractionated from a crude EVs by density gradient centrifugation. Total of 48 samples were prepared from 8 healthy volunteers. Technical replicate of 4 gave 8 x 6 x 4 x 93 = 17,856 data. As control Tris-HCl EDTA buffer (TE) was used.
Project description:We found the bone marrow stromal-derived neural progenitor cells secretome have the neural protection effect. Proteomic analysis was performed nn order to analyze the protection factor in the secretome. Keywords: Neural protection, secretome Overall design: Secretome samples were run first by HPLC. After that, 20 fractions were selected for MS/MS.
Project description:Two cultivars of Sorghum biocolor were examined from a study performed at the Kearney Research Station in California; 1) a pre-flowering drought tolerant, post-flowering drought susceptible cultivar RTx430 and 2) a pre-flowering drought susceptible, post-flowering drought-tolerant cultivar BTx642. Samples are from leaves and roots collected at 2, 3, 4, 6, 8, 9, 10, 11, 13, 15, 17 weeks post soil emergence and under a perturbation of either well-watered (control), pre-flowering drought, or post-flowering drought. A liquid-based bottom up proteomics analysis was performed using an iTRAQ labeling multiplexing approach to determine relative abundances. After the peptides were digested with trypsin and iTRAQ labeled, they were fractionated into 12 fractions offline using a C-18 column under high-pH solvent conditions Each fraction was further separated on a low pH C-18 column with direct infusion into a ThermoScientific Q-Exactive mass spectrometer. See the supplementary files for iTRAQ reporter ions details.
Project description:Fractionation of EML cells isolated based on surface expression of immunophenotypic markers reveals the existence of a subpopulation that has undergone spontaneous commitment to an erythroid fate. Uncommitted fractions were compared to committed cells, derived from both spontaneous (EryCP) and cytokine-driven (Ediff) commitment. EML cells were separated by flow cytometry based on their expression of the markers Sca1, CD34 and cKit as described.
Project description:Exosomes were isolated from the mouse CSF using total exosome isolation kit (Life Technologies) from 0h and 6h LPS treated mice. These exosomes were separated on the RP-HPLC in to 20 fractions and analysed on the Qexactive.
Project description:This a model from the article:
Critical study of and improvements in chromatographic methods for the analysis
of type B trichothecenes.
Mateo JJ, Llorens A, Mateo R, Jimenez M. J Chromatogr A
2001 May 18;918(1):99-112 11403460
Various analytical methods used in the analysis of type B trichothecenes
(deoxynivalenol, nivalenol, 3- and 15-acetyldeoxynivalenol) in cereals were
compared and optimised in this work. These methods use either
GC-electron-capture detection (ECD) of trimethylsilyl, trifluoroacetyl and
heptafluorobutyryl derivatives or HPLC with UV or photodiode array detection of
analytes. A new HPLC procedure using fluorescence detection prior derivatisation
with coumarin-3-carbonyl chloride has been also tested. Five extraction solvents
and two solid-phase extraction cartridges (silica, Florisil) plus a especial
clean-up column (MycoSep 225) were compared in order to obtain the best recovery
of the mycotoxins with minimal presence of coextractives in the chromatograms.
The chosen extraction solvent was a mixture of acetonitrile-water (84:16, v/v).
The MycoSep 225 column was chosen as the best alternative for clean-up of grain
samples. For GC-ECD analysis, derivatisation of analytes with heptafluorobutyric
anhydride prior the final determination was chosen as the most suitable
procedure. HPLC-photodiode array (at 221 nm) analysis was more suitable for
determination of type B trichothecenes than HPLC of the fluorescent
coumarin-3-carbonyl derivatives. Recoveries obtained in spiked corn, rice and
wheat are reported. The utility of the proposed methodology was assayed in
cereal cultures of various Fusarium strains.
This model was taken from the CellML repository
and automatically converted to SBML.
The original model was:
Mateo JJ, Llorens A, Mateo R, Jimenez M. (2001) - version=1.0
The original CellML model was created by:
The University of Auckland
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Project description:Adipose tissue from 6 non-obese patients was collagenase treated and adipocytes separated from the stromal vascular fraction(SVF). SVF was then FACS sorted for the following fractions CD45-/CD34+/CD31+ (endothelial), CD45-/CD34+/CD31- (progenitor), CD45+/CD14+ (monocyte/macrophage), CD45+/CD14-(Leukocyte). RNA was isolated from adipocyte, SVF, progenitor, macrophage/monocyte and leukocyte fractions and analyzed on the Affymetrix Human Transcriptome 2.0 array. We also sorted SVF from an additional 13 (10 non-obese, 9 obese) patients and sent progenitor RNA for Affymetrix Human Transcriptome 2.0 array analysis. Overall design: Adipose tissue from 6 non-obese patients was collagenase treated and adipocytes separated from the stromal vascular fraction(SVF). SVF was then FACS sorted for the following fractions CD45-/CD34+/CD31+ (endothelial), CD45-/CD34+/CD31- (progenitor), CD45+/CD14+ (monocyte/macrophage), CD45+/CD14-(Leukocyte). RNA was isolated from adipocyte, SVF, progenitor, macrophage/monocyte and leukocyte fractions and analyzed on the Affymetrix Human Transcriptome 2.0 array. We also sorted SVF from an additional 13 (10 non-obese, 9 obese) patients and sent progenitor RNA for Affymetrix Human Transcriptome 2.0 array analysis.
Project description:Samples of oil and production water were collected from five wells of the Qinghai Oilfield, China, and subjected to GeoChip hybridization experiments for microbial functional diversity profiling. Unexpectedly, a remarkable microbial diversity in oil samples, which was higher than that in the corresponding water samples, was observed, thus challenging previously believed assumptions about the microbial diversity in this ecosystem. Hierarchical clustering separated oil and water samples, thereby indicating distinct functional structures in the samples. Genes involved in the degradation of hydrocarbons, organic remediation, stress response, and carbon cycling were significantly abundant in crude oil, which is consistent with their important roles in residing in oil. Association analysis with environmental variables suggested that oil components comprising aromatic hydrocarbons, aliphatic hydrocarbons, and a polar fraction with nitrogen-, sulfur-, and oxygen-containing compounds were mainly influential on the structure of the microbial community. Furthermore, a comparison of microbial communities in oil samples indicated that the structures were depth/temperature-dependent. To our knowledge, this is the first thorough study to profile microbial functional diversity in crude oil samples. From the Qinghai Oilfield located in the Tibetan Plateau, northwest China, oil production mixtures were taken from four oil production wells (No. 813, 516, 48 and 27) and one injection well (No. 517) in the Yue-II block. The floating oil and water phases of the production mixtures were separated overnight by gravitational separation. Subsequently, the microbial community and the characteristics of the water solution (W813, W516, W48, and W27) and floating crude oil (O813, O516, O48, and O27) samples were analyzed. A similar analysis was performed with the injection water solution (W517).
Project description:Since few years, yeast cell wall components and especially beta-glucans (BG) have been identified as potential stimulators of the innate immune system in murine and human species. A large screening of crude and BG-enriched components from Saccharomyces cerevisiae has been performed on murine macrophages. A priming effect with bacterial ligands was revealed in terms of pro-inflammatory cytokines release. To further characterize the responsiveness of bone marrow derived-macrophages which express high levels of dectin-1, the major receptor of BG, transcriptional analysis would provide more hypotheses about the genes and signaling pathways triggered by yeast cell wall compounds in macrophages. Gene expression profiling was performed in murine BMDM pretreated with a set of three BG-containing cell wall compounds and then stimulated with LPS. Conditions with BG-enriched pretreatment clustered together in contrast to the crude compound and mock pretreatment conditions that remained separated whatever the time point analyzed, with a greater number of differentially-expressed genes following the crude compound treatment compared to BG-enriched pretreatment. BG-enriched pretreatment induced a specific set of genes in mouse macrophages, involving the PI3K/AKT signaling pathway. Among them, the two main upregulated genes by BG-enriched priming condition were considered for further analysis and their associated-protein production were consistently increased in BMDM pretreated with BG-enriched compound. Microarray results were confirmed using RT-qPCR on a different set of samples. Overall design: Gene expression was measured in murine BMDM pretreated with ScCW (A), BG65 (C) and BG75 (D), or mock controls for 8 h, and further stimulated with LPS for 4 and 8 h. Four independent experiments were performed at each time using 4 individuals for each experiment.