GNPS-rat blood plasma (1 to 4 days) (new candidate entity)
Ontology highlight
ABSTRACT:
INSTRUMENT(S): HRMS(Orbitrab)
ORGANISM(S): Crl:wi(han)
SUBMITTER: 
Kyung Hwa Kee
PROVIDER: MSV000096385 | GNPS | Tue Nov 12 04:16:00 GMT 2024
REPOSITORIES: GNPS
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Project description:Excerpt from a larger study which characterized the transcriptional effects of a spinal cord contusion injury in rats. This is the data from the almost chronic contusion state (35 days) at the injury site (Thoracic 8) - where we saw significant changes in several areas, including cholesterol metabolism genes. Other spinal cord areas (rostral, caudal) and time-points (3 hours, 24 hours, 7 days and 35 days) were analyzed as well and are discussed in our paper and at www.crpf.org/microarray.
2007-10-08 | E-GEOD-2599 | biostudies-arrayexpress
Project description:BackgroundExercise training promotes brain plasticity and is associated with protection against cognitive impairment and Alzheimer's disease (AD). These beneficial effects may be partly mediated by blood-borne factors. Here we used an in vitro model of AD to investigate effects of blood plasma from exercise-trained donors on neuronal viability, and an in vivo rat model of AD to test whether such plasma impacts cognitive function, amyloid pathology, and neurogenesis.MethodsMouse hippocampal neuronal cells were exposed to AD-like stress using amyloid-β and treated with plasma collected from human male donors 3 h after a single bout of high-intensity exercise. For in vivo studies, blood was collected from exercise-trained young male Wistar rats (high-intensity intervals 5 days/week for 6 weeks). Transgenic AD rats (McGill-R-Thy1-APP) were injected 5 times/fortnight for 6 weeks at 2 months or 5 months of age with either (a) plasma from the exercise-trained rats, (b) plasma from sedentary rats, or (c) saline. Cognitive function, amyloid plaque pathology, and neurogenesis were assessed. The plasma used for the treatment was analyzed for 23 cytokines.ResultsPlasma from exercised donors enhanced cell viability by 44.1% (p = 0.032) and reduced atrophy by 50.0% (p < 0.001) in amyloid-β-treated cells. In vivo exercised plasma treatment did not alter cognitive function or amyloid plaque pathology but did increase hippocampal neurogenesis by ∼3 fold, regardless of pathological stage, when compared to saline-treated rats. Concentrations of 7 cytokines were significantly reduced in exercised plasma compared to sedentary plasma.ConclusionOur proof-of-concept study demonstrates that plasma from exercise-trained donors can protect neuronal cells in culture and promote adult hippocampal neurogenesis in the AD rat brain. This effect may be partly due to reduced pro-inflammatory signaling molecules in exercised plasma.
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Project description:Previously, we published a dataset of human blood plasma and serum samples of 10 healthy males and 10 healthy females, fractionated on a set of sorbents (cation exchange Toyopearl CM-650M, CM Bio-Gel A, SP Sephadex C-25 and anion exchange QAE Sephadex A-25) and analyzed by LC-MS/MS individually and pooled in equal amounts (Supplementary Table S1, Sheet 1) [33]. The mass spectrometry peptidomics data was deposited to the ProteomeXchange Consortium via the PRIDE partner repository (dataset identifiers PXD008141 and 10.6019/PXD008141). Direct download link: http://www.ebi.ac.uk/pride/archive/projects/PXD008141. We analyzed this dataset again within this work. The detailed information about the dataset of blood plasma/serum samples of 20 healthy donors fractionated on a set of sorbents is available in the original paper [33], including the clinical parameters of the donors, sample collection, plasma/serum fractionation, peptide extraction and LC-MS/MS analysis. 33. Arapidi, G. et al. Peptidomics dataset: Blood plasma and serum samples of healthy donors fractionated on a set of chromatography sorbents. Data Brief 18, 1204–1211 (2018).
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Project description:Data for published paper
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Project description:This dataset contains raw mass spectrometry data (in the form of Thermo Fisher .RAW files) supporting associated publication “Variable blood processing procedures contribute to plasma proteomic variability” by Halvey et al.
The experiments characterized by these data evaluated effects on human plasma proteome of processing delay (from blood draw to the first centrifugation: 0, 6, 24, 48, 72 and 144 hours) and the type of anticoagulant tube used for blood collection (heparin or EDTA). Sample names indicate combinations of corresponding conditions - e.g. 48h_hep = 48 hours in heparin tube.
For the “6h_EDTA” experiment there were several instances of LC-MS/MS analytical replicates for this sample. It should be noted that for this experiment the .RAW file from the “./updates/2020-08-03_vfarutin_60de013e/raw/” folder under this dataset FTP address represents the actual LC-MS/MS run used to generate the data in the associated paper by Halvey et al.
2020-07-21 | MSV000085799 | MassIVE
Project description:This dataset contains raw mass spectrometry data (in the form of Thermo Fisher .RAW files) supporting associated publication “Variable blood processing procedures contribute to plasma proteomic variability” by Halvey et al.
The experiments characterized by these data evaluated effects on human plasma proteome of the following centrifugation parameters: number of spins (1 or 2), brake application (brake or no brake) and the speed of spin (1000g or 2000g). Conditions 1 through 8 correspond to following combinations of these factors - Condition 1: 1 spin 1000g no brake; Condition 2: 1 spin 1000g brake; Condition 3: 2 spins 1000g no brake; Condition 4: 2 spins 1000g brake; Condition 5: 1 spin 2000g no brake; Condition 6: 1 spin 2000g brake; Condition 7: 2 spins 2000g no brake; Condition 8: 2 spins 2000g brake.
For the experiments investigating Conditions 1 and 4 there were several instances of LC-MS/MS analytical replicates for each individual sample. It should be noted that for these two experiments the corresponding .RAW files from the “./updates/2020-08-03_vfarutin_3259f343/raw/” folder under this dataset FTP address represent the actual LC-MS/MS runs used to generate the data in the associated paper by Halvey et al.
2020-07-16 | MSV000085763 | MassIVE
Project description:In this study 3 pooling experiments were performed. In each of the 3 cohorts, a 'case' and a 'control' blood pool was compared - the goal being to identify single nucleotide polymorphisms with significantly different estimated pooling allele frequencies between cases and controls. For cohort 1, 100 individuals with blue eye color were placed in one pool (the 'control' pool) and 100 individuals with brown eye color were placed in another pool ( the 'case' pool). In cohort 2, 131 individuals with age-related macular degeneration were placed in one pool, with 216 control individuals in another pool. In cohort 3, 100 individuals with pseudoexfoliation syndrome were placed in a case pool - in this case the cohort 2 control sample was used as 'controls'. The blue/brown pools were hybridized to Illumina HumanHap550 arrays. The cohort 2 and 3 pools were hybridized to Illumina 1M arrays. After processing, the raw data are summarized to give pooling allele frequency estimates for each pool. The abstract from the paper describing these data is as follows: Genome-wide association studies (GWAS) have now successfully identified important genetic variants associated with many human traits and diseases. The high cost of genotyping arrays in large datasets remains the major barrier to wider utilization of GWAS. We have developed a novel method in which whole blood from cases and controls respectively is pooled prior to DNA extraction for genotyping. We demonstrate proof of principle by clearly identifying the associated variants for eye color, age-related macular degeneration and pseudoexfoliation syndrome in cohorts not previously studied. Blood pooling has the potential to reduce GWAS cost by several orders of magnitude and dramatically shorten gene discovery time. This method has profound implications for translation of modern genetic approaches to a multitude of diseases and traits yet to be analysed by GWAS, and will enable developing nations to participate in GWAS.
2009-08-08 | GSE17557 | GEO
Project description:Interventions: FOBT with collection paper vs FOBT without collection paper
Primary outcome(s): - Attendance rate
Study Design: Randomized controlled trial, Open (masking not used), Active, Parallel
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Project description:The effects of environmental hypoxia on cardiac and skeletal muscle metabolism are dependent on the duration and severity of hypoxic exposure, though factors which dictate the nature of the metabolic response to hypoxia are poorly understood. We therefore set out to investigate the time-dependence of metabolic acclimatisation to hypoxia in rat cardiac and skeletal muscle. Rats were housed under normoxic conditions, or exposed to short-term (2 d) or sustained (14 d) hypoxia (10% O2), after which samples were obtained from the left ventricle of the heart and the soleus for assessment of metabolic regulation and mitochondrial function. Mass-corrected maximal oxidative phosphorylation was 20% lower in the left ventricle following sustained but not short-term hypoxia, though no change was observed in the soleus. After sustained hypoxia, the ratio of octanoyl carnitine- to pyruvate- supported respiration was 11% and 12% lower in the left ventricle and soleus, respectively, whilst hexokinase activity increased by 33% and 2.1-fold in these tissues. mRNA levels of PPARα targets fell after sustained hypoxia in both tissues, but those of PPARα remained unchanged. Despite decreased Ucp3 expression after short-term hypoxia, UCP3 protein levels and mitochondrial coupling remained unchanged. Protein carbonylation was 40% higher after short-term but not sustained hypoxic exposure in the left ventricle, but was unchanged in the soleus at both timepoints. Our findings therefore demonstrate that 14 days, but not 2 days, of hypoxia induces a loss of oxidative capacity in the left ventricle but not the soleus, and a substrate switch away from fatty acid oxidation in both tissues.
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