13 research outputs found
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Dietary Omega-3 Fatty Acids Do Not Change Resistance of Rat Brain or Liver Mitochondria to Ca2+ and/or Prooxidants
Omega-3 polyunsaturated fatty acids (n-3 PUFAs) block apoptotic neuronal cell death and are strongly neuroprotective in acute and chronic neurodegeneration. Theoretical considerations, indirect data, and consideration of parsimony lead to the hypothesis that modulation of mitochondrial pathway(s) underlies at least some of the neuroprotective effects of n-3 PUFAs. We therefore systematically tested this hypothesis on healthy male FBFN1 rats fed for four weeks with isocaloric, 10% fat-containing diets supplemented with 1, 3, or 10% fish oil (FO). High resolution mass spectrometric analysis confirmed expected diet-driven increases in docosahexaenoic acid (DHA, 22:6, n-3) and eicosapentaenoic acid (EPA, 20:5, n-3) in sera, liver and nonsynaptosomal brain mitochondria. We further evaluated the resistance of brain and liver mitochondria to Ca2+ overload and prooxidants. Under these conditions, neither mitochondrial resistance to Ca2+ overload and prooxidants nor mitochondrial physiology is altered by diet, despite the expected incorporation of DHA and EPA in mitochondrial membranes and plasma. Collectively, the data eliminate one of the previously proposed mechanism(s) that n-3 PUFA induced augmentation of mitochondrial resistance to the oxidant/calcium-driven dysfunction. These data furthermore allow us to define a specific series of follow-up experiments to test related hypotheses about the effect of n-3 PUFAs on brain mitochondria
An SVM Based Tool for the Curation of Biomedical Literature
Information in genome databases is maintained and updated by curators, ensuring that it is current and authentic. To achieve this goal, curators refer to research articles to refine the scientific knowledge stored in these databases, as this literature is an important source for such information. Curators have to pick papers relevant to the database they are maintaining from the literature. The vastly growing literature makes it a challenge to find crucial and relevant information, making curators fall behind the latest publications. The identification of papers relevant to a particular subject is an example of text categorization. In this research we focus on creating a web based software tool that utilizes support vector machines (SVM) as a classifier. The SVM classifies papers as relevant or irrelevant by categorizing text from abstracts. By creating software tools that implement text categorization algorithms, biomedical literature can be more effectively curated. Software tools that can help curators with the task of selecting highly relevant papers out of the large volume of literature would greatly benefit the curation process. This tool achieves an average accuracy of 94.45% and precision and recall of 96.34% and 94.74% respectively when classifying papers relevant to needs of the Rat Genome Database (RGD)
Data & R Code from: Dietary macronutrients modulate the Fatty Acyl composition of rat liver mitochondrial cardiolipins.
The zip file contains all data and R code used to analyze Cardiolipin and related data. Please refer to README within the zip file for instructions on how to run the R code to produce all figures, including those found in the supplement and statistical tables in the supplement
Separation of Cis–Trans Phospholipid Isomers Using Reversed Phase LC with High Resolution MS Detection
The increased presence of synthetic trans fatty acids
into western
diets has been shown to have deleterious effects on physiology and
raising an individual’s risk of developing metabolic disease,
cardiovascular disease, and stroke. The importance of these fatty
acids for health and the diversity of their (patho) physiological
effects suggest that not only should the free trans fatty acids be
studied but also monitoring the presence of these fats into the side
chains of biological lipids, such as glycerophospholipids, is also
essential. We developed a high resolution LC-MS method that quantitatively
monitors the major lipid classes found in biospecimens in an efficient,
sensitive, and robust manner while also characterizing individual
lipid side chains through the use of high energy collisional dissociation
(HCD) fragmentation and chromatographic alignment. We herein show
how this previously described reversed phase method can baseline separate
the cis–trans isomers of phosphatidylglycerol and phosphatidylcholine
(PC) with two 18:1 side chains, in both positive and negative mode,
as neat solutions and when spiked into a biological matrix. Endogenous
PC (18:1/18:1)-cis and PC (18:1/18:1)-trans isomers were examined
in mitochondrial and serum profiling studies, where rats were fed
diets enriched in either trans 18:1 fatty acids or cis 18:1 fatty
acids. In this study, we determined the cis:trans isomer ratios of
PC (18:1/18:1) and related this ratio to dietary composition. This
generalized LC-MS method enables the monitoring of trans fats in biological
lipids in the context of a nontargeted method, allowing for relative
quantitation and enhanced identification of unknown lipids in complex
matrixes
Method Development for Fecal Lipidomics Profiling
Robust methodologies for the analysis of fecal material
will facilitate
the understanding of gut (patho)physiology and its role in health
and disease and will help improve care for individual patients, especially
high-risk populations, such as premature infants. Because lipidomics
offers a biologically and analytically attractive approach, we developed
a simple, sensitive, and quantitatively precise method for profiling
intact lipids in fecal material. The method utilizes two separate,
complementary extraction chemistries, dichloromethane (DCM) and a
methyl <i>tert</i>-butyl ether/hexafluoroisopropanol (MTBE)
mixture, alone or with high pressure cycling. Extracts were assessed
by liquid chromatography–high-resolution mass spectrometry-based
profiling with all ion higher energy collisional dissociation fragmentation
in both positive and negative ionization modes. This approach provides
both class-specific and lipid-specific fragments, enhancing lipid
characterization. Solvents preferentially extracted lipids based on
hydrophobicity. More polar species preferred MTBE; more hydrophobic
compounds preferred DCM. Pressure cycling differentially increased
the yield of some lipids. The platform enabled analysis of >500
intact
lipophilic species with over 300 lipids spanning 6 LIPID MAPS categories
identified in the fecal matter from premature infants. No previous
report exists that provides these data; thus, this study represents
a new paradigm for assessing nutritional health, inflammation, and
infectious disease in vulnerable populations
Method Development for Fecal Lipidomics Profiling
Robust methodologies for the analysis of fecal material
will facilitate
the understanding of gut (patho)physiology and its role in health
and disease and will help improve care for individual patients, especially
high-risk populations, such as premature infants. Because lipidomics
offers a biologically and analytically attractive approach, we developed
a simple, sensitive, and quantitatively precise method for profiling
intact lipids in fecal material. The method utilizes two separate,
complementary extraction chemistries, dichloromethane (DCM) and a
methyl <i>tert</i>-butyl ether/hexafluoroisopropanol (MTBE)
mixture, alone or with high pressure cycling. Extracts were assessed
by liquid chromatography–high-resolution mass spectrometry-based
profiling with all ion higher energy collisional dissociation fragmentation
in both positive and negative ionization modes. This approach provides
both class-specific and lipid-specific fragments, enhancing lipid
characterization. Solvents preferentially extracted lipids based on
hydrophobicity. More polar species preferred MTBE; more hydrophobic
compounds preferred DCM. Pressure cycling differentially increased
the yield of some lipids. The platform enabled analysis of >500
intact
lipophilic species with over 300 lipids spanning 6 LIPID MAPS categories
identified in the fecal matter from premature infants. No previous
report exists that provides these data; thus, this study represents
a new paradigm for assessing nutritional health, inflammation, and
infectious disease in vulnerable populations
Age-related changes in circadian regulation of the human plasma lipidome
Abstract Aging alters the amplitude and phase of centrally regulated circadian rhythms. Here we evaluate whether peripheral circadian rhythmicity in the plasma lipidome is altered by aging through retrospective lipidomics analysis on plasma samples collected in 24 healthy individuals (9 females; mean ± SD age: 40.9 ± 18.2 years) including 12 younger (4 females, 23.5 ± 3.9 years) and 12 middle-aged older, (5 females, 58.3 ± 4.2 years) individuals every 3 h throughout a 27-h constant routine (CR) protocol, which allows separating evoked changes from endogenously generated oscillations in physiology. Cosinor regression shows circadian rhythmicity in 25% of lipids in both groups. On average, the older group has a ~14% lower amplitude and a ~2.1 h earlier acrophase of the lipid circadian rhythms (both, p ≤ 0.001). Additionally, more rhythmic circadian lipids have a significant linear component in addition to the sinusoidal across the 27-h CR in the older group (44/56) compared to the younger group (18/58, p < 0.0001). Results from individual-level data are consistent with group-average results. Results indicate that prevalence of endogenous circadian rhythms of the human plasma lipidome is preserved with healthy aging into middle-age, but significant changes in rhythmicity include a reduction in amplitude, earlier acrophase, and an altered temporal relationship between central and lipid rhythms