Project description:Lipidomics refers to the full characterization of lipids present within a cell, tissue, organism, or biological system. One of the bottlenecks affecting reliable lipidomic analysis is the extraction of lipids from biological samples. An ideal extraction method should have a maximum lipid recovery and the ability to extract a broad range of lipid classes with acceptable reproducibility. The most common lipid extraction relies on either protein precipitation (monophasic methods) or liquid-liquid partitioning (bi- or triphasic methods). In this study, three monophasic extraction systems, isopropanol (IPA), MeOH/MTBE/CHCl3 (MMC), and EtOAc/EtOH (EE), alongside three biphasic extraction methods, Folch, butanol/MeOH/heptane/EtOAc (BUME), and MeOH/MTBE (MTBE), were evaluated for their performance in characterization of the mouse lipidome of six different tissue types, including pancreas, spleen, liver, brain, small intestine, and plasma. Sixteen lipid classes were investigated in this study using reversed-phase liquid chromatography/mass spectrometry. Results showed that all extraction methods had comparable recoveries for all tested lipid classes except lysophosphatidylcholines, lysophosphatidylethanolamines, acyl carnitines, sphingomyelines, and sphingosines. The recoveries of these classes were significantly lower with the MTBE method, which could be compensated by the addition of stable isotope-labeled internal standards prior to lipid extraction. Moreover, IPA and EE methods showed poor reproducibility in extracting lipids from most tested tissues. In general, Folch is the optimum method in terms of efficacy and reproducibility for extracting mouse pancreas, spleen, brain, and plasma. However, MMC and BUME methods are more favored when extracting mouse liver or intestine.
Project description:As the primary solid phase, amorphous calcium phosphate (ACP) is a pivotal precursor in cellular biomineralization. The intrinsic interplay between ACP and Howard factor underscores the significance of understanding their association for advancing biomimetic ACP development. While organic compounds play established roles in biomineralization, this study presents the synthesis of ACP with naturally occurring organic compounds (ascorbate, glutamate, and itaconate) ubiquitously found in mitochondria and vital for bone remodeling and healing. The developed ACP with organic compounds was meticulously characterized using XRD, FTIR, and solid-state 13C and 31P NMR. The morphological analysis revealed the characteristic spherical morphology with particle size close to 20 nm of all synthesized ACP variants. Notably, the type of organic compound strongly influences true density, specific surface area, particle size, and transformation. The in vitro analysis was performed with MC3T3-E1 cells, indicating the highest cell viability with ACP_ASC (ascorbate), followed by ACP_ITA (itaconate). The lowest cell viability was observed with 10 %w/v of ACP_GLU (glutamate); however, 1 %w/v of ACP_GLU was cytocompatible. Further, the effect of small organic molecules on the transformation of ACP to low crystalline apatite (Ap) was examined in Milli-Q® water, PBS, and α-MEM.
Project description:The untargeted approach to mass spectrometry-based metabolomics has a wide potential to investigate health and disease states, identify new biomarkers for diseases, and elucidate metabolic pathways. All this holds great promise for many applications in biological and chemical research. However, the complexity of instrumental parameters on advanced hybrid mass spectrometers can make the optimization of the analytical method immensely challenging. Here, we report a strategy to optimize the selected settings of a hydrophilic interaction liquid chromatography-tandem mass spectrometry method for untargeted metabolomics studies of human plasma, as a sample matrix. Specifically, we evaluated the effects of the reconstitution solvent in the sample preparation procedure, the injection volume employed, and different mass spectrometry-related operating parameters including mass range, the number of data-dependent fragmentation scans, collision energy mode, duration of dynamic exclusion time, and mass resolution settings on the metabolomics data quality and output. This study highlights key instrumental variables influencing the detection of metabolites along with suggested settings for the IQ-X tribrid system and proposes a new methodological framework to ensure increased metabolome coverage.
Project description:RNAi experiments are ubiquitously used in cell biology and are achieved by transfection of small interfering RNAs (siRNAs) into cells using a transfection reagent. These results in knock-down of proteins of interest, and the phenotypic consequences are then analyzed. It is reported here that two common RNA interference (RNAi) transfection reagents, DharmaFECT 1 and INTERFERin, in mock transfections using non-targeting siRNAs, cause alterations in the lipidome of HeLa cells. Some lipids change in response to both, presumably chemically different, transfection reagents, while other lipid species change only in response to one of the reagents. While the functional implications of these lipidomic alterations remain to be investigated, the authors' experiments suggest that it is important to use appropriate mock transfection controls during RNAi experiments, ideally complemented by an orthogonal perturbation, especially when investigating membrane-associated phenomena.
Project description:A study to investigate the effect of small molecule lipid inducing compounds that leads to hyper-accumulation of lipids in N replete cells of Chlamydomonas reinhardtii. These compounds were identified through a high throughput screening designed for that purpose. The highthrouhput screen (HTS) evaluated 43,783 compounds and identified 367 primary hits. These 367 hits were further retested using a 8-point dilution series (from 0.25 to 30 uM) and verified the activity of 243 compounds that induce the hyper lipid accumulating phenotype in algae. Once the hit compounds were identified and confirmed, we then performed extensive chemoinformatics analysis to look for common scaffolds and identified several common substructures. We then selected 15 top performing compounds from 5 diverse structural groups and tested for biochemical parameters such as growth, lipid accumulating capacity, effect on photosynthetic rates, respiration rates, oxygen consumption rates, analysis of different lipid species to identify and quantify fatty acid species using GC-MS, transcriptome analysis using next generation sequencing (RNASeq), untargeted metabolomics using LC-MS, lipidome analysis using FT-ICR MS. To understand the global changes in the proteome, 2 structurally different compounds were selected and compared to the control without compound treatment.
Project description:Matrix-assisted laser desorption/ionization mass spectrometry imaging allows for the study of metabolic activity in the tumor microenvironment of brain cancers. The detectable metabolites within these tumors are contingent upon the choice of matrix, deposition technique, and polarity setting. In this study, we compared the performance of three different matrices, two deposition techniques, and the use of positive and negative polarity in two different brain cancer types and across two species. Optimal combinations were confirmed by a comparative analysis of lipid and small-molecule abundance by using liquid chromatography-mass spectrometry and RNA sequencing to assess differential metabolites and enzymes between normal and tumor regions. Our findings indicate that in the tumor-bearing brain, the recrystallized α-cyano-4-hydroxycinnamic acid matrix with positive polarity offered superior performance for both detected metabolites and consistency with other techniques. Beyond these implications for brain cancer, our work establishes a workflow to identify optimal matrices for spatial metabolomics studies.
Project description:1. The changes in membrane permeability to small molecules caused by Sendai virus [Pasternak & Micklem (1973) J. Membr. Biol. 14, 293-303] have been further characterized. The uptake of substances that are concentrated within cells is inhibited. Choline and 2-deoxyglucose, which become phosphorylated, and aminoisobutyrate and glycine, which are driven by a Na+-linked mechanism, are examples. The uptake of each compound under conditons where its diffusion across the plasma membrane is rate-limiting is stimulated by virus. Choline, 2-deoxyglucose and amino acids at high concentration, amino acids in Na+-free medium, and most substances at low temperature, are examples. It is concluded that virally mediated decrease of uptake is due to one of two causes. Substances that are accumulated by phosphorylation are not retained because of leakage of the phosphorylated metabolites out of cells. Substances that are accumulated by linkage to a Na+ gradient are no longer accumulated because of collapse of the gradient resulting from an increased permeability to Nat 2. Increased permeability to K+ and Na+ results in (a) membrane depolarization and (b) cell swelling. The latter event leads to haemolysis (for erythrocytes) and can lead to giant-cell (polykaryon) formation (for several cell types). 3. Recovery of cells can be temporarily achieved by the addition of Ca2+; permanent recovery requires incubation for some hours at 37 degrees C. 4. The possible significance of virally mediated permeability changes, with regard to clinical situations and to cell biology, is discussed.