Metabolic fingerprinting of rat urine by LC/MS Part 1. Analysis by hydrophilic interaction liquid chromatography-electrospray ionization mass spectrometry

Complex biological samples, such as urine, contain a very large number of endogenous metabolites reflecting the metabolic state of an organism. Metabolite patterns can provide a comprehensive signature of the physiological state of an organism as well as insights into specific biochemical processes. Although the metabolites excreted in urine are commonly highly polar, the samples are generally analyzed using reversed-phase liquid chromatography mass spectrometry (RP-LC/MS). In Part 1 of this work, a method for detecting highly polar metabolites by hydrophilic interaction liquid chromatography-electrospray ionization mass spectrometry (HILIC/ESI-MS) is described as a complement to RP-LC/ESI-MS. In addition, in an accompanying paper (Part 2), different multivariate approaches to extracting information from the resulting complex data are described to enable metabolic fingerprints to be obtained. The coverage of the method for the screening of as many metabolites as possible is highly improved by analyzing the urine samples using both a C(18) column and a ZIC-HILIC column. The latter was found to be a good alternative when analyzing highly polar compounds, e.g., hydroxyproline and creatinine, to columns typically used for reversed-phase liquid chromatography.     

Simultaneous analysis of homovanillic acid, 5-hydroxyindoleacetic acid, 3-methoxy-4-hydroxy-phenylethylene glycol and vanilmandelic acid in plasma from alcoholics by high-performance liquid chromatography with electrochemical detection Critical comparison of solid-phase and liquid—liquid extraction methods

A method is described for the simultaneous determination of vanilmandelic acid, 3-methoxy-4-hydroxyphenylethylene glycol, 5-hydroxyindoleacetic acid, and homovanillic acid in a human plasma sample using reversed-phase high-performance liquid chromatography with column switching and amperometric detection. Two methods of sample preparation were tested. Liquid—liquid extraction yields better recoveries, is more selective and precise than solid-phase extraction and allows a shorter time of chromatographic analysis. Estimated plasma values of the metabolites from healthy controls are in good agreement with previously reported levels. Studies of alcoholics at the beginning of the delirium tremens provided different plasma levels of the metabolites, dependent on the different duration — and hence the severity — of the delirium.     

An ultraperformance liquid chromatography method for the normal-phase separation of lipids

An ultraperformance liquid chromatography method using normal-phase solvents, a silica column, and evaporative light-scattering detection is presented. The method is based on a quaternary gradient profile and is capable of resolving the major neutral and polar lipids present in plasma and animal tissue in under 5 min, with a total cycle time of 11 min. Limits of quantitation for 7 different lipid classes were on the order of 200 ng of material on column which enables an accurate analysis from as little as 20 μL of plasma or 50 mg of tissue for typical samples. Intraday and interday precision for the determination of the major lipid classes in human plasma ranged from 3.6 to 10.5% CV with a variability in retention time of less than 6%. The utility of the method is demonstrated through the separation and quantitation of lipids in mouse plasma, liver, and heart tissue.     

Micronutrients (Other than iron) and Helicobacter pylori infection: a systematic review

Background: Many micronutrients depend on a healthy stomach for absorption. Helicobacter pylori chronic gastritis may alter gastric physiology affecting homeostasis of vitamins and minerals. Objectives: Systematic review to assess whether H. pylori infection is associated with reduced micronutrient levels (other than iron) in the plasma or gastric juice and whether low micronutrient levels are modified by eradication treatment. Method: Medline was searched for relevant publications from inception to June 2010. Studies describing micronutrient levels in H. pylori‐infected and not‐infected adults and/or the effect of eradication treatment on micronutrient levels were included. Findings: Fifty‐two publications were selected: 46 investigated the association between H. pylori infection and reduced micronutrient levels and 14 the effect of eradication treatment on micronutrient levels. Sixty‐four studies investigated vitamins (23 ascorbic acid, four ß‐carotene, 21 cobalamin, 11 folate, and five α‐tocopherol) and 10 addressed minerals (one calcium, one copper, one magnesium, one phosphorus, three selenium, and three zinc). Pooled standardized mean differences in micronutrient levels showed positive associations with H. pylori infection for ascorbic acid (gastric juice, ?1.087) and cobalamin (?0.744), and a positive effect of eradication treatment, which increased ascorbic acid in the gastric juice (?1.408) and serum cobalamin (?1.910). No significant association between infection and low folate levels was observed. Meta‐analyses for other micronutrients were not performed owing to insufficient data. Conclusions: Meta‐analyses indicate that H. pylori infection is associated with reduced levels of ascorbic acid and cobalamin, supported by the positive effect of eradication treatment. For other micronutrients, further studies are needed.     

Comparison of sample preparation techniques for large‐scale proteomics

Numerous workflows exist for large‐scale bottom‐up proteomics, many of which achieve exceptional proteome depth. Herein, we evaluated the performance of several commonly used sample preparation techniques for proteomic characterization of HeLa lysates [unfractionated in‐solution digests, SDS‐PAGE coupled with in‐gel digestion, gel‐eluted liquid fraction entrapment electrophoresis (GELFrEE) technology, SCX StageTips and high‐/low‐pH reversed phase fractionation (HpH)]. HpH fractionation was found to be superior in terms of proteome depth (>8400 proteins detected) and fractionation efficiency compared to other techniques. SCX StageTip fractionation required minimal sample handling and was also a substantial improvement over SDS‐PAGE separation and GELFrEE technology. Sequence coverage of the HeLa proteome increased to 38% when combining all workflows, however, total proteins detected improved only slightly to 8710. In summary, HpH fractionation and SCX StageTips are robust techniques and highly suited for complex proteome analysis.     

Comparison of two high-performance liquid chromatographic methods for the determination of oxmetidine and its metabolites in plasma, bile and urine samples

Two high-performance liquid chromatographic methods for the assay of oxmetidine are described: both utilize the same liquid extraction from plasma, urine and bile samples. A normal-phase technique is considered most suitable for the analysis of plasma extracts and a reversed-phase method is preferred for the assay of excretory fluids such as urine and bile which will contain polar metabolites in detectable quantity as well as unchanged oxmetidine.The methods are sensitive enough to follow the kinetic changes in concentration for up to 8 h after the administration of recommended therapeutic doses. Both methods can be automated in respect of the high-performance liquid chromatograph and the samples can be stored for several weeks at −20°C without prejudicing the accuracy of the analysis.     

The effects of drying of the topsoil and of micronutrients in the subsoil on micronutrient uptake by an intermittently defoliated ryegrass

Summary A glasshouse experiment was conducted to study the effects of water content of the topsoil on the micronutrient nutrition of Italian ryegrass (Lolium multiflorum Lam.) growing in a siliceous sandy soil of marginal micronutrient status, with and without a supply of micronutrients at lower depths. The main objectives were to investigate whether micronutrient supplies would be sustained for the regrowth of defoliated grass after the topsoil had dried, and to assess the contribution made by small amounts of micronutrients in the subsoil to nutrient supply.In the absence of supply from deeper layers, topsoil drying rapidly induced deficiency of micronutrients, particularly of manganese, resulting in significant yield depression. When small amounts of micronutrients were present in a deeper, wet layer there was little reduction in yield after the topsoil had dried.The evidence suggests that, provided the roots had access to water in the subsoils, significant amounts of manganese, zinc and copper can be absorbed from topsoils as dry or drier than wilting point. Supply of micronutrients to the subsoil appears to have enhanced the efficiency of manganese absorption from dry topsoil.     

Validated liquid chromatographic method for the determination of bexarotene in human plasma

A new liquid chromatographic method is described for the determination of the anti-tumour agent bexarotene in human plasma over the range 0.500-1500 ng/ml, using 1 ml of sample. Sample preparation consists of liberating the analyte from plasma lipids by adding acetonitrile, followed by acidification of the plasma and liquid extraction using a mixture of isoamyl alcohol and pentane or hexane. Separation and quantitation are performed by reversed-phase column liquid chromatography with fluorescence detection. Parameters affecting the performance of these steps are discussed. Validation results on linearity, selectivity, accuracy, precision, recovery and stability are shown, as well as the application of the method to samples from clinical trials.     

Comparative Analysis of Techniques to Purify Plasma Membrane Proteins

The aim of this project was to identify the best method for the enrichment of plasma membrane (PM) proteins for proteomics experiments. Following tryptic digestion and extended liquid chromatography-tandem mass spectrometry acquisitions, data were processed using MaxQuant and Gene Ontology (GO) terms used to determine protein subcellular localization. The following techniques were examined for the total number and percentage purity of PM proteins identified: (a) whole cell lysate (total number, 84–112; percentage purity, 9–13%); (b) crude membrane preparation (104–111; 17–20%); (c) biotinylation of surface proteins with N-hydroxysulfosuccinimydyl-S,S-biotin and streptavidin pulldown (78–115; 27–31%); (d) biotinylation of surface glycoproteins with biocytin hydrazide and streptavidin pulldown (41–54; 59–85%); or (e) biotinylation of surface glycoproteins with amino-oxy-biotin (which labels the sialylated fraction of PM glycoproteins) and streptavidin pulldown (120; 65%). A two- to threefold increase in the overall number of proteins identified was achieved by using stop and go extraction tip (StageTip)-based anion exchange (SAX) fractionation. Combining technique (e) with SAX fractionation increased the number of proteins identified to 281 (54%). Analysis of GO terms describing these proteins identified a large subset of proteins integral to the membrane with no subcellular assignment. These are likely to be of PM location and bring the total PM protein identifications to 364 (68%). This study suggests that selective biotinylation of the cell surface using amino-oxy-biotin in combination with SAX fractionation is a useful method for identification of sialylated PM proteins.     

Quantitative determination of unchanged cisplatin in rat kidney and liver by high-performance liquid chromatography

A quantitative analytical method for measuring unchanged cisplatin (CDDP) and high- and low-molecular-mass metabolites (fixed and mobile metabolites) in rat kidney and liver was developed. Unchanged CDDP, separated from fixed and mobile metabolites in tissue homogenates by consecutive procedures of fractionation and ultrafiltration, was determined by high-performance liquid chromatography (HPLC) with post-column derivatization. Although unchanged CDDP was found to be partly metabolized to fixed metabolites during the preparation of cytosolic ultrafiltrates, the recovery of unchanged CDDP gave a constant value (about 70%), which was independent of tissue type and CDDP concentration (from 1 to 10 μg/ml). The detection limit for unchanged CDDP in the cytosolic ultrafiltrate was 20 ng/ml, corresponding to a concentration detection limit of 65 ng Pt per g of tissue in the kidney and liver. The concentrations of fixed and mobile metabolites were determined as platinum concentrations in the tissue homogenate and in the cytosolic ultrafiltrate using atomic absorption spectrometry after correcting for transformation of unchanged CDDP to fixed metabolites. The distribution of unchanged CDDP, mobile metabolites and fixed metabolites in rat kidney and liver, after bolus injection of CDDP (5 mg/kg), was determined using this method.     

Acquisition of Cu, Zn, Mn and Fe by mycorrhizal maize (Zea mays L.) grown in soil at different P and micronutrient levels

Sustainability of soil-plant systems requires, among other things, good development and function of mycorrhizal symbioses. The effects of P and micronutrient levels on development of an arbuscular mycorrhizal fungus (AMF) and uptake of Zn, Cu, Mn and Fe by maize (Zea mays L.) were studied. A pot experiment with maize either inoculated or not with Glomus intraradices was conducted in a sand:soil (3 :1) mix (pH 6.5) in a greenhouse. Our goal was to evaluate the contribution of mycorrhizae to uptake of Cu, Zn, Mn and Fe by maize as influenced by soil P and micronutrient levels. Two levels of P (10 and 40 mg kg⁻¹ soil) and three levels of a micronutrient mixture: 0, 1X and 2X (1X contained, in mg kg⁻¹ soil, 4.2 Fe, 1.2 Mn, 0.24 Zn, 0.06 Cu, 0.78 B and 0.036 Mo), were applied to pots. There were more extraradical hyphae at the low P level than at the high P level when no micronutrients were added to the soil. Root inoculation with mycorrhiza and application of micronutrients increased shoot biomass. Total Zn content in shoots was higher in mycorrhizal than non-mycorrhizal plants grown in soils with low P and low or no micronutrient addition. Total Cu content in shoots was increased by mycorrhizal colonization when no micronutrients were added. Mycorrhizal plants had lower Mn contents than non-mycorrhizal plants only at the highest soil micronutrient level. AMF increased total shoot Fe content when no micronutrients were added, but decreased shoot Fe when plants were grown at the high level of micronutrient addition. The effects of G. intraradices on Zn, Cu, Mn, and Fe uptake varied with micronutrient and P levels added to soil. Accepted: 27 December 1999     

Maternal micronutrient disturbance as risks of offspring metabolic syndrome

Metabolic syndrome (MetS) is defined as a constellation of individual metabolic disturbances, including central obesity, hypertension, dyslipidemia, and insulin resistance. The established pathogenesis of MetS varies extensively with gender, age, ethnic background, and nutritional status. In terms of nutritional status, micronutrients are more likely to be discounted as essential components of required nutrition than macronutrients due to the small amount required. Numerous observational studies have shown that pregnant women frequently experience malnutrition, especially in developing and low-income countries, resulting in chronic MetS in the offspring due to the urgent and increasing demands for micronutrients during gestation and lactation. Over the past few decades, scientific developments have revolutionized our understanding of the association between balanced maternal micronutrients and MetS in the offspring. Examples of successful individual, dual, or multiple maternal micronutrient interventions on the offspring include iron for hypertension, selenium for type 2 diabetes, and a combination of folate and vitamin D for adiposity. In this review, we aim to elucidate the effects of maternal micronutrient intake on offspring metabolic homeostasis and discuss potential perspectives and challenges in the field of maternal micronutrient interventions.     

Fractionation and lipase-catalyzed conversion of microalgal lipids to biodiesel

This study was conducted to evaluate the lipid fractionation and purification procedures of lipase-catalyzed conversion of neutral lipids to microalgal biodiesel. Microalgae lipids were efficiently recovered and purified by a combined extraction method and crude lipid extracts were separated into neutral lipids, glycolipids, and phospholipids by solid-phase extraction. The high purity of the neutral lipids fraction was confirmed by its low concentration of phosphorous (< 2.0 ppm). Transesterification was catalyzed by immobilized Candida antarctica lipase for 72 h with stepwise addition of methanol. The reaction displayed Michaelis–Menten kinetics and produced high yields of microalgal biodiesel (91.2% in the case of Dunaliella salina) with a high content of unsaturated fatty acids (81.5%). Neutral lipids were converted to biodiesel by three-step transesterification, while the removal of polar lipids maintained the activity of the immobilized lipase by reducing both reaction mixture viscosity and contamination risk.     

Preparation of lipid-free tissue extracts for chromatographic determination of thyroid hormones and metabolites

We have developed a new method of preparing tissues for analysis of thyroid hormones and metabolites which eliminates troublesome lipids and proteins. Frozen tissue is homogenized by grinding with dry ice in a Waring blender, and the moist powder obtained is extracted with chloroform:methanol (2:1). In a modification of the Folch procedure for the total separation of lipids, the filtered extracts then are partitioned into polar and nonpolar layers by the addition of 0.05% aqueous calcium chloride. The upper phase contains the iodocompounds of interest as well as all salts and small polar molecules. The lipids remain dissolved in the lower phase after it is back-extracted with pure upper phase. The combined upper or aqueous methanol layers are lyophilized and the residue is taken up in methanol to yield a concentrated solution ready for analysis of iodocompounds. The greater clarity of the extract permits application of larger samples for two-dimensional paper chromatography than has been customary. For gradient analysis by reverse-phase ion-pair high-performance liquid chromatography (HPLC), the nitrogen-evaporated methanol extract is dissolved in the initial mobile phase, 0.1% H₃PO₄, for injection onto the column. Using these methods we have achieved the first reported separation of ¹²⁵I-labeled tissue iodothyronine metabolites by HPLC. The new method of extraction is of general applicability to any biological sample which might be analyzed in thyroid hormone metabolism research.     

Evaluation of metabolite extraction strategies from tissue samples using NMR metabolomics

Metabolomic analysis of tissue samples can be applied across multiple fields including medicine, toxicology, and environmental sciences. A thorough evaluation of several metabolite extraction procedures from tissues is therefore warranted. This has been achieved at two research laboratories using muscle and liver tissues from fish. Multiple replicates of homogenous tissues were extracted using the following solvent systems of varying polarities: perchloric acid, acetonitrile/water, methanol/water, and methanol/chloroform/water. Extraction of metabolites from ground wet tissue, ground dry tissue, and homogenized wet tissue was also compared. The hydrophilic metabolites were analyzed using 1-dimensional (1D) ¹H nuclear magnetic resonance (NMR) spectroscopy and projections of 2-dimensional J-resolved (p-JRES) NMR, and the spectra evaluated using principal components analysis. Yield, reproducibility, ease, and speed were the criteria for assessing the quality of an extraction protocol for metabolomics. Both laboratories observed that the yields of low molecular weight metabolites were similar among the solvent extractions; however, acetonitrile-based extractions provided poorer fractionation and extracted lipids and macromolecules into the polar solvent. Extraction using perchloric acid produced the greatest variation between replicates due to peak shifts in the spectra, while acetonitrile-based extraction produced highest reproducibility. Spectra from extraction of ground wet tissues generated more macromolecules and lower reproducibility compared with other tissue disruption methods. The p-JRES NMR approach reduced peak congestion and yielded flatter baselines, and subsequently separated the metabolic fingerprints of different samples more clearly than by 1D NMR. Overall, single organic solvent extractions are quick and easy and produce reasonable results. However, considering both yield and reproducibility of the hydrophilic metabolites as well as recovery of the hydrophobic metabolites, we conclude that the methanol/chloroform/water extraction is the preferred method. C. Y. Lin and H. Wu contributed equally.     

Extraction parameters for metabolomics from cultured cells

The successful extraction of metabolites is a critical step in metabolite profiling. By optimizing metabolite extraction, the range and quantitative capacity of metabolomics studies can be improved. We considered eight separate extraction protocols for the preparation of a metabolite extract from cultured mammalian cells. Parameters considered included temperature, pH, and cell washing before extraction. The effects on metabolite recovery were studied using a liquid chromatography high-resolution mass spectrometry (LC–HRMS) platform that measures metabolites of diverse chemical classes, including amino acids, lipids, and sugar derivatives. The temperature considered during the extraction or the presence of formic acid, a commonly used additive, was shown to have minimal effects on the measured ion intensities of metabolites. However, washing of samples before metabolite extraction, whether with water or phosphate-buffered saline, exhibited dramatic effects on measured intensities of both intracellular and extracellular metabolites. Together, these findings present a systematic assessment of extraction conditions for metabolite profiling.     

Applying genomic resources to accelerate wheat biofortification

Wheat has low levels of the micronutrients iron and zinc in the grain, which contributes to 2 billion people suffering from micronutrient deficiency globally. While wheat flour is commonly fortified during processing, an attractive and more sustainable solution is biofortification, which could improve micronutrient content in the human diet, without the sustainability issues and costs associated with conventional fortification. Although many studies have used quantitative trait loci mapping and genome-wide association to identify genetic loci to improve micronutrient contents, recent developments in genomics offer an opportunity to accelerate marker discovery and use gene-focussed approaches to engineer improved micronutrient content in wheat. The recent publication of a high-quality wheat genome sequence, alongside gene expression atlases, variation datasets and sequenced mutant populations, provides a foundation to identify genetic loci and genes controlling micronutrient content in wheat. We discuss how novel genomic resources can identify candidate genes for biofortification, integrating knowledge from other cereal crops, and how these genes can be tested using gene editing, transgenic and TILLING approaches. Finally, we highlight key challenges remaining to develop wheat cultivars with high levels of iron and zinc.Subject terms: Agricultural genetics, Plant genetics     

Accessibility of glucose 6-phosphate: phosphohydrolase to antibody attack in modified microsomal vesicles

Upon subcellular fractionation of (murine) Friend erythroleukaemic cells (FELCs), purified plasma membranes were identified by their high enrichment in specific marker enzymes and typical plasma membrane lipids. When FELCs were incubated for short periods with ³²P_i before cell fractionation, the lipid-bound radioactivity was almost exclusively present in phosphatidylinositol-4-phosphate (DPI) and phosphatidylinositol-4,5-bisphosphate (TPI), and its distribution closely matched that of the plasma membrane markers. In addition, purified plasma membranes actively incorporated ³²P from [γ-³²P]ATP into polyphosphoinositides, and the specific activities of the involved kinases were again mostly enriched in the plasma membrane fraction.