Quantitative sphingosine measurement as a surrogate for total ceramide concentration—preclinical and potential translational applications

Biomarkers are an increasingly important constituent of the drug development process, offering the potential of increased efficiency through reduced compound attrition and earlier proof of mechanism and/or efficacy. Assays developed for compound screening that can be directly translated for clinical trials are especially valuable, but their successful adoption requires a careful balance between assay performance and implementation costs. One such ‘fit‐for‐purpose’ biomarker assay, the indirect measurement of pharmacological modulation of sphingolipid biosynthesis and disposition, is presented here. Among spingolipids, numerous ceramide species are readily detectable in different lipoprotein fractions of mammalian plasma, but their parallel quantification can be prohibitively expensive and time consuming. Ceramides differ in their fatty acid moiety, which is readily removed by hydrolysis, yielding a common sphingosine derivative, the measurement of which serves as an indicator of total ceramide. When followed by liquid chromatography tandem mass spectrometry (LC/MS/MS) for detection, robust analyte quantification becomes relatively straightforward. The practical utility of a method developed to be fit for the purpose of rapidly and quantitatively measuring treatment‐induced variations in total ceramide from hamster plasma and individual lipoprotein fractions is described. With a linear calibration range from 0.003 to 33.4 μm sphingosine, precision and accuracy error in plasma‐based quality controls spiked with ceramides was less than 15%. The specificity of the assay for ceramides was also assessed. The simplicity of the method would allow for its potential translation to other preclinical species, as well as for clinical applications in later‐stage drug development. Copyright © 2009 John Wiley & Sons, Ltd.     

Temperature dependence of the resolution of diastereomeric isoprenoids in capillary GC. Experiments with 50 μm, 100 μm,and 250 μm i.d. Columns

The resolution of the diastereoisomers of norpristane, pristane, and phytane was studied as a function of the column internal diameter and/or the residence time of the compounds in the column. Increasing the residence time in the column by operating the column at a lower temperature program rate enhances the resolution more than reducing the internal diameter of the column. Practical experience with ultra narrow bore columns is also presented.     

Polypyridyl-Based Copper Phenanthrene Complexes: Combining Stability with Enhanced DNA Recognition

We report a series of copper(II) artificial metallo-nucleases (AMNs) and demonstrate their DNA damaging properties and in-vitro cytotoxicity against human-derived pancreatic cancer cells. The compounds combine a tris-chelating polypyridyl ligand, di-(2-pycolyl)amine (DPA), and a DNA intercalating phenanthrene unit. Their general formula is Cu-DPA-N,N' (where N,N'=1,10-phenanthroline (Phen), dipyridoquinoxaline (DPQ) or dipyridophenazine (DPPZ)). Characterisation was achieved by X-ray crystallography and continuous-wave EPR (cw-EPR), hyperfine sublevel correlation (HYSCORE) and Davies electron-nuclear double resonance (ENDOR) spectroscopies. The presence of the DPA ligand enhances solution stability and facilitates enhanced DNA recognition with apparent binding constants (K_app) rising from 10⁵ to 10⁷ m ⁻¹ with increasing extent of planar phenanthrene. Cu-DPA-DPPZ, the complex with greatest DNA binding and intercalation effects, recognises the minor groove of guanine–cytosine (G-C) rich sequences. Oxidative DNA damage also occurs in the minor groove and can be inhibited by superoxide and hydroxyl radical trapping agents. The complexes, particularly Cu-DPA-DPPZ, display promising anticancer activity against human pancreatic tumour cells with in-vitro results surpassing the clinical platinum(II) drug oxaliplatin.     

A data-driven,high-throughput methodology to determine tissue-specific differentially methylated regions able to discriminate body fluids

Tissue-specific differentially methylated regions (tDMRs) are regions of the genome with methylation patterns that modulate gene expression in those tissue types. The detection of tDMRs in forensic evidence can permit the identification of body fluids at trace levels. In this report, we have performed a bioinformatic analysis of an existing array dataset to determine if new tDMRs could be identified for use in body fluid identification from forensic evidence. Once these sites were identified, primers were designed and bisulfite modification was performed. The relative methylation level for each body fluid at a given locus was then determined using qPCR with high-resolution melt analysis (HRM). After screening 127 tDMR's in multiple body fluids, we were able to identify four new markers able to discriminate blood (2 markers), vaginal epithelia (1 marker) and buccal cells (1 marker). One marker for each target body fluid was also tested with pyrosequencing showing results consistent with those obtained by HRM. This work successfully demonstrates the ability of in silico analysis to develop a novel set of tDMRs capable of being differentiated by real time PCR/HRM. The method can rapidly determine the body fluids left at crime scenes, assisting the triers of fact in forensic casework.     

Elucidating dynamic behavior of synthetic supramolecular polymers in water by hydrogen/deuterium exchange mass spectrometry

A comprehensive understanding of the structure, self-assembly mechanism, and dynamics of one-dimensional supramolecular polymers in water is essential for their application as biomaterials. Although a plethora of techniques are available to study the first two properties, there is a paucity in possibilities to study dynamic exchange of monomers between supramolecular polymers in solution. We recently introduced hydrogen/deuterium exchange mass spectrometry (HDX-MS) to characterize the dynamic nature of synthetic supramolecular polymers with only a minimal perturbation of the chemical structure. To further expand the application of this powerful technique some essential experimental aspects have been reaffirmed and the technique has been applied to a diverse library of assemblies. HDX-MS is widely applicable if there are exchangeable hydrogen atoms protected from direct contact with the solvent and if the monomer concentration is sufficiently high to ensure the presence of supramolecular polymers during dilution. In addition, we demonstrate that the kinetic behavior as probed by HDX-MS is influenced by the internal order within the supramolecular polymers and by the self-assembly mechanism.     

The Formation of Methyl Ketones during Lipid Oxidation at Elevated Temperatures

Lipid oxidation and the resulting volatile organic compounds are the main reasons for a loss of food quality. In addition to typical compounds, such as alkanes, aldehydes and alcohols, methyl ketones like heptan-2-one, are repeatedly described as aroma-active substances in various foods. However, it is not yet clear from which precursors methyl ketones are formed and what influence amino compounds have on the formation mechanism. In this study, the formation of methyl ketones in selected food-relevant fats and oils, as well as in model systems with linoleic acid or pure secondary degradation products (alka-2,4-dienals, alken-2-als, hexanal, and 2-butyloct-2-enal), has been investigated. Elevated temperatures were chosen for simulating processing conditions such as baking, frying, or deep-frying. Up to seven methyl ketones in milk fat, vegetable oils, and selected model systems have been determined using static headspace gas chromatography-mass spectrometry (GC-MS). This study showed that methyl ketones are tertiary lipid oxidation products, as they are derived from secondary degradation products such as deca-2,4-dienal and oct-2-enal. The study further showed that the position of the double bond in the precursor compound determines the chain length of the methyl ketone and that amino compounds promote the formation of methyl ketones to a different degree. These compounds influence the profile of the products formed. As food naturally contains lipids as well as amino compounds, the proposed pathways are relevant for the formation of aroma-active methyl ketones in food.     

Common Trends and Differences in Antioxidant Activity Analysis of Phenolic Substances Using Single Electron Transfer Based Assays

Numerous assays were developed to measure the antioxidant activity, but each has limitations and the results obtained by different methods are not always comparable. Popular examples are the DPPH and ABTS assay. Our aim was to study similarities and differences of these two assay regarding the measured antioxidant potentials of 24 phenolic compounds using the same measurement and evaluation methods. This should allow conclusions to be drawn as to whether one of the assays is more suitable for measuring specific subgroups like phenolic acids, flavonols, flavanones, dihydrochalcones or flavanols. The assays showed common trends for the mean values of most of the subgroups. Some dihydrochalcones and flavanones did not react with the DPPH radical in contrast to the ABTS radical, leading to significant differences. Therefore, to determine the antioxidant potential of dihydrochalcone or flavanone-rich extracts, the ABTS assay should be preferred. We found that the results of the flavonoids in the DPPH assay were dependent on the Bors criteria, whereas the structure–activity relationship in the ABTS assay was not clear. For the phenolic acids, the results in the ABTS assay were only high for pyrogallol structures, while the DPPH assay was mainly determined by the number of OH groups.     

Ultrasound as a Promising Tool for the Green Extraction of Specialized Metabolites from Some Culinary Spices

Spices are a popular food of plant origin, rich in various phytochemicals and recognized for their numerous properties. The aim of the study was to evaluate the antioxidant and antimicrobial activity, as well as the content of specialized metabolites, of aqueous extracts of three spice species––garlic (Allium sativum L.), ginger (Zingiber officinalle L.) and turmeric (Curcuma longa L.)––prepared by green extraction methods. Ultrasound treatment increased the chromaticity parameter b value of turmeric and ginger extracts, thus indicating a higher yellow color predominantly due to curcuminoids characteristic of these species. Ultrasound-assisted extraction significantly increased the content of total soluble solids, phenolic compounds, total carotenoids and vitamin C. The temperature of the system was also an important factor, with the highest (70 °C) conditions in ultrasound-assisted extraction having a positive effect on thermolabile compounds (vitamin C, phenolics, total carotenoids). For example, turmeric extract treated with ultrasound at 70 °C had up to a 67% higher vitamin C content and a 69.4% higher total carotenoid content compared to samples treated conventionally at the same temperature, while ginger extracts had up to 40% higher total phenols. All different concentrations of spice extracts were not sufficient for complete inhibition of pathogenic bacterial strains of Salmonella, L. monocytogenes and S. aureus; however, only garlic extracts had an effect on slowing down the growth and number of L. monocytogenes colonies. Spice extracts obtained by ultrasonic treatment contained a significantly higher level of bioactive compounds and antioxidant capacity, suggesting that the extracts obtained have significant nutritional potential and thus a significant possibility for phytotherapeutic uses.     

Capillary gas chromatographic separation of C10–C12 secondary phenylalkanes on modified cyclodextrin stationary phases

The separation of isomers and enantiomers of branched C₁₀-C₁₂ phenylalkanes by gas chromatography on fused silica capillary columns coated with some modified β- and γ-cyclodextrins was studied. It was shown that the separation of positional isomers of C₁₀-C₁₂ phynylalkanes on modified cyclodextrin capillary columns is not better than that on a column coated with modified polyethylene glycol. Differences were found in the enantioselectivity of modified β- and γ-cyclodextrins for the separation of C₁₀-C₁₂ secondary phenylalkane enantiomers. While alkylderivatives of β-CDs resolve enantiomers of 3-phenylalkanes, alkyl derivatives of γ-CD resolve enantiomers of 2-phenylalkanes. Since shape selectivity factors of modified cyclodextrins have indicated no inclusion of the considered solutes in cyclodextrin cavities, enantioselective interactions most probably occur on the outer sphere of cyclodextrins.     

FTIR Spectroscopy as a Tool to Study Age-Related Changes in Cardiac and Skeletal Muscle of Female C57BL/6J Mice

Studying aging is important to further understand the molecular mechanisms underlying this physiological process and, ideally, to identify a panel of aging biomarkers. Animals, in particular mice, are often used in aging studies, since they mimic important features of human aging, age quickly, and are easy to manipulate. The present work describes the use of Fourier Transform Infrared (FTIR) spectroscopy to identify an age-related spectroscopic profile of the cardiac and skeletal muscle tissues of C57BL/6J female mice. We acquired ATR-FTIR spectra of cardiac and skeletal muscle at four different ages: 6; 12; 17 and 24 months (10 samples at each age) and analyzed the data using multivariate statistical tools (PCA and PLS) and peak intensity analyses. The results suggest deep changes in protein secondary structure in 24-month-old mice compared to both tissues in 6-month-old mice. Oligomeric structures decreased with age in both tissues, while intermolecular β-sheet structures increased with aging in cardiac muscle but not in skeletal muscle. Despite FTIR spectroscopy being unable to identify the proteins responsible for these conformational changes, this study gives insights into the potential of FTIR to monitor the aging process and identify an age-specific spectroscopic signature.