Automated Morphological and Morphometric Analysis of Mass Spectrometry Imaging Data: Application to Biomarker Discovery

Mass spectrometry imaging datasets are mostly analyzed in terms of average intensity in regions of interest. However, biological tissues have different morphologies with several sizes, shapes, and structures. The important biological information, contained in this highly heterogeneous cellular organization, could be hidden by analyzing the average intensities. Finding an analytical process of morphology would help to find such information, describe tissue model, and support identification of biomarkers. This study describes an informatics approach for the extraction and identification of mass spectrometry image features and its application to sample analysis and modeling. For the proof of concept, two different tissue types (healthy kidney and CT-26 xenograft tumor tissues) were imaged and analyzed. A mouse kidney model and tumor model were generated using morphometric – number of objects and total surface – information. The morphometric information was used to identify m/z that have a heterogeneous distribution. It seems to be a worthwhile pursuit as clonal heterogeneity in a tumor is of clinical relevance. This study provides a new approach to find biomarker or support tissue classification with more information.

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Quantification of plasma phospholipids by ultra performance liquid chromatography tandem mass spectrometry

We describe a fast and robust ultra performance liquid chromatography tandem mass spectrometry method for the quantification of phospholipid (PL) species in EDTA-plasma samples. We quantified total phosphatidylcholine (PC), phosphatidylethanolamine (PE), lysophosphatidylcholine (LPC), and sphingomyelin (SM) and several species within these classes using one or two external calibrators and one internal standard for each class. Inter-assay coefficients of variation were <10% for the most abundant species and <20% for all quantified PC, LPC, and SM species and the three most abundant PE species. Coefficients of linear regression were R ² > 0.98. Mean recoveries were between 83% and 123%. The limits of detection were 0.37 μmol/L for PC, 4.02 μmol/L for LPC, 3.75 μmol/L for PE, and 0.86 μmol/L for SM. Quantification was linear over the physiological ranges for PE, LPC, and SM and up to 500 μmol/L for PC. The concentrations of PLs in the plasma of healthy donors yielded results that were comparable with those of previous works.     

The Effects of Prolonged Storage on ARPE-19 Cells Stored at Three Different Storage Temperatures

This study aimed to investigate how prolonged storage of adult retinal pigment epithelial (ARPE-19) cell sheets affects cell metabolism, morphology, viability, and phenotype. ARPE-19 cell sheets were stored at three temperatures (4 °C, 16 °C, and 37 °C) for three weeks. Metabolic status and morphology of the cells were monitored by sampling medium and examining cells by phase-contrast microscopy, respectively, throughout the storage period. Cell viability was analyzed by flow cytometry, and phenotype was determined by epifluorescence microscopy after the storage. Lactate production and glucose consumption increased heavily, while pH dropped considerably, through storage at 37 °C compared to 4 °C and 16 °C. During storage, morphology started to deteriorate first at 4 °C, then at 37 °C, and was maintained the longest at 16 °C. Viability of the cells after three weeks of storage was best preserved at 16 °C, while cells stored at 4 °C and 37 °C had reduced viability. Dedifferentiation indicated by reduced expression of retinal pigment epithelium-specific protein 65 (RPE65), zonula occludens protein 1 (ZO-1), and occludin after three weeks of storage was noticed in all experimental groups compared to control. We conclude that storage temperature affects the metabolic status of ARPE-19 cells and that 16 °C reduces metabolic activity while protecting viability and morphology.     

Structurally original oxathioethers macrocycles containing an exocyclic double-bond: synthesis,characterization, reactivity,and coordination

New oxathioethers macrocycles have been synthesized and characterized. Each macrocycle consists in structurally defined ether and thioether moieties and an exocyclic double-bond (2a–c) or a hydroxymethyl group (3a–c). Macrocycles (2a–c) have been synthesized by reaction of dianions of thioethers diols (1a–c) with 3-chloro-2-chloromethylprop-1-ene. Their hydroboration/oxidation led to corresponding primary alcohols (3a–c). Structures of compounds (2b) and (3a) have been determined by X-ray diffraction. The reactivity of the hydroxyl group allowed the preparation of oxathioethers macrocycles bearing a polyether chain or a benzyl group (4a,b) and the synthesis of new bicyclic sandwich-type compounds (5a,b). The ability of these functionalized macrocycles to coordinate to palladium has been investigated.     

Radioprotective activity of metalladithioacetals derived from N‐substituted naphthylethylimidazoline

A number of organosilicon and organogermanium derivatives of N‐substituted 2‐[1‐(1‐naphthyl)ethyl]‐2‐imidazoline have been reported and the toxicity of these compounds has been determined in mice. In this paper we report the evaluation of the radioprotective activity of new sila‐ and germa‐dithioacetals derived from N‐substituted 2‐[1‐(1‐naphthyl)ethyl]‐2‐imidazoline. Copyright © 2003 John Wiley & Sons, Ltd.     

Identification of Non-Macrocyclic Small Molecule Inhibitors against the NS3/4A Serine Protease of Hepatitis C Virus through in Silico Screening

Drug discovery and design for inhibition of the Hepatitis C Virus (HCV) NS3/4A serine protease is a major challenge. The broad, shallow, and generally featureless nature of the active site makes it a difficult target for "hit" selection especially using standard docking programs. There are several macrocyclic NS3/4A protease inhibitors that have been approved or are in clinical trials to treat chronic HCV (alone or as combination therapy), but most of the current therapies for HCV infection have untoward side effects, indicating a continuing medical need for the discovery of novel therapeutics with improved efficacy. In this study, we designed and implemented a two-tiered and progressive docking regime that successfully identified five non-macrocyclic small molecules that show inhibitory activity in the low micromolar range. Of these, four compounds show varying inhibition against HCV subgenotypes 1b, 1a, 2a, and 4d. The top inhibitor (3) has an IC(50) value of 15 μM against both subgenotypes 1b and 2a of the NS3/4A protease enzyme. Another inhibitor, 1, inhibits all four subgenotypes with moderate activity, showing highest activity for genotype 2a (24 μM). The five inhibitors presented in this study could be valuable candidates for future hit to lead optimization. Additionally, enzyme-inhibitor interaction models presented herein provide key information regarding structural differences between the active sites of the NS3/4A protease of the HCV subgenotype 1a and 1b that might explain the variable inhibitory activity between subgenotypes of the small molecule inhibitors identified here.     

Novel route to the synthesis of 4-quinolyl isothiocyanates

4-Quinolyl isothiocyanates were synthesized in a regiospecific fashion from the corresponding 4-chloroquinolines and silver thiocyanate in refluxing toluene. The products were isolated in quantitative yield and high purity (>95%) by simple filtration and concentration. Reactivity and mechanism of the reaction are discussed. The new approach would provide a new mean which had been lacking for the synthesis of functionalized 4-quinolinyl isothiocyanate.     

The use of amidoximated cellulose for the removalof metal ions and dyes from waste waters

The adsorption of metal ions such as Cu(II), Cr(III), Cd(II) and Ni(II)and dyes such as Acid Blue 25, Calmagite and Eriochrome Blue Black Bis performed onto amidoximated cellulose (Am-Cell). Different ways are possible for theadsorption of these pollutants onto Am-Cell : adsorption of each pollutantaloneon the support, or cumulative adsorption of both metal ions and dyes on the samesupport. In the last case, the pollutants may be adsorbed simultaneously from aunique solution, or successively from two different solutions, whatever theorder. Am-Cell loaded or not with metal ions shows a high capacity for dyeadsorption. Ternary complexes involving metal/dye/amidoxime are formed. Theobserved stoichiometries are 1/1/1 with Cu(II), Cr(III) and Cd(II) ions and1/1/2with Ni(II) ion. A quasi-total and specific desorption of either metal ions (bytreatment with ethylenediaminetetracetic salt) or of dyes (by heating inaqueoussolution) is possible from these ternary complexes. Concerning the dyes, manysuccessive adsorption/desorption cycles are possible without a noticeablechange in the adsorption capacity.     

Synthetic approaches to indolo[6,7-a]pyrrolo[3,4-c]carbazoles: potent cyclin D1/CDK4 inhibitors

Synthesis of indolo[6,7-a]pyrrolo[3,4-c]carbazoles 1, a new class of cyclin D1/CDK4 inhibitors, by oxidation of the corresponding aryl indolylmaleimides 2, will be described. Two approaches to the synthesis of 2 were identified that required new methods for the synthesis of 7-substituted indole acetamides 3 and N-methyl (indol-7-yl)oxoacetates 6. The chemistry developed enabled introduction of functionality (-OR, NR(2)) at C(12) and N(13) facilitating structure-activity relationship (SAR) evaluation of this indolocarbazole platform.     

Effect of n-alkyl chain length on the complexation of phenanthrene and 9-alkyl-phenanthrene with beta-cyclodextrin

The characteristics of host-guest complexation between beta-cyclodextrin (beta-CD) and phenanthrene derivatives (phenanthrene, n-propyl, n-butyl and n-hexyl-phenanthrene) were investigated by fluorescence spectrometry. Linear and non-linear regression methods were used to estimate the formation constants (K1). A 1:1 stoichiometric ratio and an effect of n-alkyl chain length on the formation constant were observed for the binary inclusion complex between guest and beta-CD. The formation constant dramatically increases with the length of n-alkyl, it starts from the value of 140 l mol(-1) for the phenanthrene to reach the value of 580 l mol(-1) for hexyl-phenanthrene. The effect of the temperature on the fluorescence intensity of each complex (guest-host) was also studied; and then the thermodynamic parameters were calculated. The main inclusion site seems to be aromatic moiety for short chain molecules, and it moves toward the alkyl chain part, as the chain becomes longer.