Extended specificity studies of mRNA assays used to infer human organ tissues and body fluids

Messenger RNA (mRNA) profiling is a technique increasingly applied for the forensic identification of body fluids and skin. More recently, an mRNA‐based organ typing assay was developed which allows for the inference of brain, lung, liver, skeletal muscle, heart, kidney, and skin tissue. When applying this organ typing system in forensic casework for the presence of animal, rather than human, tissue is an alternative scenario to be proposed, for instance that bullets carry cell material from a hunting event. Even though mRNA profiling systems are commonly in silico designed to be primate specific, physical testing against other animal species is generally limited. In this study, human specificity of the organ tissue inferring system was assessed against organ tissue RNAs of various animals. Results confirm human specificity of the system, especially when utilizing interpretation rules considering multiple markers per cell type. Besides, we cross‐tested our organ and body fluid mRNA assays against the target types covered by the other assay. Marker expression in the nontarget organ tissues and body fluids was observed to a limited extent, which emphasizes the importance of involving the case‐specific context of the forensic samples in deciding which mRNA profiling assay to use and when for interpreting results.     

Local Ions Distribution Inhomogeneities in Polymer Based Light Emitting Cells

 In the last years the development of light emitting electrochemical cells on a polymer base has made a great progress. They are extremely interesting due to their low cost, but still, problems concerning the stability and lifetime of these elements remain. The performance of light-emitting electrochemical cells (LEC) is strongly influenced by the inhomogeneous distribution of the three main components (light emitting polymer, ion conductive polymer, ionic molecules) in the device. The local ions distribution of lithium and triflate (short for the CF₃SO₃ ⁻ species) ions in a blend with the ionic conducting polymer poly(ethylene oxide) (PEO) and the conjugated polymer m-LPPP (methyl substituted poly(para phenylene)) throughout the polymer layer has been investigated by secondary ion mass spectroscopy (SIMS). Different combinations of top- and base-electrodes have been investigated and have been found to influence the distribution of the ions strongly. Received January 13, 1999. Revision June 16, 2000.     

Antimony as a traffic-related element in size-fractionated road dust samples collected in Buenos Aires

The growing interest of public opinion in environmental problems conducted us to investigate the levels of a toxic traffic-related element such antimony in 19 size-fractionated street dust samples. Samples were collected in the megacity of Buenos Aires during two months at 19 sites with different urban characteristics and traffic profile. Samples were sieved in four fractions (F1 < 37 µm, F2: 37-55 µm, F3: 55-75 µm and F4: 55-100 µm) before elemental analysis. A mixture of aqua regia and hydrofluoric acid was used to digest all samples. Antimony concentrations were quantified by inductively coupled plasma optical emission spectrometry (ICP OES) or flow injection hydride generation-atomic absorption spectrometry (FI-HG-AAS).Twenty four out of 73 sub-samples analyzed showed Sb levels < 0.05 µg g^− 1; in the rest of the samples mean Sb concentrations varied from 1.4 to 20.4 µg g^− 1. Maximum and minimum concentrations (in µg g^− 1) found in individual samples in the four fractions were: Fraction 1, < 0.05-20.4; Fraction 2, < 0.05-18.4; Fraction 3, < 0.05-6.3; Fraction 4, < 0.05-7.7.Antimony was found to be enriched in the smallest size fraction of road dust, with mean enrichment factors varying between 27 (F3) and 272 (F1). Concentrations of Sb were correlated with those of other traffic-related elements such as Cu and Pb and higher levels were found in areas with medium and high traffic densities.     

A chemometric method to identify enzymatic reactions leading to the transition from glycolytic oscillations to waves

In the present work we demonstrate that FTIR-spectroscopy is a powerful tool for the time resolved and noninvasive measurement of multi-substrate/product interactions in complex metabolic networks as exemplified by the oscillating glycolysis in a yeast extract. Based on a spectral library constructed from the pure glycolytic intermediates, chemometric analysis of the complex spectra allowed us the identification of many of these intermediates. Singular value decomposition and multiple level wavelet decomposition were used to separate drifting substances from oscillating ones. This enabled us to identify slow and fast variables of glycolytic oscillations. Most importantly, we can attribute a qualitative change in the positive feedback regulation of the autocatalytic reaction to the transition from homogeneous oscillations to travelling waves. During the oscillatory phase the enzyme phosphofructokinase is mainly activated by its own product ADP, whereas the transition to waves is accompanied with a shift of the positive feedback from ADP to AMP. This indicates that the overall energetic state of the yeast extract determines the transition between spatially homogeneous oscillations and travelling waves.     

Direct chemical profiling of olive (Olea europaea) fruit epicuticular waxes by direct electrospray‐ultrahigh resolution mass spectrometry

In the present paper, an electrospray ionization (ESI)‐Orbitrap method is proposed for the direct chemical profiling of epicuticular wax (EW) from Olea europaea fruit. It constitutes a rapid and efficient tool suitable for a wide‐ranging screening of a large number of samples. In a few minutes, the method provides a comprehensive characterization of total EW extracts, based on the molecular formula of their components. Accurate mass measurements are obtained by ultrahigh resolution mass spectrometry, and compositional restrictions are set on the basis of the information available from previous studies of olive EW. By alternating positive and negative ESI modes within the same analysis, complementary results are obtained and a wide range of chemical species is covered. This provides a detailed compositional overview that otherwise would only be available by applying multiple analytical techniques. Copyright © 2015 John Wiley & Sons, Ltd.     

Reversed‐phase liquid chromatography with electrospray mass detection and 1H and 13C NMR characterization of new process‐related impurities,including forced degradants of Efavirenz: Related substances correlated to the synthetic pathway

In this study, a stability‐indicating reversed‐phase liquid chromatographic electrospray mass spectrometric method was developed and validated for the determination of process‐related impurities and forced degradants of Efavirenz in bulk drugs. Efavirenz was subjected to acid, alkaline hydrolysis, H₂O₂ oxidation, photolysis, and thermal stress. Significant degradation was observed during alkaline hydrolysis, and the degradants were isolated on a mass‐based purification system and characterized by high‐resolution mass spectrometry, positive electrospray ionization tandem mass spectrometry, and ¹H and ¹³C NMR spectroscopy. Accurate mass measurement and NMR spectroscopy revealed the possible structure of process‐related impurities and degradant under stress conditions. The acceptable separation was accomplished on Waters bondapak C₁₈ column (250 mm × 4.6 mm; 5 μm), using 5 mM ammonium acetate and acetonitrile as a mobile phase in a gradient elution mode at a flow rate of 1.0 mL/min. The eluents were monitored by diode array detector at 247 nm and quantitation limits were obtained in the range of 0.1–2.5 μg/mL for Efavirenz, degradants, and process‐related impurities. The liquid chromatography method was validated with respect to accuracy, precision, linearity, robustness, and limits of detection and quantification as per International Conference on Harmonization guidelines.     

Comparing Cyclophellitol N‐Alkyl and N‐Acyl Cyclophellitol Aziridines as Activity‐Based Glycosidase Probes

The synthesis and evaluation as activity‐based probes (ABPs) of three configurationally distinct, fluorescent N‐alkyl cyclophellitol aziridine isosteres for profiling GH1 β‐glucosidase (GBA), GH27 α‐galactosidase (GLA) and GH29 α‐fucosidase (FUCA) is described. In comparison with the corresponding acyl aziridine ABPs reported previously, the alkyl aziridine ABPs are synthesized easily and are more stable in mild acidic and basic media, and are thus easier to handle. The β‐glucose‐configured alkyl aziridine ABP proves equally effective in labeling GBA as its N‐acyl counterpart, whereas the N‐acyl aziridines targeting GLA and FUCA outperform their N‐alkyl counterparts. Alkyl aziridines can therefore be an attractive alternative in retaining glycosidase ABP design, but in targeting a new retaining glycosidase both N‐alkyl and N‐acyl aziridines are best considered at the onset of a new study.     

脂质组学及其分析方法

脂质组学的研究属于生命科学的范畴,与人类的健康密切相关。目前,脂质组学已成为代谢组学最重要的分支之一,且是一个非常活跃的研究领域,尤其在研究疾病方面的重要性已经引起了科学界的广泛关注。该文简要介绍了脂质组学的研究内容,重点评述了脂质组学分析方法,包括样品处理、轮廓分析、目标分析、成像分析以及数据处理。最后提出了脂质组学分析技术和方法的展望。     

Identification of Proteins Interacting with Ubiquitin Chains

Ubiquitylation, the modification of proteins with ubiquitin (Ub), is one of the most versatile post‐translational modifications in eukaryotic cells. Since Ub also serves as its own substrate, proteins can be modified by numerous different Ub chains, in which the individual moieties are linked via one or several of the seven lysines of Ub. Homogeneous Ub chains, in which the moieties are sequentially linked via the same residue, have been most extensively studied. However, due to their restricted availability, the functions of Ub chains linked via K27, K29, or K33 are poorly understood. We have developed an approach that, for the first time, allows the generation of all seven homogeneous Ub chains in large quantities. The potential of our approach is demonstrated by the identification of previously unknown interaction partners of K27‐, K29‐, and K33‐linked Ub chains by affinity‐based proteomics.     

A Whole Proteome Inventory of Background Photocrosslinker Binding

Affinity‐based protein profiling (AfBPP) is a widely applied method for the target identification of bioactive molecules. Probes containing photocrosslinkers, such as benzophenones, diazirines, and aryl azides, irreversibly link the molecule of interest to its target protein upon irradiation with UV light. Despite their prevalent application, little is known about photocrosslinker‐specific off‐targets, affecting the reliability of results. Herein, we investigated background protein labeling by gel‐free quantitative proteomics. Characteristic off‐targets were identified for each photoreactive group and compiled in a comprehensive inventory. In a proof‐of‐principle study, H8 , a protein kinase A inhibitor, was equipped with a diazirine moiety. Application of this photoprobe revealed, by alignment with the diazirine background, unprecedented insight into its in situ proteome targets. Taken together, our findings guide the identification of biologically relevant binders in photoprobe experiments.