Explorative data analysis of two-dimensional electrophoresis gels

Methods for classification of two-dimensional (2-DE) electrophoresis gels based on multivariate data analysis are demonstrated. Two-dimensional gels of ten wheat varieties are analyzed and it is demonstrated how to classify the wheat varieties in two qualities and a method for initial screening of gels is presented. First, an approach is demonstrated in which no prior knowledge of the separated proteins is used. Alignment of the gels followed by a simple transformation of data makes it possible to analyze the gels in an automated explorative manner by principal component analysis, to determine if the gels should be further analyzed. A more detailed approach is done by analyzing spot volume lists by principal components analysis and partial least square regression. The use of spot volume data offers a mean to investigate the spot pattern and link the classified protein patterns to distinct spots on the gels for further investigation. The explorative approach in analysis of 2-D gels makes it possible, in a fast and convenient way, to screen many gels in order to determine the protein patterns that form clusters and could be selected for further examination.     

Femtosecond midinfrared study of aggregation behavior in aqueous solutions of amphiphilic molecules

We study the spectral and orientational dynamics of HDO molecules in aqueous solutions of different concentrations of tertiary butyl alcohol (TBA) and trimethylamine-N-oxide (TMAO). The spectral dynamics is investigated with femtosecond two-dimensional infrared spectroscopy of the O-H stretch vibration of HDO:D(2)O, and the orientational dynamics is studied with femtosecond polarization-resolved pump-probe spectroscopy of the O-D stretch vibration of HDO:H(2)O. Both the spectral and orientational dynamics are observed to show bimodal behavior: part of the water molecules shows spectral and orientational dynamics similar to bulk liquid water and part of the water molecules displays a much slower dynamics. For low solute concentrations, the latter fraction of slow water increases linearly as a function of solute molality, indicating that the slow water is contained in the solvation shells of TBA and TMAO. At higher concentrations, the fraction of slow water saturates. The saturation behavior is much stronger for TBA solutions than for TMAO solutions, indicating the aggregation of the TBA molecules.     

A tetrathiafulvalene–perylene diimide conjugate prepared via click chemistry

A new tetrathiafulvalene (TTF)–perylene diimide (PDI) conjugate is prepared from an azide-functionalized TTF and an acetylenic PDI employing a Cu(I)-catalyzed Huisgen-Meldal-Sharpless reaction (‘click chemistry’). Thus, the TTF donor and PDI acceptor units are linked together by a 1,2,3-triazole unit. The molecules are found to assemble on a mica surface, forming fibrilar structures.     

Laboratory intercomparison study on the analysis of short-chain chlorinated paraffins in an extract of industrial soil

Short-chain chlorinated paraffins (SCCPs) comprise a class of organic pollutants used in many industrial applications and released into the environment. The analytical determination of SCCPs is very challenging. Although there is at present no fully validated measurement procedure that might be applied in routine monitoring, the European Union Water Framework Directive (WFD) has required regular monitoring of this class of compounds at river-basin scale since 2007.To assess the status quo of the analysis of SCCPs in relation to the requirements of the WFD, we organized an interlaboratory comparison on the quantification of SCCPs in an extract of an industrial soil. Six laboratories participated in the exercise using three different techniques [i.e. gas chromatography (GC) coupled to mass spectrometry (MS) in electron-capture negative ionization mode, GC with atomic emission detection, and carbon-skeleton GC-MS]. The results reported were in the range 8.5–3200 mg/L. This confirms that reliable quantification of SCCPs is still very difficult to achieve and that the comparability of SCCP data reported to the European Commission is at least questionable.     

Absorption Spectra of 4‐Nitrophenolate Ions Measured in Vacuo and in Solution

From blue to red: While four π‐conjugated nitrophenolates absorb within a relatively narrow region in solution, they cover the entire visible spectrum when isolated in vacuo (see picture). The work combines gas‐ and solution‐phase spectroscopy and provides the first benchmark of theoretical excitation energies for nitrophenolates.

     

Euphohelioscopin A Is a PKC Activator Capable of Inducing Macrophage Differentiation

To identify small molecules that selectively control hematopoietic stem cell differentiation, we performed an unbiased screen using primary human CD34(+) cells. We identified a plant-derived natural product, euphohelioscopin A, capable of selectively differentiating CD34(+) cells down the granulocyte/monocytic lineage. Euphohelioscopin A also inhibits proliferation and induces differentiation of the myeloid leukemia cell lines THP-1 and HL-60. Mechanistic studies revealed that euphohelioscopin A is an activator of protein kinase C (PKC), and that the promonocytic effects of this natural product are mediated by PKC activation. In addition to shedding insights into normal hematopoiesis, this work may ultimately facilitate the application of stem cell therapies to a host of myeloid dysfunctions.     

Analysis of poly-beta-hydroxybutyrate in environmental samples by GC-MS/MS

Application of gas chromatography-mass spectrometry (GC-MS) can significantly improve trace analyses of compounds in complex matrices from natural environments compared to gas chromatography only. A GC-MS/MS technique for determination of poly-beta-hydroxybutyrate (PHB), a bacterial storage compound, has been developed and used for analysis of two soils stored for up to 319 d, fresh samples of sewage sludge, as well as a pure culture of Bacillus megaterium. Specific derivatization of beta-hydroxybutyrate (3-OH C4:0) PHB monomer units by N-tert-butyl-dimethylsilyl-N-methyltrifluoracetamide (MTBSTFA) improved chromatographic and mass spectrometric properties of the analyte. The diagnostic fragmentation scheme of the derivates tert-butyldimethylsilyl ester and ether of beta-hydroxybutyric acid (MTBSTFA-HB) essential for the PHB identification was shown. The ion trap MS was used, therefore the scan gave the best sensitivity and with MS/MS the noise decreased, so the S/N was better and also with second fragmentation the amount of ions increased compared to SIM. The detection limit for MTBSTFA-HB by GC-MS/MS was about 10(-13) g microL(-1) of injected volume, while by GC (FID) and GC-MS (scan) it was around 10(-10) g microL(-1) of injected volume. Sensitivity of GC-MS/MS measurements of PHB in arable soil and activated sludge samples was down to 10 pg of PHB g(-1) dry matter. Comparison of MTBSTFA-HB detection in natural soil sample by GC (FID), GC-MS (scan) and by GC-MS/MS demonstrated potentials and limitations of the individual measurement techniques.     

Synthesis of C-8 Deuterated Glycosides of 3-Deoxy-D-manno-oct-2-ulosonic Acid (Kdo) Related to Chlamydial Lipopolysaccharides

Summary.  Methyl glycosides of Kdo and a (2→8)-linked Kdo disaccharide were prepared which contain a deuterium label at C-8 of the reducing unit. The label was introduced in fair diastereoselectivity upon reduction of an aldehyde group using a chiral borane complex derived from N-benzyloxycarbonyl-(S)-proline which produced the 8-(S)-deuterated derivative as the major isomer. Further coupling with a Kdo bromide gave the α-(2→8)-linked disaccharide in good yield. The deprotected disaccharide serves as a model for NMR spectroscopic studies on the side chain conformation of a carbohydrate epitope from the bacterial pathogen Chlamydia. Received September 17, 2001. Accepted October 17, 2001