Outer-membrane proteomic maps and surface-exposed proteins of <Emphasis Type="Italic">Legionella pneumophila</Emphasis> using cellular fractionation and fluorescent labelling

Bacterial surface-associated proteins play crucial roles in host–pathogen interactions and pathogenesis. The identification of these proteins represents an important goal of bacterial proteomics for vaccine development, but also for environmental concerns such as microbial biosensing. Here, we developed such an approach for Legionella pneumophila, a bacterium that causes severe pneumonia. We propose a complementary strategy consisting of (1) a fluorescent labelling of surface-exposed proteins in parallel with (2) a fractionation of the outer-membrane protein extract. These two distinct protein populations were subsequently separated using two-dimensional gel electrophoresis and characterised by mass spectrometry. Within these populations, we found proteins which were expected for the compartments studied, but also a great number of proteins never experimentally described, and also a non-negligible fraction of proteins never described in these fractions. These data provided new routes of inspection for transport and host recognition for Legionella pneumophila. In addition, these results on the membranome and surfaceome show that Legionella in the stationary phase of growth possesses the major determinants to infect host cells. Figure Electron micrograph of Legionella pneumophila in stationnary phase of growth Electronic supplementary material The online version of this article (doi:) contains supplementary material, which is available to authorized users. Presented at the Annual French National Symposium on Mass Spectrometry, Electrophoresis and Proteomics, 20–23 September 2007 in Pau, France     

Plasticity and robustness of protein patterns during reversible development in the honey bee (<Emphasis Type="Italic">Apis mellifera</Emphasis>)

With age, worker honey bees normally proceed from performing activities inside the nest to foraging in the field, creating an age-related division of labor. We previously established that the whole-body protein profiles of nest workers and foragers are different, and proposed that this proteomic divergence in part is explained by a shift in metabolic requirements as worker bees initiate intense flight. The unique plasticity of honey bee worker ontogeny, however, provides further opportunities to investigate if such changes in the proteome are dynamic or, alternatively, are permanently induced. Through manipulation of the social structure of colonies, foragers can be forced to revert to nest tasks, and in the current study we investigate how protein profiles respond to such reverse development. By using a quantitative LC-MS/MS-based approach in conjunction with robust statistical validation we show that after reversal from foraging to nest activities, subsets of proteins are detected at relative concentrations that characterize nest bees, whereas other proteins remain unchanged at relative concentrations normally found in foragers. In all, we quantified the levels of 81 proteins, and for 22 of these we found significant differences between worker groups before and after reversion. We interpret these patterns as examples of plasticity and robustness at the proteome level that are linked to characteristics of behavior and aging in Apis mellifera. Figure Quantitative LC-MS/MS in conjunction with robust statistical validation reveals plasticity and robustness of protein patterns during reversible development in the honey bee (Apis mellifera) Electronic supplementary material The online version of this article (doi:) contains supplementary material, which is available to authorized users.     

Comparison of planar SDS-PAGE,CGE-on-a-chip,and MALDI-TOF mass spectrometry for analysis of the enzymatic de-<Emphasis Type="Italic">N</Emphasis>-glycosylation of antithrombin III and coagulation factor IX with PNGase F

Three different analytical techniques (planar SDS-PAGE, CGE-on-a-chip and MALDI-TOF-MS) applied for determination of the molecular weight of intact and partly and completely de-N-glycosylated human serum glycoproteins (antithrombin III and coagulation factor IX) have been compared. N-Glycans were removed from the protein backbone of both complex glycoproteins using PNGase F, which cleaves all types of asparagine-attached N-glycan provided the oligosaccharide has at least the length of a chitobiose core unit. Two of the applied techniques were based on gel electrophoretic separation in the liquid phase while the third technique was the gas-phase technique mass spectrometry. It was demonstrated that the enzymatic de-N-glycosylation generally worked well (completely or partially) with both glycoproteins (one containing only N-glycans and the second N- and O-glycans). All three methods were suitable for monitoring the de-N-glycosylation progress. While the molecular weights determined with MALDI-TOF-MS were most accurate, both gel electrophoretic methods provided molecular weights that were too high because of the attached glycan structures. Figure CGE-on-a-chip, SDS-PAGE and MALDI mass spectrometric pattern obtained from therapeutic glycoprotein     

DNA molecule manipulation by motor proteins for analysis at the single-molecule level

Massively parallel and individual DNA manipulation for analysis has been demonstrated by designing a fully self-assembled molecular system using motor proteins. DNA molecules were immobilized by trapping in a polyacrylamide gel replica, and were digested by a restriction enzyme, XhoI, for DNA analysis. One end of the λDNA was modified with biotin and the other end was modified with digoxin molecules by fragment labeling and ligation methods. The digoxin-functionalized end was immobilized on a glass surface coated with anti-digoxigenin antibody. The biotinylated end was freely suspended and experienced Brownian motion in a buffer solution. The free end was attached to a biotinylated microtubule via avidin–biotin biding and the DNA was stretched by a kinesin-based gliding assay. A stretched DNA molecule was fixed between the gel and coverslip to observe the cleavage of the DNA by the enzyme, which was supplied through the gel network structure. This simple process flow from DNA manipulation to analysis offers a new method of performing molecular surgery at the single-molecule scale. Figure DNA molecule manipulation by motor proteins for analysis at the single-molecule level     

Electrospray mass spectrometry analysis of dendritic branches bearing peripheral fullerene subunits

The electrospray mass spectrometric characterization of neutral dendrons with a carboxylic acid function or a t-butyl ester moiety at the central point and up to eight peripheral C₆₀ subunits has been performed and is described in detail. Molecules bearing a carboxylic acid group at the center turned out to be preferentially ionized by deprotonation, whereas those with a t-butyl ester head group were ionized by reduction of the C₆₀ units in the infusion capillary of the electrospray source. Electronic supplementary material Supplementary material is available for this article at and is accessible for authorized users.     

Biosensor for total cholesterol estimation using N-(2-aminoethyl)-3-aminopropyltrimethoxysilane self-assembled monolayer

Cholesterol oxidase (ChOx), cholesterol esterase (ChEt), and horseradish peroxidase (HRP) have been co-immobilized covalently on a self-assembled monolayer (SAM) of N-(2-aminoethyl)-3-aminopropyltrimethoxysilane (AEAPTS) deposited on an indium–tin–oxide (ITO) glass surface. These enzyme-modified (ChOx-ChEt-HRP/AEAPTS/ITO) biosensing electrodes have been used to estimate cholesteryl oleate from 10 to 500 mg dL⁻¹. The sensitivity, K _m value, and shelf-life of these ChEt-ChOx-HRP/AEAPTS/ITO biosensing electrodes have been found to be 124 nA mg⁻¹ dL, 95.098 mg dL⁻¹ (1.46 mmol L⁻¹), and ten weeks, respectively. The ChEt-ChOx-HRP/AEAPTS/ITO bio-electrodes have been used to estimate total cholesterol in serum samples. Figure Covalent immobilization of enzymes onto AEAPTS/ITO surface using EDC/NHS chemistry Electronic supplementary material The online version of this article (doi:) contains supplementary material, which is available to authorized users.     

Surface modification using a novel type I hydrophobin HGFI

Surface wettability conversion with hydrophobins is important for its applications in biodevices. In this work, the application of a type I hydrophobin HGFI in surface wettability conversion on mica, glass, and poly(dimethylsiloxane) (PDMS) was investigated. X-ray photoelectron spectroscopy (XPS) and water-contact-angle (WCA) measurements indicated that HGFI modification could efficiently change the surface wettability. Data also showed that self-assembled HGFI had better stability than type II hydrophobin HFBI. Protein patterning and the following immunoassay illustrated that surface modification with HGFI should be a feasible strategy for biosensor device fabrication. Figure A hydrophobin HGFI has been applied into surface wettability conversion for protein immobilization Electronic supplementary material  The online version of this article (doi:) contains supplementary material, which is available to authorized users.     

Prediction of retention times of polycyclic aromatic hydrocarbons and <Emphasis Type="Italic">n</Emphasis>-alkanes in temperature-programmed gas chromatography

We have developed an iterative procedure for predicting the retention times of polycyclic aromatic hydrocarbons (PAHs) and n-alkanes during separations by temperature-programmed gas chromatography. The procedure is based on estimates of two thermodynamic properties for each analyte (the differences in enthalpy and entropy associated with movements between the stationary and mobile phases) derived from data acquired experimentally in separations under isothermal conditions at temperatures spanning the range covered by the temperature programs in ten-degree increments. The columns used for this purpose were capillary columns containing polydimethylsiloxane-based stationary phases with three degrees of phenyl substitution (0%, 5%, and 50%). Predicted values were mostly within 1% of experimentally determined values, implying that the method is stable and precise. Figure Predicted values were mostly within 1 % of experimentally determined values, thus implying that the method is stable and precise     

Diagonal chromatographic selection of cysteinyl peptides modified with benzoquinones

The derivatization of cysteine-containing peptides with benzoquinone compounds is rapid, quantitative and specific in acidic media. The conversion of cysteines into hydrophobic benzoquinone-adducted residues in peptides is used here to alter the chromatographic properties of cysteinyl peptides during liquid chromatography separation. The benzoquinone derivatization is shown to allow the accurate selection of cysteine-containing peptides of bovine serum albumin tryptic digest by diagonal reversed-phase chromatography, which consists of one primary and a series of secondary identical liquid chromatographic separations, before and after a cysteinyl-targeted modification of the peptides by benzoquinone compounds. Figure Diagonal chromatographic selection of cysteinyl peptides modified with benzoquinones Electronic supplementary material The online version of this article (doi:) contains supplementary material, which is available to authorized users.     

Disposable screen-printed chemiluminescent biochips for the simultaneous determination of four point-of-care relevant proteins

A screen-printed (SP) microarray is presented as a platform for the achievement of multiparametric biochips. The SP platform is composed of eight (0.28-mm²) working electrodes modified with electroaddressed protein A-aryl diazonium adducts. The electrode surfaces are then used as an affinity immobilisation support for the orientated binding of capture monoclonal antibodies, having specificity against four different point-of-care related proteins (myoglobin, cardiac troponin I, C-reactive protein and brain natriuretic peptide). The immobilised capture antibodies are involved in sandwich assays of the four proteins together with biotinylated detection antibodies and peroxidase-labelled streptavidin in order to permit a chemiluminescent imaging of the SP platform and a sensitive detection of the assayed proteins. The performances of the system in pure buffered solutions, using a 25-min assay duration, were characterised by dynamic ranges of 0.5–50, 0.1–120, 0.2–20 and 0.67–67 μg/L for C-reactive protein, myoglobin, cardiac troponin I and brain natriuretic peptide, respectively. The four different assays were also validated in spiked 40-times-diluted human sera, using LowCross buffer, and were shown to work simultaneously in this complex medium. Figure Principle of the screen-printed POC microarray and a schematic representation of the assay architecture. Electronic supplementary material  The online version of this article (doi:) contains supplementary material, which is available to authorized users.     

Collision-induced reporter fragmentations for identification of covalently modified peptides

Collision-induced reporter fragmentations of the currently most important covalent peptide modifications as detected by tandem mass spectrometry are summarized. These fragmentations comprise the formation of reporter ions, which are preferentially immonium ions, immonium ion-derived fragments or side chain fragments. In addition, the reporter neutral loss reactions for covalently modified amino acid residues are summarized. For each individual covalent modification which can be recognized by a reporter fragmentation, the accurate mass shift and the gross formula shift of the modified amino acid residue are given. The same set of data is provided for the reporter fragmentations. Finally, an extensive accurate mass and gross formula list is presented as supplementary material, describing mostly regular and modified y₁ and dipeptide a and b ions, which are helpful for identification of the peptide ends of covalently modified peptides. Figure When modified peptides are fragmented by collision-induced dissociation in a tandem mass spectrometer, the modification is either lost as part of a charged fragment, so that a reporter ion for the modification is generated or it is lost as part of a neutral fragment, so that a modification-specific reporter neutral loss is observed in the fragment ion spectrum. Electronic supplementary material The online version of this article (doi:) contains supplementary material, which is available to authorized users. Chien-Wen Hung and Andreas Schlosser contributed equally to this work.     

Metal-binding molecules in the organs of <Emphasis Type="Italic">Mus musculus</Emphasis> by size-exclusion chromatography coupled with UV spectroscopy and ICP-MS

Mus musculus mice have been investigated for the total elements content in different organs (lung, liver, spleen, kidney, brain, testicle, heart and muscle) and molecular mass distribution patterns of Mn, Ni, Cu, Zn, As, Pb, Cr, Fe, Co, Se and Cd. Some differences have been found in the organs studied, with especially relevant being the Cu-containing fraction present only in the brain and the As-containing one in the liver. Other differences related to the abundance of the metallospecies have also been found. The present paper is the first step in the study of the “metallome” of this inbred laboratory species from which the genome is completely known. This organism could be used as a model in future studies focused on wild mice and the analytical approach developed could be applied to wild mice to find markers of environmental pollution. Figure The present paper is the first step in the study of the “metallome” of the inbred laboratory specie Mus musculus from which the genome is completely known. Some interesting differences have been found in the extracts from the organs that are discussed along the text. Electronic suplementary material The online version of this article (doi:) contains supplementary material, which is available to authorized users. The present paper is the first step in the study of the “metallome” of the inbred laboratory species Mus musculus from which the genome is completely known. Some interesting differences have been found in the extracts from the organs that are discussed in the text.     

Rapid determination of p<Emphasis Type="Italic">K</Emphasis><Subscript>a</Subscript> values of 20 amino acids by CZE with UV and capacitively coupled contactless conductivity detections

A rapid and universal capillary zone electrophoresis (CZE) method was developed to determine the dissociation constants (pK _a) of the 20 standard proteogenic amino acids. Since some amino acids are poorly detected by UV, capacitively coupled contactless conductivity detection (C⁴D) was used as an additional detection mode. The C⁴D coupling proved to be very successful on a conventional CE-UV instrument, neither inducing supplementary analyses nor instrument modification. In order to reduce the analysis time for pK _a determination, two strategies were applied: (i) a short-end injection to reduce the effective length, and (ii) a dynamic coating procedure to generate a large electroosmotic flow (EOF), even at pH values as low as 1.5. As a result, the analysis time per amino acid was less than 2 h, using 22 optimized buffers covering a pH range from 1.5 to 12.0 at a constant ionic strength of 50 mM. pK _a values were calculated using an appropriate mathematical model describing the relationship between effective mobility and pH. The obtained pK _a values were in accordance with the literature. Figure a UV (1) and C⁴D (2) detectors placed on-line on the CE capillary. b Curve of effective mobility as a function of pH for histidine     

Study of thiazole orange in aptamer-based dye-displacement assays

We screened a series of RNA and DNA aptamers for their ability to serve in the dye displacement assays in which analytes compete with TO dye. We conclude that, while the performance of the TO dye displacement approach is not always predictable, it is still a simple and sensitive assay to detect binding between RNA aptamers and small molecules. In particular, we describe efficient assays for tobramycin and theophylline, with up to 90% displacement of TO observed, and we describe the first aptameric assay for cAMP. Figure An RNA or DNA aptamer against a molecule (circle) binds TO dye, resulting in a fluorescent complex. Presence of free molecule in solution results in the displacement of TO from the complex and a reduction in fluorescence Electronic supplementary material The online version of this article (doi:) contains supplementary material, which is available to authorized users.     

Preparation of Fe<Subscript>3</Subscript>O<Subscript>4</Subscript>-C18 nano-magnetic composite materials and their cleanup properties for organophosphorous pesticides

Magnetic Fe₃O₄-C18 composite nanoparticles of approximately 5–10 nm in size were synthesized and characterized by IR spectroscopy, atomic absorption spectroscopy, X-ray diffraction, and transmission electron microscopy. The magnetic Fe₃O₄-C18 composite nanoparticles were applied for cleanup and enrichment of organophosphorous pesticides. Comparative studies were carried out between magnetic Fe₃O₄-C18 composite nanoparticles and common C18 materials. Residues of organophosphorous pesticides were determined by gas chromatography in combination with a nitrogen/phosphorus detector. The cleanup and enrichment properties of magnetic Fe₃O₄-C18 composite nanoparticles are comparable with those of common C18 materials for enrichment of organophosphorous pesticides, but the cleanup and enrichment are faster and easier to perform. Figure Presumed mechanism for the adhesion of the OPs to the Fe₃O₄-C18 magnetic nanoparticles     

Different iron-chelating properties of pyochelin diastereoisomers revealed by LC/MS

Pyochelin is a siderophore and virulence factor common to Burkholderia cepacia and several Pseudomonas strains. It is isolated from bacterial media as a mixture of two epimers, which readily equilibrate in most solvents. Experiments based on high-performance liquid chromatography/electrospray ionization mass spectrometry are reported here, allowing the investigation of the different Fe(III)-chelating properties of pyochelin diastereomers in solution without the need for labourious isolation. It is demonstrated in this study that only one of the two pyochelin diastereomers is able to chelate Fe(III); no Fe(III) complexes of the other diastereomer could be detected. The Fe(III)–pyochelin complex exhibited a 1:1 metal-to-siderophore ratio and no evidence for other stoichiometries was found.      

Determination of total <Emphasis Type="Italic">trans</Emphasis> fats and oils by infrared spectroscopy for regulatory compliance

The mandatory requirement in many countries to declare the amount of trans fat present in food products and dietary supplements has led to a need for sensitive and accurate methodologies for the rapid quantitation of total trans fats and oils. Capillary gas chromatography (GC) and infrared spectroscopy (IR) are the two methods most commonly used to identify and quantify trans fatty acids for food labeling purposes (see the article by Delmonte and Rader in this ABC issue for a detailed presentation of GC methodology). The present article provides a comprehensive review of the IR technique and the current attenuated total reflection (ATR) Fourier-transform (FT) IR methodologies for the rapid determination of total trans fats and oils. This review also addresses potential sources of interferences and inaccuracies in FTIR determinations, particularly those done at low trans levels. Recent observations have shown that the presence of saturated fats caused interferences in the FTIR spectra observed for trans triacylglycerols. The recognition and resolution of previously unresolved quantitative issues improved the accuracy and sensitivity of the FTIR methodology. Once validated, it is anticipated that the new negative second-derivative ATR-FTIR procedure will make IR spectroscopy more suitable than ever, and a rapid alternative and/or complementary method to GC, for the rapid determination of total trans fats for regulatory compliance. Figure Infrared light bouncing inside an internal reflection crystal     

Monitoring surface-assisted biomolecular assembly by means of evanescent-field-coupled waveguide-mode nanobiosensors

Biological self-assembly is a natural process that involves various biomolecules, and finding the missing partner in these interactions is crucial for a specific biological function. Previously, we showed that evanescent-field-coupled waveguide-mode sensor in conjunction with a SiO₂ waveguide, the surfaces which contain cylindrical nanometric holes produced by atomic bombardment, allowed us to detect efficiently the biomolecular interactions. In the present studies, we showed that the assembly of biomolecules can be monitored using the evanescent-field-coupled waveguide-mode biosensor and thus provide a methodology in monitoring assembly process in macromolecular machines while they are assembling. Evanescent-field-coupled waveguide-mode sensor Electronic supplementary material  The online version of this article (doi:) contains supplementary material, which is available to authorized users.     

In situ electrochemical contact angle study of hemoglobin and hemoglobin–Fe3O4 nanocomposites

The electrochemical redox-induced contact angle changes of hemoglobin droplets in the absence and presence of tetraheptylammonium-capped Fe₃O₄ nanoparticles have been explored by using in situ electrochemical contact angle measurements. The results indicate that the electrochemical redox process may lead to some structure changes of hemoglobin (Hb), which could further induce the hydrophobic-to-hydrophilic changes of the relative droplets. Our observations demonstrate that hemoglobin could self-assemble on the surface of the functionalized Fe₃O₄ nanoparticles as Hb–Fe₃O₄ nanocomposites, which may contribute to much more significant change of the electrochemical redox-induced contact angle values than that with free nano-Fe₃O₄. These results suggest that in situ electrochemical contact angle measurements could be readily applied as a new and convenient method to detect some specific biological process. Figure Schematic drawing of the possible process and contact angle changes for the self-assembly of hemoglobin on the tetraheptylammonium-capped Fe₃O₄ nanoparticles Electronic supplementary material Supplementary material is available in the online version of this article at and is accessible for authorized users.     

Headspace mass spectrometry methodology: application to oil spill identification in soils

In the present work we report the results obtained with a methodology based on direct coupling of a headspace generator to a mass spectrometer for the identification of different types of petroleum crudes in polluted soils. With no prior treatment, the samples are subjected to the headspace generation process and the volatiles generated are introduced directly into the mass spectrometer, thereby obtaining a fingerprint of volatiles in the sample analysed. The mass spectrum corresponding to the mass/charge ratios (m/z) contains the information related to the composition of the headspace and is used as the analytical signal for the characterization of the samples. The signals obtained for the different samples were treated by chemometric techniques to obtain the desired information. The main advantage of the proposed methodology is that no prior chromatographic separation and no sample manipulation are required. The method is rapid, simple and, in view of the results, highly promising for the implementation of a new approach for oil spill identification in soils. Figure PCA score plots illustrate clear discrimination of types of crude oil in polluted soil samples (e.g. results are shown for vertisol)