Serodiagnosis of Echinococcus spp. infection: explorative selection of diagnostic antigens by peptide microarray

BACKGROUND: Production of native antigens for serodiagnosis of helminthic infections is laborious and hampered by batch-to-batch variation. For serodiagnosis of echinococcosis, especially cystic disease, most screening tests rely on crude or purified Echinococcus granulosus hydatid cyst fluid. To resolve limitations associated with native antigens in serological tests, the use of standardized and highly pure antigens produced by chemical synthesis offers considerable advantages, provided appropriate diagnostic sensitivity and specificity is achieved. METHODOLOGY/PRINCIPAL FINDINGS: Making use of the growing collection of genomic and proteomic data, we applied a set of bioinformatic selection criteria to a collection of protein sequences including conceptually translated nucleotide sequence data of two related tapeworms, Echinococcus multilocularis and Echinococcus granulosus. Our approach targeted alpha-helical coiled-coils and intrinsically unstructured regions of parasite proteins potentially exposed to the host immune system. From 6 proteins of E. multilocularis and 5 proteins of E. granulosus, 45 peptides between 24 and 30 amino acids in length were designed. These peptides were chemically synthesized, spotted on microarrays and screened for reactivity with sera from infected humans. Peptides reacting above the cut-off were validated in enzyme-linked immunosorbent assays (ELISA). Peptides identified failed to differentiate between E. multilocularis and E. granulosus infection. The peptide performing best reached 57% sensitivity and 94% specificity. This candidate derived from Echinococcus multilocularis antigen B8/1 and showed strong reactivity to sera from patients infected either with E. multilocularis or E. granulosus. CONCLUSIONS/SIGNIFICANCE: This study provides proof of principle for the discovery of diagnostically relevant peptides by bioinformatic selection complemented with screening on a high-throughput microarray platform. Our data showed that a single peptide cannot provide sufficient diagnostic sensitivity whereas pooling several peptide antigens improved sensitivity; thus combinations of several peptides may lead the way to new diagnostic tests that replace, or at least complement conventional immunodiagnosis of echinococcosis. Our strategy could prove useful for diagnostic developments in other pathogens.

Metabolomics reveals a novel vitamin E metabolite and attenuated vitamin E metabolism upon PXR activation

Pregnane X receptor (PXR) is an important nuclear receptor xenosensor that regulates the expression of metabolic enzymes and transporters involved in the metabolism of xenobiotics and endobiotics. In this study, ultra-performance liquid chromatography (UPLC) coupled with electrospray time-of-flight mass spectrometry (TOFMS), revealed altered urinary metabolomes in both Pxr-null and wild-type mice treated with the mouse PXR activator pregnenolone 16alpha-carbonitrile (PCN). Multivariate data analysis revealed that PCN significantly attenuated the urinary vitamin E metabolite alpha-carboxyethyl hydroxychroman (CEHC) glucuronide together with a novel metabolite in wild-type but not Pxr-null mice. Deconjugation experiments with beta-glucuronidase and beta-glucosidase suggested that the novel urinary metabolite was gamma-CEHC beta-D-glucoside (Glc). The identity of gamma-CEHC Glc was confirmed by chemical synthesis and by comparing tandem mass fragmentation of the urinary metabolite with the authentic standard. The lower urinary CEHC was likely due to PXR-mediated repression of hepatic sterol carrier protein 2 involved in peroxisomal beta-oxidation of branched-chain fatty acids (BCFA). Using a combination of metabolomic analysis and a genetically modified mouse model, this study revealed that activation of PXR results in attenuated levels of the two vitamin E conjugates, and identification of a novel vitamin E metabolite, gamma-CEHC Glc. Activation of PXR results in attenuated levels of the two vitamin E conjugates that may be useful as biomarkers of PXR activation.

Independent measurement of biogenic silica in sediments by FTIR spectroscopy and PLS regression

We present an independent calibration model for the determination of biogenic silica (BSi) in sediments, developed from analysis of synthetic sediment mixtures and application of Fourier transform infrared spectroscopy (FTIRS) and partial least squares regression (PLSR) modeling. In contrast to current FTIRS applications for quantifying BSi, this new calibration is independent from conventional wet-chemical techniques and their associated measurement uncertainties. This approach also removes the need for developing internal calibrations between the two methods for individual sediments records. For the independent calibration, we produced six series of different synthetic sediment mixtures using two purified diatom extracts, with one extract mixed with quartz sand, calcite, 60/40 quartz/calcite and two different natural sediments, and a second extract mixed with one of the natural sediments. A total of 306 samples—51 samples per series—yielded BSi contents ranging from 0 to 100 %. The resulting PLSR calibration model between the FTIR spectral information and the defined BSi concentration of the synthetic sediment mixtures exhibits a strong cross-validated correlation ( R2cv = 0.97) and a low root-mean square error of cross-validation (RMSECV = 4.7 %). Application of the independent calibration to natural lacustrine and marine sediments yields robust BSi reconstructions. At present, the synthetic mixtures do not include the variation in organic matter that occurs in natural samples, which may explain the somewhat lower prediction accuracy of the calibration model for organic-rich samples.

Optimization of TRPV6 Calcium Channel Inhibitors Using a 3D Ligand-Based Virtual Screening Method

Herein, we report the discovery of the first potent and selective inhibitor of TRPV6, a calcium channel overexpressed in breast and prostate cancer, and its use to test the effect of blocking TRPV6-mediated Ca2+-influx on cell growth. The inhibitor was discovered through a computational method, xLOS, a 3D-shape and pharmacophore similarity algorithm, a type of ligand-based virtual screening (LBVS) method described briefly here. Starting with a single weakly active seed molecule, two successive rounds of LBVS followed by optimization by chemical synthesis led to a selective molecule with 0.3 μM inhibition of TRPV6. The ability of xLOS to identify different scaffolds early in LBVS was essential to success. The xLOS method may be generally useful to develop tool compounds for poorly characterized targets.

A cross-sectional study of human symptomatology and residential formaldehyde concentrations

The cross-sectional study was performed to quantify the prevalence of symtomatology in residents of mobile homes as a function of indoor formaldehyde concentration. Formaldehyde concentrations were monitored for a seven hour period with an automated wet-chemical colorimetric analyzer. The health status of family members was ascertained by administration of questionnaires and physical exams. This is the first investigation to perform clinical assessments on residents undergoing concurrent exposure assessment in the home.^ Only 22.8% of households eligible for participation chose to cooperate. Monitoring data and health evaluations were obtained from 155 households in four Texas counties. A total of 428 residents (86.1%) were available for examination during the sampling hours. The study population included 45 infants, 126 children, and 257 adults.^ Formaldehyde concentration was not found to be significantly associated with increased risks for symptoms and signs of ocular irritation, dermal anomalies, or malaise. Three associations were identified that warrant further investigation. The relative odds associated with a doubling of formaldehyde concentration was significantly associated with parenchymal rales in adults and children. However, risk was modified by log respirable suspended particulate concentrations. Due to the presence of modification by a continuous variable, prevalence odds ratios (POR) and 95% confidence intervals (95% CI) for these associations are presented in tables. A doubling of formaldehyde concentration was also associated with an increased risk of perceived tightness in the chest in adults. Prevalence odds ratios are presented in a table due to effect modification by the average number of hours spent indoors on weekdays. Furthermore, a doubling of formaldehyde concentration was associated with an increased risk of drowsiness in children (POR = 2.60; 95% CI 1.04-6.51) and adults (POR = 1.94; 95% CI 1.20-3.14). ^

Mineralogy and inorganic geochemistry of sediments at DSDP Leg 65 Holes

During Leg 65, 15 holes were drilled at four sites located on young crust in the mouth of the Gulf of California. Quaternary to upper Pliocene hemipelagic sediments above and interlayered within the young basaltic basement were cored. The influence of hot lava, high temperature gradients, and hydrothermal activity on the mineralogy and geochemistry of the terrigenous sediments near contacts with basalts might therefore be expected. The purpose of the present study was to determine the mineralogy and inorganic geochemistry of these sediments and to analyze the nature and extent of low temperature alteration. To this end we studied the mineralogy and inorganic geochemistry of 75 sediment samples, including those immediately overlying uppermost basalts and those from layers alternating with basalts within the basement. We separated three size fractions - <2 µm (clay), 2-20 µm (intermediate), and >20 µm (coarse) - and applied the following mineralogical determinations: x-ray diffraction (XRD), infrared spectroscopy, transmission and scanning electron microscopy, and optical microscopy (for coarse fractions, using thin sections and smear slides). We calculated the percentages of clay minerals using Biscaye's (1964) method, and used routine wet chemical analyses to determine bulk composition and quantitative spectral analyses for trace elements.

Iodine speciation at time series station DYFAMED

Iodine speciation analysis was carried out upon seawater samples collected in July 1993 at the DYFAMED station (43 °25?N, 7 °52?E) located in the northwestern Mediterranean Sea. Dissolved iodate and iodide were directly determined by differential pulse polarography and cathodic stripping square wave voltammetry, respectively, and organically bound iodine was estimated by wet-chemical oxidation with sodium hypochlorite. Iodate is the predominant species ranging from 416 nM in surface waters to 480 nM in bottom waters. Iodide is present in significant concentrations up to 60 nM in surface waters, undetectable between 500 and 1000 m depth and present in very low but measurable concentrations (about 6 nM) in deep waters. The vertical profile of total free iodine demonstrates observable removal from surface waters, slight enrichment at about 200 m depth and constant there below. Up to 40 nM of organically bound iodine has been estimated between 20 to 30 m. Factorial analysis of different iodine species with biologically relevant parameters provided strong evidence for iodine biophilic features.

Geochemistry measured on sediment core GeoB12309-5

Laminated sediment records from the oxygen minimum zone in the Arabian Sea offer unique ultrahigh-resolution archives for deciphering climate variability in the Arabian Sea region. Although numerous analytical techniques are available it has become increasingly popular during the past decade to analyze relative variations of sediment cores' chemical signature by non-destructive X-ray fluorescence (XRF) core scanning. We carefully selected an approximately 5 m long sediment core from the northern Arabian Sea (GeoB12309-5: 24°52.3' N; 62°59.9' E, 956 m water depth) for a detailed, comparative study of high-resolution techniques, namely non-destructive XRF core scanning (0.8 mm resolution) and ICP-MS/OES analysis on carefully selected, discrete samples (1 mm resolution). The aim of our study was to more precisely define suitable chemical elements that can be accurately analyzed and to determine which elemental ratios can be interpretated down to sub-millimeter-scale resolutions. Applying the Student's t-test our results show significantly correlating (1% significance level) elemental patterns for all S, Ca, Fe, Zr, Rb, and Sr, as well as the K/Ca, Fe/Ti and Ti/Al ratios that are all related to distinct lithological changes. After careful consideration of all errors for the ICP analysis we further provide respective factors of XRF Core Scanner software error's underestimation by applying Chi-square-tests, which is especially relevant for elements with high count rates. As demonstrated by these new, ultra-high resolution data core scanning has major advantages (high-speed, low costs, few sample preparation steps) and represents an increasingly required alternative over the time consuming, expensive, elaborative, and destructive wet chemical analyses (e.g., by ICP-MS/OES after acid digestions), and meanwhile also provides high-quality data in unprecedented resolution.

Geochemistry of peridotites from ODP Leg 125 diapiric serpentinites

Refractory spinel peridotites were drilled during Leg 125 from two diapiric serpentinite seamounts: Conical Seamount in the Mariana forearc (Sites 778-780) and Torishima Forearc Seamount (Sites 783-784) in the Izu-Ogasawara forearc. Harzburgite is the predominant rock type in the recovered samples, with subordinate dunite; no lherzolite was found. The harzburgite is diopside-free to sparsely diopside-bearing, with modal percentages of diopside that range from 0% to 2%. Spinels in the harzburgites are chrome-rich (Cr/[Cr + Al] = 0.38-0.83; Fe3+/[Fe3+ + Cr + Al] = 0.01-0.07). Olivine and orthopyroxene are magnesian (Mg# = 0.92). Discrete diopsides reveal extreme depletion of light rare earth elements. Primary hornblende is rare. The bulk major-element chemistry shows low average values of TiO2 (trace), Al2O3 (0.55%) and CaO (0.60%), but high Mg# (0.90). These rocks are more depleted than the abyssal peridotites from the mid-oceanic ridge. They are interpreted as residues of extensive partial melting (= 30%), of which the last episode was in the mantle wedge, probably associated with the generation of incipient island-arc magma, including boninite and/or arc-tholeiite. These depleted peridotites probably represent the residues of melting within mantle diapirs that developed within the mantle wedge.

Vanadium-Doped In and Sn Sulphides: Photocatalysts able to use the whole visible light spectrum

Using photocatalysis for energy applications depends, more than for environmental purposes or selective chemical synthesis, on converting as much of the solar spectrum as possible; the best photocatalyst, titania, is far from this. Many efforts are pursued to use better that spectrum in photocatalysis, by doping titania or using other materials (mainly oxides, nitrides and sulphides) to obtain a lower bandgap, even if this means decreasing the chemical potential of the electron-hole pairs. Here we introduce an alternative scheme, using an idea recently proposed for photovoltaics: the intermediate band (IB) materials. It consists in introducing in the gap of a semiconductor an intermediate level which, acting like a stepstone, allows an electron jumping from the valence band to the conduction band in two steps, each one absorbing one sub-bandgap photon. For this the IB must be partially filled, to allow both sub-bandgap transitions to proceed at comparable rates; must be made of delocalized states to minimize nonradiative recombination; and should not communicate electronically with the outer world. For photovoltaic use the optimum efficiency so achievable, over 1.5 times that given by a normal semiconductor, is obtained with an overall bandgap around 2.0 eV (which would be near-optimal also for water phtosplitting). Note that this scheme differs from the doping principle usually considered in photocatalysis, which just tries to decrease the bandgap; its aim is to keep the full bandgap chemical potential but using also lower energy photons. In the past we have proposed several IB materials based on extensively doping known semiconductors with light transition metals, checking first of all with quantum calculations that the desired IB structure results. Subsequently we have synthesized in powder form two of them: the thiospinel In2S3 and the layered compound SnS2 (having bandgaps of 2.0 and 2.2 eV respectively) where the octahedral cation is substituted at a â?10% level with vanadium, and we have verified that this substitution introduces in the absorption spectrum the sub-bandgap features predicted by the calculations. With these materials we have verified, using a simple reaction (formic acid oxidation), that the photocatalytic spectral response is indeed extended to longer wavelengths, being able to use even 700 nm photons, without largely degrading the response for above-bandgap photons (i.e. strong recombination is not induced) [3b, 4]. These materials are thus promising for efficient photoevolution of hydrogen from water; work on this is being pursued, the results of which will be presented.

Sewage sludge gasification. Dolomite performance under different operating conditions

Gasification is a technology that can replace traditional management alternatives used up to date to deal with this waste (landfilling, composting and incineration) and which fulfils the social, environmental and legislative requirements. The main products of sewage sludge gasification are permanent gases (useful to generate energy or to be used as raw material in chemical synthesis processes), liquids (tars) and char. One of the main problems to be solved in gasification is tar production. Tars are organic impurities which can condense at relatively high temperatures making impossible to use the produced gases for most applications. This work deals with the effect of some primary tar removal processes (performed inside the gasifier) on sewage sludge gasification products. For this purpose, analysis of the gas composition, tar production, cold gas efficiency and carbon conversion were carried out. The tests were performed with air in a laboratory scale plant consisting mainly of a bubbling bed gasifier. No catalyzed and catalyzed (10% wt of dolomite in the bed and in the feeding) tests were carried out at different temperatures (750ºC, 800ºC and 850ºC) in order to know the effect of these parameters in the gasification products. As far as tars were concerned, qualitative and quantitative tar composition was determined. In all tests the Equivalence Ratio (ER) was kept at 0.3. Temperature is one of the most influential variables in sewage sludge gasification. Higher temperatures favoured hydrogen and CO production while CO2 content decreased, which might be partially explained by the effect of the cracking, Boudouard and CO2 reforming reactions. At 850ºC, cold gas efficiency and carbon conversion reached 49% and 76%, respectively. The presence of dolomite as catalyst increased the production of H2 reaching contents of 15.5% by volume at 850 °C. Similar behaviour was found for CO whereas CO2 and CnHm (light hydrocarbons) production decreased. In the presence of dolomite, a tar reduction of up to 51% was reached in comparison with no catalyzed tests, as well as improvements on cold gas efficiency and carbon conversion. Several assays were developed in order to test catalyst performance under more rough gasification conditions. For this purpose, the throughput value (TR), defined as kg sludge “as received” fed to the gasifier per hour and per m2 of cross sectional area of the gasifier, was modified. Specifically, the TR values used were 110 (reference value), 215 and 322 kg/h·m2. When TR increased, the H2, CO and CH4 production decreased while the CO2 and the CnHm production increased. Tar production increased drastically with TR during no catalysed tests what is related to the lower residence time of the gas inside the reactor. Nevertheless, even at TR=322 kg/h·m2, tar production decreased by nearly 50% with in-bed use of dolomite in comparison with no catalyzed assays under the same operating conditions. Regarding relative tar composition, there was an increase in benzene and naphthalene content when temperature increased while the content of the rest of compounds decreased. The dolomite seemed to be effective all over the range of molecular weight studied showing tar removal efficiencies between 35-55% in most cases. High values of the TR caused a significant increase in tar production but a slight effect on tar composition.

Photovoltaic LiNbO3particles: Applications to Biomedicine/Biophotonics

Recently, a novel method to trap and pattern ensembles of nanoparticles has been proposed and tested. It relies on the photovoltaic (PV) properties of certain ferroelectric crystals such as LiNbO3 [1,2]. These crystals, when suitably doped, develop very high electric fields in response to illumination with light of suitable wavelength. The PV effect lies in the asymmetrical excitation of electrons giving rise to PV currents and associated space-charge fields (photorefractive effect). The field generated in the bulk of the sample propagates to the surrounding medium as evanescent fields. When dielectric or metal nanoparticles are deposited on the surface of the sample the evanescent fields give rise to either electrophoretic or dielectrophoretic forces, depending on the charge state of the particles, that induce the trapping and patterning effects [3,4]. The purpose of this work has been to explore the effects of such PV fields in the biology and biomedical areas. A first work was able to show the necrotic effects induced by such fields on He-La tumour cells grown on the surface of an illuminated iron-doped LiNbO3 crystal [5]. In principle, it is conceived that LiNbO3 nanoparticles may be advantageously used for such biomedical purposes considering the possibility of such nanoparticles being incorporated into the cells. Previous experiments using microparticles have been performed [5] with similar results to those achieved with the substrate. Therefore, the purpose of this work has been to fabricate and characterize the LiNbO3 nanoparticles and assess their necrotic effects when they are incorporated on a culture of tumour cells. Two different preparation methods have been used: 1) mechanical grinding from crystals, and 2) bottom-up sol-gel chemical synthesis from metal-ethoxide precursors. This later method leads to a more uniform size distribution of smaller particles (down to around 50 nm). Fig. 1(a) and 1(b) shows SEM images of the nanoparticles obtained with both method. An ad hoc software taking into account the physical properties of the crystal, particullarly donor and aceptor concentrations has been developped in order to estimate the electric field generated in noparticles. In a first stage simulations of the electric current of nanoparticles, in a conductive media, due to the PV effect have been carried out by MonteCarlo simulations using the Kutharev 1-centre transport model equations [6] . Special attention has been paid to the dependence on particle size and [Fe2+]/[Fe3+]. First results on cubic particles shows large dispersion for small sizes due to the random number of donors and its effective concentration (Fig 2). The necrotic (toxicity) effect of nanoparticles incorporated into a tumour cell culture subjected to 30 min. illumination with a blue LED is shown in Fig.3. For each type of nanoparticle the percent of cell survival in dark and illumination conditions has been plot as a function of the particle dilution factor. Fig. 1a corresponds to mechanical grinding particles whereas 1b and 1c refer to chemically synthesized particles with two oxidation states. The light effect is larger with mechanical grinding nanoparticles, but dark toxicity is also higher. For chemically synthesized nanoparticles dark toxicity is low but only in oxidized samples, where the PV effect is known to be larger, the light effect is appreciable. These preliminary results demonstrate that Fe:LiNbO· nanoparticles have a biological damaging effect on cells, although there are many points that should be clarified and much space for PV nanoparticles optimization. In particular, it appears necessary to determine the fraction of nanoparticles that become incorporated into the cells and the possible existence of threshold size effects. This work has been supported by MINECO under grant MAT2011-28379-C03.

Crystal structure of chemically synthesized [N33A] stromal cell-derived factor 1α, a potent ligand for the HIV-1 “fusin” coreceptor

Stromal cell-derived factor-1α (SDF-1α ) is a member of the chemokine superfamily and functions as a growth factor and chemoattractant through activation of CXCR4/LESTR/Fusin, a G protein-coupled receptor. This receptor also functions as a coreceptor for T-tropic syncytium-inducing strains of HIV-1. SDF-1α antagonizes infectivity of these strains by competing with gp120 for binding to the receptor. The crystal structure of a variant SDF-1α ([N33A]SDF-1α ) prepared by total chemical synthesis has been refined to 2.2-Å resolution. Although SDF-1α adopts a typical chemokine β-β-β-α topology, the packing of the α-helix against the β-sheet is strikingly different. Comparison of SDF-1α with other chemokine structures confirms the hypothesis that SDF-1α may be either an ancestral protein from which all other chemokines evolved or the chemokine that is the least divergent from a primordial chemokine. The structure of SDF-1α reveals a positively charged surface ideal for binding to the negatively charged extracellular loops of the CXCR4 HIV-1 coreceptor. This ionic complementarity is likely to promote the interaction of the mobile N-terminal segment of SDF-1α with interhelical sites of the receptor, resulting in a biological response.

Activity-based protein profiling: The serine hydrolases

With the postgenome era rapidly approaching, new strategies for the functional analysis of proteins are needed. To date, proteomics efforts have primarily been confined to recording variations in protein level rather than activity. The ability to profile classes of proteins on the basis of changes in their activity would greatly accelerate both the assignment of protein function and the identification of potential pharmaceutical targets. Here, we describe the chemical synthesis and utility of an active-site directed probe for visualizing dynamics in the expression and function of an entire enzyme family, the serine hydrolases. By reacting this probe, a biotinylated fluorophosphonate referred to as FP-biotin, with crude tissue extracts, we quickly and with high sensitivity detect numerous serine hydrolases, many of which display tissue-restricted patterns of expression. Additionally, we show that FP-biotin labels these proteins in an activity-dependent manner that can be followed kinetically, offering a powerful means to monitor dynamics simultaneously in both protein function and expression.

Nucleic acid duplexes incorporating a dissociable covalent base pair

We have used molecular modeling techniques to design a dissociable covalently bonded base pair that can replace a Watson-Crick base pair in a nucleic acid with minimal distortion of the structure of the double helix. We introduced this base pair into a potential precursor of a nucleic acid double helix by chemical synthesis and have demonstrated efficient nonenzymatic template-directed ligation of the free hydroxyl groups of the base pair with appropriate short oligonucleotides. The nonenzymatic ligation reactions, which are characteristic of base paired nucleic acid structures, are abolished when the covalent base pair is reduced and becomes noncoplanar. This suggests that the covalent base pair linking the two strands in the duplex is compatible with a minimally distorted nucleic acid double-helical structure.