HPLC-based analysis of serum N-glycans on a 96-well plate platform with dedicated database software

We present a robust, fully automatable technology platform that includes computer software for the detailed analysis of low femtomoles of N-linked sugars released from glycoproteins. Features include (i) sample immobilization in 96-well plates, glycan release, and fluorescent labeling; (ii) quantitative HPLC analysis, including monosaccharide sequence, linkage, and arm-specific information for charged and neutral glycans; (iii) automatic structural assignment of peaks from HPLC profiles via web-based software that accesses our database (GlycoBase) of more than 350 N-glycan structures, including 117 present in the human serum glycome; and (iv) software (autoGU) that progressively analyzes data from exoglycosidase digestions to produce a refined list of final structures. The N-glycans from a plate of 96 samples can be released and purified in 2 or 3 days and profiled in 2 days. This strategy can be used for (i) identification and screening of disease biomarkers and (ii) monitoring the production of therapeutic glycoproteins, allowing optimization of production conditions. This technology is also suitable for preparing released glycans for other analytical techniques. Here we demonstrate its application to rheumatoid arthritis using 5 μl of patient serum.     

CD23-bound IgE augments and dominates recall responses through human naive B cells

Human peripheral blood BCRμ(+) B cells express high levels of CD23 and circulate preloaded with IgE. The Ag specificity of CD23-bound IgE presumably differs from the BCR and likely reflects the Ag-specific mix of free serum IgE. CD23-bound IgE is thought to enhance B cell Ag presentation to T cells raising the question of how a B cell might respond when presented with a broad mix of Ags and CD23-bound IgE specificities. We recently reported that an increase in CD23(+) B cells is associated with the development of resistance to schistosomiasis, highlighting the potential importance of CD23-bound IgE in mediating immunity. We sought to determine the relationship between BCR and CD23-bound IgE-mediated B cell activation in the context of schistosomiasis. We found that crude schistosome Ags downregulate basal B cell activation levels in individuals hyperexposed to infectious worms. Schistosome-specific IgE from resistant, occupationally exposed Kenyans recovered responses of B cells to schistosome Ag. Furthermore, cross-linking of CD23 overrode intracellular signals mediated via the BCR, illustrating its critical and dominating role in B cell activation. These results suggest that CD23-bound IgE augments and dominates recall responses through naive B cells.     

DNA recognition by the EcoRV restriction endonuclease probed using base analogues

The EcoRV restriction endonuclease recognises palindromic GATATC sequences and cuts between the central T and dA bases in a reaction that has an absolute requirement for a divalent metal ion, physiologically Mg(2+). Use has been made of base analogues, which delete hydrogen bonds between the protein and DNA (or hydrophobic interactions in the case of the 5-CH(3) group of thymine), to evaluate the roles of the outer two base-pairs (GATATC) in DNA recognition. Selectivity arises at both the binding steps leading to the formation of the enzyme-DNA-metal ion ternary complex (assayed by measuring the dissociation constant in the presence of the non-reactive metal Ca(2+)) and the catalytic step (evaluated using single-turnover hydrolysis in the presence of Mg(2+)), with each protein-DNA contact contributing to recognition. With the A:T base-pair, binding was reduced by the amount expected for the simple loss of a single contact; much more severe effects were observed with the G:C base-pair, suggesting additional conformational perturbation. Most of the modified bases lowered the rate of hydrolysis; furthermore, the presence of an analogue in one strand of the duplex diminished cutting at the second, unmodified strand, indicative of communication between DNA binding and the active site. The essential metal ion Mg(2+) plays a key role in mediating interactions between the DNA binding site and active centre and in many instances rescue of hydrolysis was seen with Mn(2+). It is suggested that contacts between the GATATC site are required for tight binding and for the correct assembly of metal ions and bound water at the catalytic site, functions important in providing acid/base catalysis and transition state stabilisation.     

Improving plant functional groups for dynamic models of biodiversity: at the crossroads between functional and community ecology

The pace of on‐going climate change calls for reliable plant biodiversity scenarios. Traditional dynamic vegetation models use plant functional types that are summarized to such an extent that they become meaningless for biodiversity scenarios. Hybrid dynamic vegetation models of intermediate complexity (hybrid‐DVMs) have recently been developed to address this issue. These models, at the crossroads between phenomenological and process‐based models, are able to involve an intermediate number of well‐chosen plant functional groups (PFGs). The challenge is to build meaningful PFGs that are representative of plant biodiversity, and consistent with the parameters and processes of hybrid‐DVMs. Here, we propose and test a framework based on few selected traits to define a limited number of PFGs, which are both representative of the diversity (functional and taxonomic) of the flora in the Ecrins National Park, and adapted to hybrid‐DVMs. This new classification scheme, together with recent advances in vegetation modeling, constitutes a step forward for mechanistic biodiversity modeling.     

Antimicrobial action of palmarosa oil (Cymbopogon martinii) on Saccharomyces cerevisiae

The essential oil extracted from palmarosa (Cymbopogon martinii) has proven anti-microbial properties against cells of Saccharomyces cerevisiae. Low concentrations of the oil (0.1%) inhibited the growth of S. cerevisiae cells completely. The composition of the sample of palmarosa oil was determined as 65% geraniol and 20% geranyl acetate as confirmed by GC-FTIR. The effect of palmarosa oil in causing K(+) leakage from yeast cells was attributed mainly to geraniol. Some leakage of magnesium ions was also observed. Blocking potassium membrane channels with caesium ions before addition of palmarosa oil did not change the extent of K(+) ion leakage, which was equal to the total sequestered K(+) in the cells. Palmarosa oil led to changes in the composition of the yeast cell membrane, with more saturated and less unsaturated fatty acids in the membrane after exposure of S. cerevisiae cells to the oil. Some of the palmarosa oil was lost by volatilization during incubation of the oil with the yeast cells. The actual concentration of the oil components affecting the yeast cells could not therefore be accurately determined.     

Estimating true prevalence of Schistosoma mansoni from population summary measures based on the Kato-Katz diagnostic technique

BackgroundThe prevalence of Schistosoma mansoni infection is usually assessed by the Kato-Katz diagnostic technique. However, Kato-Katz thick smears have low sensitivity, especially for light infections. Egg count models fitted on individual level data can adjust for the infection intensity-dependent sensitivity and estimate the ‘true’ prevalence in a population. However, application of these models is complex and there is a need for adjustments that can be done without modeling expertise. This study provides estimates of the ‘true’ S. mansoni prevalence from population summary measures of observed prevalence and infection intensity using extensive simulations parametrized with data from different settings in sub-Saharan Africa.MethodologyAn individual-level egg count model was applied to Kato-Katz data to determine the S. mansoni infection intensity-dependent sensitivity for various sampling schemes. Observations in populations with varying forces of transmission were simulated, using standard assumptions about the distribution of worms and their mating behavior. Summary measures such as the geometric mean infection, arithmetic mean infection, and the observed prevalence of the simulations were calculated, and parametric statistical models fitted to the summary measures for each sampling scheme. For validation, the simulation-based estimates are compared with an observational dataset not used to inform the simulation.Principal findingsOverall, the sensitivity of Kato-Katz in a population varies according to the mean infection intensity. Using a parametric model, which takes into account different sampling schemes varying from single Kato-Katz to triplicate slides over three days, both geometric and arithmetic mean infection intensities improve estimation of sensitivity. The relation between observed and ‘true’ prevalence is remarkably linear and triplicate slides per day on three consecutive days ensure close to perfect sensitivity.Conclusions/significanceEstimation of ‘true’ S. mansoni prevalence is improved when taking into account geometric or arithmetic mean infection intensity in a population. We supply parametric functions and corresponding estimates of their parameters to calculate the ‘true’ prevalence for sampling schemes up to 3 days with triplicate Kato-Katz thick smears per day that allow estimation of the ‘true’ prevalence.     

Aromatization and androgen stimulation of sexual behavior in male and female rats

6α-Fluorotestosterone, an androgen that is not aromatized in a standard assay system, stimulated sexual behavior in both male and female rats. In males, it was as effective as testosterone. 19-Nortestosterone also stimulated more male sexual behavior than would be expected on the basis of its aromatizability in standard assays. In other tests of the aromatization hypo we used the anti-estrogen, CI-628. This drug inhibited androgen-induced sexual receptivity in female rats, but did not inhibit androgen-induced sexual behavior in male rats. In females, CI-628 antagonized testosterone and 6α-fluorotestosterone equally. These data suggest that the structures of androgens, rather than their abilities to be aromatized, determine behavioral effectiveness.     

Synthesis and characterisation of bis(2,2′-bipyridine)(4-carboxy-4′-(pyrid-2-ylmethylamido)-2,2′-bipyridine)ruthenium(II) di(hexafluorophosphate): Comparison of spectroelectrochemical properties with related complexes

The new complex, [Ru^II(bpy)₂(4-HCOO-4′-pyCH₂ NHCO-bpy)](PF₆)₂ · 3H₂O (1), where 4-HCOO-4′-pyCH₂NHCO-bpy is 4-(carboxylic acid)-4′-pyrid-2-ylmethylamido-2,2′-bipyridine, has been synthesised from [Ru(bpy)₂(H₂dcbpy)](PF₆)₂ (H₂dcbpy is 4,4′-(dicarboxylic acid)-2,2′-bipyridine) and characterised by elemental analysis and spectroscopic methods. An X-ray crystal structure determination of the trihydrate of the [Ru(bpy)₂(H₂dcbpy)](PF₆)₂ precursor is reported, since it represented a different solvate to an existing structure. The structure shows a distorted octahedral arrangement of the ligands around the ruthenium(II) centre and is consistent with the carboxyl groups being protonated. A comparative study of the electrochemical and photophysical properties of [Ru^II(bpy)₂(4-HCOO-4′-pyCH₂NHCO-bpy)]²⁺ (1), [Ru(bpy)₂(H₂dcbpy)]²⁺ (2), [Ru(bpy)₃]²⁺ (3), [Ru(bpy)₂Cl₂] (4) and [Ru(bpy)₂Cl₂]⁺ (5) was then undertaken to determine their variation upon changing the ligands occupying two of the six ruthenium(II) coordination sites. The ruthenium(II) complexes exhibit intense ligand centred (LC) transition bands in the UV region, and broad MLCT bands in the visible region. The ruthenium(III) complex, 5, displayed overlapping LC bands in the UV region and a LMCT band in the visible. 1, 2 and 3 were found, via cyclic voltammetry at a glassy carbon electrode, to exhibit very positive reversible formal potentials of 996, 992 and 893 mV (versus Fc/Fc⁺) respectively for the Ru(III)/Ru(II) half-cell reaction. As expected the reversible potential derived from oxidation of 4 (−77 mV (versus Fc/Fc⁺)) was in excellent agreement with that found via reduction of 5 (−84 mV (versus Fc/Fc⁺)). Spectroelectrochemical experiments in an optically transparent thin-layer electrochemical cell configuration allowed UV-Vis spectra of the Ru(III) redox state to be obtained for 1, 2, 3 and 4 and also confirmed that 5 was the product of oxidative bulk electrolysis of 4. These spectrochemical measurements also confirmed that the oxidation of all Ru(II) complexes and reduction of the corresponding Ru(III) complex are fully reversible in both the chemical and electrochemical senses.