New Real-Time Quantitative PCR Procedure for Quantification of Bifidobacteria in Human Fecal Samples

The application of a real-time quantitative PCR method (5′ nuclease assay), based on the use of a probe labeled at its 5′ end with a stable, fluorescent lanthanide chelate, for the quantification of human fecal bifidobacteria was evaluated. The specificities of the primers and the primer-probe combination were evaluated by conventional PCR and real-time PCR, respectively. The results obtained by real-time PCR were compared with those obtained by fluorescent in situ hybridization, the current gold standard for intestinal microbiota quantification. In general, a good correlation between the two methods was observed. In order to determine the detection limit and the accuracy of the real-time PCR procedure, germfree rat feces were spiked with known amounts of bifidobacteria and analyzed by both methods. The detection limit of the method used in this study was found to be about 5 × 10⁴ cells per g of feces. Both methods, real-time PCR and fluorescent in situ hybridization, led to an accurate quantification of the spiked samples with high levels of bifidobacteria, but real-time PCR was more accurate for samples with low levels. We conclude that the real-time PCR procedure described here is a specific, accurate, rapid, and easy method for the quantification of bifidobacteria in feces.     

Water chemistry of mires in relation to the poor-rich vegetation gradient and contrasting geochemical zones of the north-eastern fennoscandian Shield

The relationship of the poor-rich vegetation gradient with water chemistry and geochemical bedrock zones was studied with a data set from 36 pristine mire sites in the middle boreal zone, Finland. The bipartition of bedrock zones into a granitoid zone and three other, more alkaline bedrock zones was clearly connected to the poor-rich gradient in the study area. Mires in the granitoid bedrock zone were predominantly bogs and poor fens, while most of the rich fen sites were located in other bedrock zones. In fens with strongly minerogenous hydrology, the geochemically distinct bedrock zones showed significant differences in concentrations of calcium, manganese, phosphorus, as well as in the total equivalent charge of base cations and the ratio of calcium and magnesium. In light of the indicator species baseda priori poor-rich classification anda posteriori correlations with vegetation ordinations and a poor-rich indicator cover index, pH showed the strongest relationship of the water chemical variables with the poor-rich gradient. High calcium concentrations only separated extremely rich fens from other categories. The poor-rich gradient of mires is considered as a primarily pH-related vegetation continuum. A more general use of pH-classes along with hydrological and vegetation based classification is suggested for mire classification instead of the “poor-rich” terminology.     

Fimbrial Subunit Protein FaeG Expressed in Transgenic Tobacco Inhibits the Binding of F4ac Enterotoxigenic Escherichia coli to Porcine Enterocytes

Plants offer a promising alternative for the production of foreign proteins for pharmaceutical purposes in tissues that are consumed as food and/or feed. Our long-term strategy is to develop edible vaccines against piglet diarrhoea caused by enterotoxigenic Escherichia coli (F4 ETEC) in feed plants. In this work, we isolated a gene, faeG, encoding for a major F4ac fimbrial subunit protein. Our goal was to test whether the FaeG protein, when isolated from its fimbrial background and produced in a plant cell, would retain the key properties of an oral vaccine, that is, stability in gastrointestinal conditions, binding to intestinal receptors and inhibition of the F4 ETEC attachment. For this purpose, tobacco was first transformed with a faeG construct that included a transit peptide encoding sequence to target the FaeG protein to the chloroplast. The best transgenic lines produced FaeG protein in amounts of 1% total soluble protein. The stability of the plant-produced FaeG was tested in fluids simulating piglet gastric (SGF) and intestinal (SIF) conditions. Plant-produced FaeG proved to be stable up to 2 h under these conditions. The binding and inhibition properties were tested with isolated piglet villi. These results showed that the plant-produced FaeG could bind to the receptors on the villi and subsequently inhibit F4 ETEC binding in a dose-dependent manner. Thus, the first two prerequisites for the development of an oral vaccine have been met.     

Human alpha3-fucosyltransferases convert chitin oligosaccharides to products containing a GlcNAcbeta1-4(Fucalpha1-3)GlcNAcbeta1-4R determinant at the nonreducing terminus

Human alpha3-fucosyltransferases (Fuc-Ts) are known to convert N-acetyllactosamine to Galbeta1-4(Fucalpha1-3)GlcNAc (Lewis x antigen); some of them transfer fucose also to GalNAcbeta1-4GlcNAc, generating GalNAcbeta1-4(Fucalpha1-3)GlcNAc determinants. Here, we report that recombinant forms of Fuc-TV and Fuc-TVI as well as Fuc-Ts of human milk converted chitin oligosaccharides of 2-4 GlcNAc units efficiently to products containing a GlcNAcbeta1-4(Fucalpha1-3)GlcNAcbeta1-4R determinant at the nonreducing terminus. The product structures were identified by mass spectrometry and nuclear magnetic resonance experiments; rotating frame nuclear Overhauser spectroscopy data suggested that the fucose and the distal N-acetylglucosamine are stacked in the same way as the fucose and the distal galactose of the Lewis x determinant. The products closely resembled a nodulation factor of Mesorhizobium loti but were distinct from nodulation signals generated by NodZ-enzyme.     

Single-step procedure for gas chromatography-mass spectrometry screening and quantitative determination of amphetamine-type stimulants and related drugs in blood, serum, oral fluid and urine samples

We describe a rapid GC/MS assay for amphetamine-type stimulant drugs (ATSs) and structurally related common medicaments in blood, serum, oral fluid and urine samples. The drugs were extracted from their matrices and derivatized with heptafluorobutyric anhydride (HFBA) in a single step, using the following procedure: 100 microl (oral fluid) or 200 microl (blood, serum, urine) of the sample were mixed with 50 microl of alkaline buffer and 500 microl of extraction-derivatization reagent (toluene + HFBA + internal standard), centrifuged, and injected into a GC/MS apparatus. As revealed by the validation data this procedure, with its limit of quantitation being set at 20 ng/ml for oral fluid, 25 ng/ml for blood or 200 ng/ml for urine, is suitable for screening, identification and quantitative determination of the ATSs and related drugs in all the matrices examined. Thus, time-consuming and expensive multiple analyses are not needed, unless specifically required.     

The acceptor and site specificity of alpha 3-fucosyltransferase V. High reactivity of the proximal and low of the distal galbeta 1-4GlcNAc unit in i-type polylactosamines

We report here on in vitro acceptor and site specificity of recombinant alpha3-fucosyltransferase V (Fuc-TV) with 40 oligosaccharide acceptors. Galbeta1-4GlcNAc (LN) and GalNAcbeta1-4GlcNAc (LDN) reacted rapidly; Galbeta1-3GlcNAc (LNB) reacted moderately, and GlcNAcbeta1-4GlcNAc (N, N'-diacetyl-chitobiose) reacted slowly yet distinctly. In neutral and terminally alpha3-sialylated polylactosamines of i-type, the reducing end LN unit reacted rapidly and the distal (sialyl)LN group very slowly; the midchain LNs revealed intermediate reactivities. The data suggest that a distal LN neighbor enhances but a proximal LN neighbor reduces the reactivity of the midchain LNs. This implies that Fuc-TV may bind preferably the tetrasaccharide sequence Galbeta1-4GlcNAcbeta1-3Galbeta1-4GlcNAc for transfer at the underlined monosaccharide. Terminal alpha3-sialylation of i-type polylactosamines almost doubled the reactivities of the LN units at all positions of the chains. We conclude that, in comparison with human Fuc-TIV and Fuc-TIX, Fuc-TV reacted with a highly distinct site specificity with i-type polylactosamines. The Fuc-TV reactivity of free LNB resembled that of LNBbeta1-3'R of a polylactosamine, contrasting strongly with the dissimilarity of the reactivities of the analogous pair of LN and LNbeta1-3'R. This observation supports the notion that LN and LNB may be functionally bound at distinct sites on Fuc-TV surface. Our data show that Fuc-TV worked well with a very wide range of LN-glycans, showing weak reactivity only with distal (sialyl)LN units of i-type polylactosamines, biantennary N-glycans, and I branches of polylactosamines.     

Ongoing Fen–Bog Transition in a Boreal Aapa Mire Inferred from Repeated Field Sampling,Aerial Images,and Landsat Data

Ecosystems - Northern aapa mire complexes are characterized by patterned fens with flarks (wet fen surfaces) and bog zone margins with Sphagnum moss cover. Evidence exists of a recent increase in...