Resolving genetic functions within microbial populations: In situ analyses using rRNA and mRNA stable isotope probing coupled with single-cell raman-fluorescence in situ hybridization

Prokaryotes represent one-half of the living biomass on Earth, with the vast majority remaining elusive to culture and study within the laboratory. As a result, we lack a basic understanding of the functions that many species perform in the natural world. To address this issue, we developed complementary population and single-cell stable isotope (C-13)-linked analyses to determine microbial identity and function in situ. We demonstrated that the use of rRNA/mRNA stable isotope probing (SIP) recovered the key phylogenetic and functional RNAs. This was followed by single-cell physiological analyses of these populations to determine and quantify in situ functions within an aerobic naphthalene-degrading groundwater microbial community. Using these culture-independent approaches, we identified three prokaryote species capable of naphthalene biodegradation within the groundwater system: two taxa were isolated in the laboratory (Pseudomonas fluorescens and Pseudomonas putida), whereas the third eluded culture (an Acidovorax sp.). Using parallel population and single-cell stable isotope technologies, we were able to identify an unculturable Acidovorax sp. which played the key role in naphthalene biodegradation in situ, rather than the culturable naphthalene-biodegrading Pseudomonas sp. isolated from the same groundwater. The Pseudomonas isolates actively degraded naphthalene only at naphthalene concentrations higher than 30 mu M. This study demonstrated that unculturable microorganisms could play important roles in biodegradation in the ecosystem. It also showed that the combined RNA SIP-Raman-fluorescence in situ hybridization approach may be a significant tool in resolving ecology, functionality, and niche specialization within the unculturable fraction of organisms residing in the natural environment.

Rapid Surface Plasmon Resonance Immunoassay for the Determination of Deoxynivalenol in Wheat, Wheat Products, and Maize-Based Baby Food

A rapid screening assay (9 min/sample) has been developed and validated for the detection of deoxynivalenol in durum wheat, wheat products, and maize-based baby foods using an SPA biosensor. Through a single laboratory validation, the limits of detection (LOD) for wheat, wheat-based breakfast cereal, and maize-based baby food were 57, 9, and 6 mu g/kg, respectively. Intra-assay and interassay precisions were calculated for each matrix at the maximum and half-maximum European Union regulatory limits and expressed as the coefficient of variation (CV). All CVs fell below 10% with the exception of the between-run CV for breakfast cereal. Recoveries at the concentrations tested ranged from 92 to 115% for all matrices. Action limits of 161, 348, and 1378 mu g/kg were calculated for baby food, wheat-based breakfast cereal, and wheat, respectively, and the linear range of the assay was determined as 250-2000 mu g/kg.

Hapten synthesis and antibody production for the development of a melamine immunoassay

The incorporation of melamine into food products is banned but its misuse has been widely reported in both animal feeds and food. The development of a rapid screening immunoassay for monitoring of the substance is an urgent requirement. Two haptens of melamine were synthesized by introducing spacer arms of different lengths and structures on the triazine ring of the analyte molecular structure. 6-Aminocaproic acid and 3-mercaptopropionic acid were reacted with 2-chloro-4,6-diamino-1,3,5-triazine (CAAT) to produce hapten 1[3-(4,6-diamino-1,6-dihydro-1,3,5-triazin-2-ylamino) hexanoic acid] and hapten 2[3-(4,6-diamino-1,6-dihydro-1,3,5-triazin-2-ylthio) propanoic acid]. respectively. The molecular structures of the two haptens were identified by I H nuclear magnetic resonance spectrometry, mass spectrometry and infrared spectrometry. An immunogen was prepared by coupling hapten 1 to bovine serum albumin (BSA). Two plate coating antigens were prepared by coupling both haptens to egg ovalbumin (OVA). A competitive indirect enzyme-linked immunosorbent assay (ciELISA) was developed to evaluate homogeneous and heterogeneous assay formats. The results showed that polyclonal antibodies with high titers were obtained, and the heterogeneous immunoassay format demonstrated a better performance with an IC50 of 70.6 ng mL(-1), a LOD of 2.6 ng mL(-1) and a LOQ of 7.6 ng mL(-1). Except for cyromazine, no obvious cross-reactivity to common compounds was found. The data showed that the hapten synthesis was successful and the resultant antisera could be used in an immunoassay for the rapid and sensitive detection of this banned chemical. (C) 2010 Elsevier B.V. All rights reserved.

A rapid optical immunoassay for the screening of T-2 and HT-2 toxin in cereals and maize-based baby food

A rapid surface plasmon resonance (SPR) screening assay has been developed for the combined detection of T-2 and HT-2 toxins in naturally contaminated cereals using a sensor chip coated with an HT-2 toxin derivative and a monoclonal antibody. The antibody raised against HT-2 displayed high cross-reactivity with T-2 toxin while there was no cross-reaction observed with other commonly occurring trichothecenes. A simple extraction procedure using 40% methanol was applied to baby food, breakfast cereal, and wheat samples prior to biosensor analysis. Limits of detection (LOD) for each matrix were determined as 25 mu g kg(-1) for baby food and breakfast cereal and 26 mu g kg(-1) for wheat. Intra-assay precision (n = 6) was calculated for each matrix. The results were expressed as the relative standard deviation and determined as 2.8% (100 mu g kg(-1)) and 1.8% (200 mu g kg(-1)) in breakfast cereal, 4.6% (50 mu g kg(-1)) and 3.6% (100 mu g kg(-1)) in wheat and 0.97% (25 mu g kg(-1)) and 6.3% (50 mu g kg(-1)) in baby food. Between run precision (n = 3) performed at the same levels yielded relative standard deviations of 6.7% and 3.9% for breakfast cereals, 3.3% and 1.6% for wheat and 6.8% and 0.08% for baby food, respectively. (C) 2010 Elsevier B.V. All rights reserved.

Comparison of porcine urine and bile as matrices to screen for the residues of two sulfonamides using a semi-automated enzyme immunoassay.

Porcine urine enzyme immunoassays for sulfamethazine and sulfadiazine have previously been employed as screening tests to predict the concentrations of the drugs in the corresponding tissues (kidneys), If a urine was found positive (> 800 ng ml(-1)) the corresponding kidney was then analysed by an enzyme immunoassay and, if found positive, a confirmatory analysis by HPLC was performed. Urine was chosen as the screening matrix since sulfonamides are mainly eliminated through this body fluid, However, after obtaining a number of false positive predictions, an investigation was carried out to assess the possibility of using an alternative body fluid which would act as a superior indicator of the presence of sulfonamides in porcine kidney, An initial study indicated that serum, plasma and bile could all be used as screening matrices. From these, bile was chosen as the preferred sample matrix and an extensive study followed to compare the efficiencies of sulfonamide positive bile and urine at predicting sulphonamide positive kidneys, Bile was found to be 17 times more efficient than urine at predicting a sulfamethazine positive kidney and 11 times more efficient at predicting a sulfadiazine positive kidney, With this enhanced performance of the initial screening test, the need for the costly and time consuming kidney enzyme immunoassay, prior to HPLC analysis, was eliminated

Spontaneous spin polarization and charge localization in metal nanowires: the role of a geometric constriction

An idealized jellium model of conducting nanowires with a geometric constriction is investigated by density functional theory (DFT) in the local spin density (LSD) approximation. The results reveal a fascinating variety of spin and charge patterns arising in wires of sufficiently low (r(s) >= 15) average electron density, pinned at the indentation by an apparent attractive interaction with the constriction. The spin-resolved frequency-dependent conductivity shows a marked asymmetry in the two spin channels, reflecting the spontaneous spin polarization around the wire neck. The relevance of the computational results is discussed in relation to the so-called 0.7 anomaly found by experiments in the low-frequency conductivity of nanowires at near-breaking conditions (see 2008 J. Phys.: Condens Matter 20, special issue on the 0.7 anomaly). Although our mean-field approach cannot account for the intrinsic many-body effects underlying the 0.7 anomaly, it still provides a diagnostic tool to predict impending transitions in the electronic structure.

Spontaneous spin polarization in geometrically constricted metal nanowires

The electronic structure of thin conducting wires with a narrow geometric constriction has been determined by density-functional theory computations in the local spin density approximation. Spontaneous spin polarization arises in nominally paramagnetic wires at sufficiently low density (r(s)>= 15). Real-space spin-polarization maps show a fascinating variety of magnetic structures pinned at the constriction. The frequency-dependent conductivity is different for the spin-up and spin-down channels and significantly lower than in wires of identically vanishing spin polarization.

Stability of dust lattice modes in the presence of charged dust grain polarization in plasmas

We discuss the effect of the attractive force associated with overlapping Debye spheres on the dispersion properties of the longitudinal and transverse dust lattice waves in strongly coupled dust crystals. The dust grain attraction is shown to contribute to a destabilization of the longitudinal dust lattice oscillations. The (optic-like) transverse mode dispersion law is shown to change. due to the Debye sphere dressing effect, from the known inverse-dispersive ("backward wave") form into a normal dispersive law (i.e. the group velocity changes sign). The stability of one-dimensionless bi-layers, consisting of (alternating) negatively and positively charged dust particles, is also discussed. The range of parameter values (mainly in terms of the lattice parameter kappa) where the above predictions are valid, are presented. (c) 2005 Elsevier B.V. All rights reserved.

Dust lattice wave dispersion relations in two-dimensional hexagonal crystals including the effect of dust charge polarization

A dusty plasma crystalline configuration with equal charge dust grains and mass is considered. Both charge and mass of each dust species are taken to be constant. Two differential equations for a two-dimensional hexagonal crystal on the basis of a Yukawa-type potential energy and a

Phonons, Instabilities and Origin of Polarization in KDP Crystals

The -phonons of KH2PO4 (KDP) and its deuterated analog DKDP are studied via first-principles linear response calculations. The paraelectric phase shows two instabilities. One for a z-polarized mode, which leads to the spontaneous polarization Ps of the ferroelectric phase. The other corresponds to a two-fold degenerate xy-polarized mode. Other phonons are analyzed, which couple to the ferroelectric one at large amplitudes and are relevant for the ferroelectric transition. We show that Ps is mainly of electronic nature, since it arises mostly from an off-diagonal component of the Born effective charge tensor of H, with minor contribution from P atoms displacements.