Pathogen detection using engineered bacteriophages

Bacteriophages, or phages, are bacterial viruses that can infect a broad or narrow range of host organisms. Knowing the host range of a phage allows it to be exploited in targeting various pathogens. Applying phages for the identification of microorganisms related to food and waterborne pathogens and pathogens of clinical significance to humans and animals has a long history, and there has to some extent been a recent revival in these applications as phages have become more extensively integrated into novel detection, identification, and monitoring technologies. Biotechnological and genetic engineering strategies applied to phages are responsible for some of these new methods, but even natural unmodified phages are widely applicable when paired with appropriate innovative detector platforms. This review highlights the use of phages as pathogen detector interfaces to provide the reader with an up-to-date inventory of phage-based biodetection strategies.     

Revision of the absolute configurations of bethosides B and C and their aglycone

The absolute stereochemistry of the steroidal saponins bethosides B and C was previously assigned as (22R,25R) on the basis of work that employed Horeau's method. Our studies of helosides A and B created doubt about both the original assignment and consequently our conclusion that relied upon it. The absolute configurations of bethosides B and C are revised to (22S,25R) following X-ray crystallographic analysis of their aglycone. Synthesis and full spectral characterization of both the 22R and 22S aglycones is reported to facilitate future stereochemical assignments in this series of saponins.     

Comprehensive analysis of polycyclic aromatic hydrocarbons in wastewater using stir bar sorptive extraction and gas chromatography coupled to tandem mass spectrometry

The objective of this study was the optimization and comparison of two extraction methods for the determination of polycyclic aromatic hydrocarbons (PAHs) in wastewater (WW). A distribution study of the target compounds between the aqueous phase and the suspended particulate matter (SPM) has been performed in order to establish whether the analysis of both phases is necessary. In this sense, the feasibility of stir bar sorptive extraction (SBSE) and solid-phase extraction (SPE) for the determination of 24 PAHs in WW samples has been evaluated. The results demonstrated the suitability of SBSE to perform a comprehensive analysis of liquid samples containing high amounts of SPM, such as in the determination of PAHs in WWs. A gas chromatography triple quadrupole mass spectrometry (GC-QqQ-MS/MS) method has been also optimized for the separation and detection of the target compounds, avoiding the co-elution of some groups of isomers, such as benzo[b], [j] and [k] fluoranthenes and indene[1,2,3-cd]pyrene/dibenz[a,h]anthracene. For that purpose, a specific capillary column developed for PAH determination was used. The SBSE procedure was validated and adequate parameters (such as recovery, linearity, precision, limits of detection and quantification) were obtained. Finally, the validated method was applied to the analysis of real samples collected from an experimental WW treatment plant, detecting some PAHs at concentrations in the range 0.007-0.022 μg L(-1).     

Solitonic waves in polyene dications and principles of charge carrier localization in π‐conjugated organic materials

The quantum‐chemical investigations by ab initio method (restricted Hartree–Fock/6‐31G**) have been performed for a series of unsubstituted, monosubstituted, and disubstituted neutral polyenes and their double charged cations. The waves of charge alternation (characterized by the difference in the electron densities at the nearest carbon atoms or Δq function) and bond length alternation (characterized by the lengths difference of the nearest carbon–carbon bonds or Δl function) are reported. Comparisons are made with the corresponding monocationic polymethine molecules. We found that ionization by two electrons results in formation of two solitonic waves of charge alternation, rather than superposition of two overlapping solitonic waves into one. These waves behave similar to two independent elastic particles, which do not penetrate into each other despite the special confinement by the length of chromophore π‐system. In monosubstituted polyene dication, Δq and Δl functions contain two waves each; however, only one wave is mobile and sensitive to a change of the chemical nature of the terminal group, whereas the second wave remains practically unchanged. The introduction of one oxymethyl or phenyl terminal groups leads to a relatively small shift of the mobile wave from the center to a direction of the terminal group. The effect of the amino or tropilium terminal groups is much more pronounced and leads to a shift of the mobile wave to the end of the molecule. In disubstituted polyene dication, both solitonic waves become mobile and shift symmetrically to both ends. The general principles of the charge localization described in this study may be used in molecular design and fine‐tuning of the charge transport properties in plastic photovoltaics and other organic semiconducting materials. © 2012 Wiley Periodicals, Inc.     

Residual‐based stabilization of the finite element approximation to the acoustic perturbation equations for low Mach number aeroacoustics

The acoustic perturbation equations (APE) are suitable to predict aerodynamic noise in the presence of a non‐uniform mean flow. As for any hybrid computational aeroacoustics approach, a first computational fluid dynamics simulation is carried out from which the mean flow characteristics and acoustic sources are obtained. In a second step, the APE are solved to get the acoustic pressure and particle velocity fields. However, resorting to the finite element method (FEM) for that purpose is not straightforward. Whereas mixed finite elements satisfying an appropriate inf–sup compatibility condition can be built in the case of no mean flow, that is, for the standard wave equation in mixed form, these are difficult to implement and their good performance is yet to be checked for more complex wave operators. As a consequence, strong simplifying assumptions are usually considered when solving the APE with FEM. It is possible to avoid them by resorting to stabilized formulations. In this work, a residual‐based stabilized FEM is presented for the APE at low Mach numbers, which allows one to deal with the APE convective and reaction terms in its full extent. The key of the approach resides in the design of the matrix of stabilization parameters. The performance of the formulation and the contributions of the different terms in the equations are tested for an acoustic pulse propagating in sheared‐solenoidal mean flow, and for the aeolian tone generated by flow past a two‐dimensional cylinder. Copyright © 2016 John Wiley & Sons, Ltd.     

Unsaturated hydrocarbons adsorbed on low coordinated Pd surface: A periodic DFT study

In this work, the adsorption of several unsaturated hydrocarbon molecules on a stepped Pd(4 2 2) surface was studied. Using a periodic method based on the Density Functional Theory (DFT) formalism, different adsorption geometries for ethylene, three butene isomers (cis/trans-2-butene and 1-butene), acetylene and 2-butyne were investigated. The results were compared with those obtained for a free defect surface as Pd(1 1 1). The 1-butene is more stable on the free defect surface than on Pd(4 2 2). On the stepped surface, the olefins adsorb tilted towards the step and increases, in almost all the cases, the magnitude of the adsorption energy. Conversely, the 3-fold site is the most stable for the alkynes adsorption on the stepped surface, as it was found on Pd(1 1 1). The analysis of the dipole moment change indicate a charge transfer from the double bond of the olefin to the metallic surface, being higher for the Pd(1 1 1) surface. In case of the alkynes, an important back-donation is produced. Except the alkynes and the 1-butene molecule, the results show the preference of ethylene and cis/trans-2-butene to be adsorbed on the stepped surface. These observations are related with experimental catalytic results.     

Determination of the β-Glucosidase Activity in Different Soils by Pre Capillary Enzyme Assay Using Capillary Electrophoresis with Laser-Induced Fluorescence Detection

Enzyme activities can provide indication for quantitative changes in soil organic matter (SOM). It is known that the activities of most enzymes increase as native SOM content reflecting larger microbial communities and stabilization of enzymes on humic materials. β-Gucosidase (β-Glu) activities have been frequently used as indicators of changes in quantity and quality of SOM. In this study we propose a simple and very sensitive method, which has lower limit of detection compared with classic spectrophotometric method with the aim of determinate the β-Glu activity in soil samples using Fluorescein mono-β-D-glucopyranoside (FMGlc) as a substrate. The fluorescein released by the enzymatic reaction was quantified by capillary electrophoresis-laser induced fluorescence (CE-LIF) method. The background electrolyte (BGE) consisted in 40 mM phosphate buffer, pH 6. The LOD and LOQ for fluorescein were 1.3 10⁻⁷ mg mL⁻¹ and 6.4 10⁻⁶ mg mL⁻¹, respectively. This work deals with the minimization of the mixture for the enzymatic reaction and with the optimization conditions of CE separation. To the best of our knowledge, this is the first time that an enzymatic activity was detected in soil using CE-LIF system.     

Immobilized ruthenium complexes and aspects of their reactivity

Methodologies for the immobilization and characterization of ruthenium complexes into/onto functionalized silica gel, zeolites, polymers, dendrimers, sol–gel, nano and microparticles are described. The corresponding spectroscopic, electrochemical, and photochemical properties as well as chemical reactivities are used for their characterization and study. Comparison between the reactivities of immobilized and in solution species is presented. Some biological applications are also described.     

Determination of β-glucosidase activity in soils with a bioanalytical sensor modified with multiwalled carbon nanotubes

Soil microorganisms and enzymes are the primary mediators of soil biological processes, including organic matter degradation, mineralization, and nutrient recycling. They play an important role in maintaining soil ecosystem quality and functional diversity. Moreover, enzyme activities can provide an indication of quantitative changes in soil organic matter. β-Glucosidase (β-Glu) activity has been found to be sensitive to soil management and has been proposed as a soil quality indicator because it provides an early indication of changes in organic matter status and its turnover. The aims of the present study were to test and use a simple and convenient procedure for the assay of β-Glu activity in agricultural soil. The method described here is based on the enzymatic degradation of cellobiose by β-Glu present in the soil sample and the subsequent determination of glucose produced by the enzymatic reaction using screen-printed carbon electrodes modified with multiwalled carbon nanotubes (SPCE-CNT) equipped with coimmobilized glucose oxidase and horseradish peroxidase enzymes. The potential applied to the SPCE-CNT detection was −0.15 V versus a Ag/AgCl pseudo-reference electrode. A linear calibration curve was obtained in the range 2.7–11.3 mM with a correlation coefficient. In the present study, an easy and effective SPCE-CNT-modified electrode allowed an improved amperometric response to be achieved and this is attributed to the increased surface area upon electrode modification.