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.     

Sodium periodate as a primary oxidant for water-oxidation catalysts

Sodium periodate was characterized as a primary chemical oxidant for the catalytic evolution of oxygen at neutral pH using a variety of water-oxidation catalysts. The visible spectra of solutions formed from Cp*Ir(bpy)SO(4) during oxygen-evolution catalysis were measured. NMR spectroscopy suggests that the catalyst remains molecular after several turnovers with sodium periodate. Two of our [Cp*Ir(bis-NHC)][PF(6)](2) complexes, along with other literature catalysts, such as the manganese terpyridyl dimer, Hill's cobalt polyoxometallate, and Meyer's blue dimer, were also tested for activity. Sodium periodate was found to function only for water-oxidation catalysts with low overpotentials. This specificity is attributed to the relatively low oxidizing capability of sodium periodate solutions relative to solutions of other common primary oxidants. Studying oxygen-evolution catalysis by using sodium periodate as a primary oxidant may, therefore, provide preliminary evidence that a given catalyst has a low overpotential.     

Structure and diffusion of nanoparticle monolayers floating at liquid/vapor interfaces: a molecular dynamics study

Large-scale molecular dynamics simulations are used to simulate a layer of nanoparticles floating on the surface of a liquid. Both a low viscosity liquid, represented by Lennard-Jones monomers, and a high viscosity liquid, represented by linear homopolymers, are studied. The organization and diffusion of the nanoparticles are analyzed as the nanoparticle density and the contact angle between the nanoparticles and liquid are varied. When the interaction between the nanoparticles and liquid is reduced the contact angle increases and the nanoparticles ride higher on the liquid surface, which enables them to diffuse faster. In this case the short-range order is also reduced as seen in the pair correlation function. For the polymeric liquids, the out-of-layer fluctuation is suppressed and the short-range order is slightly enhanced. However, the diffusion becomes much slower and the mean square displacement even shows sub-linear time dependence at large times. The relation between diffusion coefficient and viscosity is found to deviate from that in bulk diffusion. Results are compared to simulations of the identical nanoparticles in 2-dimensions.     

Evaporation of Lennard-Jones fluids

Evaporation and condensation at a liquid/vapor interface are ubiquitous interphase mass and energy transfer phenomena that are still not well understood. We have carried out large scale molecular dynamics simulations of Lennard-Jones (LJ) fluids composed of monomers, dimers, or trimers to investigate these processes with molecular detail. For LJ monomers in contact with a vacuum, the evaporation rate is found to be very high with significant evaporative cooling and an accompanying density gradient in the liquid domain near the liquid/vapor interface. Increasing the chain length to just dimers significantly reduces the evaporation rate. We confirm that mechanical equilibrium plays a key role in determining the evaporation rate and the density and temperature profiles across the liquid/vapor interface. The velocity distributions of evaporated molecules and the evaporation and condensation coefficients are measured and compared to the predictions of an existing model based on kinetic theory of gases. Our results indicate that for both monatomic and polyatomic molecules, the evaporation and condensation coefficients are equal when systems are not far from equilibrium and smaller than one, and decrease with increasing temperature. For the same reduced temperature T/T(c), where T(c) is the critical temperature, these two coefficients are higher for LJ dimers and trimers than for monomers, in contrast to the traditional viewpoint that they are close to unity for monatomic molecules and decrease for polyatomic molecules. Furthermore, data for the two coefficients collapse onto a master curve when plotted against a translational length ratio between the liquid and vapor phase.     

Synthetic training sets for the development of discriminant functions for the detection of volatile organic compounds from passive infrared remote sensing data

A novel synthetic data generation methodology is described for use in the development of pattern recognition classifiers that are employed for the automated detection of volatile organic compounds (VOCs) during infrared remote sensing measurements. The approach used is passive Fourier transform infrared spectrometry implemented in a downward-looking mode on an aircraft platform. A key issue in developing this methodology in practice is the need for example data that can be used to train the classifiers. To replace the time-consuming and costly collection of training data in the field, this work implements a strategy for taking laboratory analyte spectra and superimposing them on background spectra collected from the air. The resulting synthetic spectra can be used to train the classifiers. This methodology is tested by developing classifiers for ethanol and methanol, two prevalent VOCs in wide industrial use. The classifiers are successfully tested with data collected from the aircraft during controlled releases of ethanol and during a methanol release from an industrial facility. For both ethanol and methanol, missed detections in the aircraft data are in the range of 4 to 5%, with false positive detections ranging from 0.1 to 0.3%.     

Cross-coupling of mesylated phenol derivatives with potassium alkoxymethyltrifluoroborates

Cross-coupling of mesylated phenol derivatives with various potassium alkoxymethyltrifluoroborates has been achieved. The corresponding aryl and heteroaryl alkoxymethyl compounds have been obtained with equal facility with both electron-rich and electron-poor substituents on the activated alcohol.     

Rapid determination of 226Ra in drinking water samples using dispersive liquid-liquid microextraction coupled with liquid scintillation counting

A new radioanalytical method was developed for rapid determination of ²²⁶Ra in drinking water samples. The method is based on extraction and preconcentration of ²²⁶Ra from a water sample to an organic solvent using a dispersive liquid-liquid microextraction (DLLME) technique followed by radiometric measurement using liquid scintillation counting. In DLLME for ²²⁶Ra, a mixture of an organic extractant (toluene doped with dibenzo-21-crown-7 and 2-theonyltrifluoroacetone) and a disperser solvent (acetonitrile) is rapidly injected into the water sample resulting in the formation of an emulsion. Within the emulsion, ²²⁶Ra reacts with dibenzo-21-crown-7 and 2-theonyltrifluoroacetone and partitions into the fine droplets of toluene. The water/toluene phases were separated by addition of acetonitrile as a de-emulsifier solvent. The toluene phase containing ²²⁶Ra was then measured by liquid scintillation counting. Several parameters were studied to optimize the extraction efficiency of ²²⁶Ra, including water immiscible organic solvent, disperser and de-emulsifier solvent type and their volume, chelating ligands for ²²⁶Ra and their concentrations, inorganic salt additive and its concentration, and equilibrium pH. With the optimized DLLME conditions, the accuracy (expressed as relative bias, B _r ) and method repeatability (expressed as relative precision, S _B ) were determined by spiking ²²⁶Ra at the maximum acceptable concentration level (0.5 Bq L⁻¹) according to the Guidelines for Canadian Drinking Water Quality. Accuracy and repeatability were found to be less than −5% (B _r ) and less than 6% (S _B ), respectively, for both tap water and bottled natural spring water samples. The minimum detectable activity and sample turnaround time for determination of ²²⁶Ra was 33 mBq L⁻¹ and less than 3 h, respectively. The DLLME technique is selective for extraction of ²²⁶Ra from its decay progenies.     

Purification and Characterisation of a Thermostable β-Xylosidase from <Emphasis Type="Italic">Aspergillus niger</Emphasis> van Tieghem of Potential Application in Lignocellulosic Bioethanol Production

A locally isolated strain of Aspergillus niger van Tieghem was found to produce thermostable β-xylosidase activity. The enzyme was purified by cation and anion exchange and hydrophobic interaction chromatography. Maximum activity was observed at 70–75 °C and pH 4.5. The enzyme was found to be thermostable retaining 91 and 87% of its original activity after incubation for 72 h at 60 and 65 °C, respectively, with 52% residual activity detected after 18 h at 70 °C. Available data indicates that the purified β-xylosidase is more thermostable over industrially relevant prolonged periods at high temperature than those reported from other A. niger strains. Maximum activity was observed on p-nitrophenyl-β-d-xylopyranoside and the enzyme also hydrolysed p-nitrophenyl β-d-glucopyranoside and p-nitrophenyl α-l-arabinofuranoside. The purified enzyme acted synergistically with A. niger endo-1,4-β-xylanase in the hydrolysis of beechwood xylan at 65 °C. During hydrolysis of pretreated straw lignocellulose at 70 °C using a commercial lignocellulosic enzyme cocktail, inclusion of the purified enzyme resulted in a 19-fold increase in the amount of xylose produced after 6 h. The results observed indicate potential suitability for industrial application in the production of lignocellulosic bioethanol where thermostable β-xylosidase activity is of growing interest to maximise the enzymatic hydrolysis of lignocellulose.     

Using LR-HSQMBC to observe long-range H–N correlations

The recently reported LR-HSQMBC experiment has been optimized for ¹H–¹⁵N long-range heteronuclear couplings. Several previously unreported four-bond correlations, consistent with the predicted by DFT calculations (0.2–0.3 Hz ⁴J_NH couplings), have been observed for strychnine using 2 Hz optimization of the LR-HSQMBC experiment. This experiment offers an advantage over accordion-optimized experiments such as IMPEACH and CIGAR for the observation of long-range ¹H–¹⁵N correlations in that the experiment is refocused and employs a CLIP pulse sequence element to bring the long-range correlations into phase, allowing broadband X-decoupling to be employed during acquisition.     

Allylic amidation. An investigation of nitrosocarbonylmethane for direct allylic functionalization of olefins

Nitrosocarbonylmethane reacts with a variety of olefins $\text{via}$ an ene pathway, yielding N-substituted hydroxamic acid products in a preparatively useful reaction. With unsymmetrical olefins, observed regiochemical preferences can be rationalized by a mechanism involving electrophilic addition of nitrogen to the olefin.