Crystallization of Arthrobacter sp. strain 1C N-(1-D-carboxyethyl)-L-norvaline dehydrogenase and its complex with NAD+

The novel NAD+-linked opine dehydrogenase from a soil isolate Arthrobacter sp. strain 1C belongs to an enzyme superfamily whose members exhibit quite diverse substrate specificites. Crystals of this opine dehydrogenase, obtained in the presence or absence of co-factor and substrates, have been shown to diffract to beyond 1.8 ? resolution. X-ray precession photographs have established that the crystals belong to space group P21212, with cell parameters a = 104.9, b = 80.0, c = 45.5 ? and a single subunit in the asymmetric unit. The elucidation of the three-dimensional structure of this enzyme will provide a structural framework for this novel class of dehydrogenases to enable a comparison to be made with other enzyme families and also as the basis for mutagenesis experiments directed towards the production of natural and synthetic opine-type compounds containing two chiral centres.     

The effects of triangle inequality on the vehicle routing problem

Routing problems often utilize experimental networks to represent real world scenarios. However most ignore the inclusion of triangle inequality violations, a phenomenon resulting from delays or rounding errors within a network. This work evaluates the effect of both frequency – the number of violations – and severity – the degree of intensity of a violation – of triangle inequality and evaluates both solution quality and solution time based on Simulated Annealing, Ant Colony Optimization and Savings Algorithm methods. Findings indicate that while both frequency and severity degrade solution quality, increased levels of frequency and severity together result in significant adverse affects to solution quality. Solution time, however, is not impacted by the presence of triangle inequality violations within the network. This information should encourage practitioners to identify delays and maintain the presence of triangle inequality violations in a network to ensure accuracy of solution quality.     

A lab-on-chip for biothreat detection using single-molecule DNA mapping

Rapid, specific, and sensitive detection of airborne bacteria, viruses, and toxins is critical for biodefense, yet the diverse nature of the threats poses a challenge for integrated surveillance, as each class of pathogens typically requires different detection strategies. Here, we present a laboratory-on-a-chip microfluidic device (LOC-DLA) that integrates two unique assays for the detection of airborne pathogens: direct linear analysis (DLA) with unsurpassed specificity for bacterial threats and Digital DNA for toxins and viruses. The LOC-DLA device also prepares samples for analysis, incorporating upstream functions for concentrating and fractionating DNA. Both DLA and Digital DNA assays are single molecule detection technologies, therefore the assay sensitivities depend on the throughput of individual molecules. The microfluidic device and its accompanying operation protocols have been heavily optimized to maximize throughput and minimize the loss of analyzable DNA. We present here the design and operation of the LOC-DLA device, demonstrate multiplex detection of rare bacterial targets in the presence of 100-fold excess complex bacterial mixture, and demonstrate detection of picogram quantities of botulinum toxoid.     

Identification and correction of spectral contamination in 2H/1H and 18O/16O measured in leaf, stem, and soil water

Plant water extracts typically contain organic materials that may cause spectral interference when using isotope ratio infrared spectroscopy (IRIS), resulting in errors in the measured isotope ratios. Manufacturers of IRIS instruments have developed post-processing software to identify the degree of contamination in water samples, and potentially correct the isotope ratios of water with known contaminants. Here, the correction method proposed by an IRIS manufacturer, Los Gatos Research, Inc., was employed and the results were compared with those obtained from isotope ratio mass spectrometry (IRMS). Deionized water was spiked with methanol and ethanol to create correction curves for δ(18)O and δ(2)H. The contamination effects of different sample types (leaf, stem, soil) and different species from agricultural fields, grasslands, and forests were compared. The average corrections in leaf samples ranged from 0.35 to 15.73‰ for δ(2)H and 0.28 to 9.27‰ for δ(18)O. The average corrections in stem samples ranged from 1.17 to 13.70‰ for δ(2)H and 0.47 to 7.97‰ for δ(18)O. There was no contamination observed in soil water. Cleaning plant samples with activated charcoal had minimal effects on the degree of spectral contamination, reducing the corrections, by on average, 0.44‰ for δ(2)H and 0.25‰ for δ(18)O. The correction method eliminated the discrepancies between IRMS and IRIS for δ(18)O, and greatly reduced the discrepancies for δ(2)H. The mean differences in isotope ratios between IRMS and the corrected IRIS method were 0.18‰ for δ(18)O, and -3.39‰ for δ(2)H. The inability to create an ethanol correction curve for δ(2)H probably caused the larger discrepancies. We conclude that ethanol and methanol are the primary compounds causing interference in IRIS analyzers, and that each individual analyzer will probably require customized correction curves.     

Thermo-mechanical response of tension panels under intense rapid heating

The temperature dependence of the fracture strength of 7075-T6 aluminum alloy was determined under rapid heating (0.02–.50 sec) conditions by exposing thin-section specimens to intense surface irradiation while under constant tensile load. When combined with a numerical thermal analysis and an appropriate limit analysis, these data enabled accurate prediction of the heating time required to produce ductile fracture in spot irradiated tension panels. The transient heat transfer model employed in the computations incorporated material removal due to melting, temperature-dependent material properties, and convection/radiation losses.     

Model study of electron beam charge compensation for positive secondary ion mass spectrometry using a positive primary ion beam

A new modeling approach has been developed to assist in the SIMS analysis of insulating samples. This approach provides information on the charging phenomena occurring when electron and positive primary ion beams impact a low conductivity material held at a high positive potential. The concept of effective leakage resistance aids in the understanding of the dynamic electrical properties of an insulating sample under dynamic analysis conditions. Modeling of steady state electron beam charge compensation involves investigation of electron injection and charge drift. Using a Monte Carlo program to simulate electron injection and dc conduction calculations to predict charge drift, detailed information regarding charging phenomena can be determined.