Pyrinomonas methylaliphatogenes gen. nov., sp. nov., a novel group 4 thermophilic member of the phylum Acidobacteria from geothermal soils.

An aerobic, thermophilic, moderately acidophilic non-spore-forming bacterium, strain K22(T), was isolated from geothermally heated soil at Mount Ngauruhoe, New Zealand. On the basis of 16S rRNA gene sequence similarity, K22(T) was shown to belong to subdivision 4 of the phylum Acidobacteria and to be most closely related to 'Candidatus Chloracidobacterium thermophilum' (86 %) and Blastocatella fastidiosa (86 %). Cells stained Gram-negative and were catalase and oxidase-positive. The major fatty acids detected were iso-C15 : 0, iso-C17 : 0, iso-C19 : 0 and iso-C21 : 0 when standard lipid extraction protocols were employed. Analysis of the total cell lipid acid hydrolysate also detected membrane-spanning and ether lipids, which made up approximately 40 % of the total membrane composition. These lipids included dicarboxylic (iso-diabolic) acid and the glyceryl ether of alkyl analogues of iso-C15 : 0 and iso-diabolic acid. The G+C content of the genomic DNA was 59.6 mol% and the primary respiratory quinone was MK-8. Strain K22(T) grew at 50-69 °C with an optimum temperature of 65 °C and at pH 4.1-7.8 with an optimum growth pH of 6.5. NaCl tolerance was up to 1 % (w/v). Cells displayed a chemoheterotrophic and obligately aerobic metabolism. Cells grew on nutrient broth, alginate, arabinose, Casamino acids, glucose, lactate, formate, mannose, sodium alginate, peptone, sucrose, tryptone, xanthan, xylan, xylose and yeast extract. Nitrogen sources included nitrate, ammonium, urea, yeast extract and Casamino acids, but not dinitrogen gas. The distinct phylogenetic position and the phenotypic characteristics separate strain K22(T) from all other members of the class Acidobacteria and indicate that it represents a novel species and genus, for which the name Pyrinomonas methylaliphatogenes gen. nov., sp. nov. is proposed. The type strain of the type species is K22(T) ( = DSM 25857(T) = ICMP 18710(T)).

Multi-contrast light profile microscopy for the depth-resolved imaging of the properties of multi-ply thin films.

Light profile microscopy (LPM) is a direct method for the spectral depth imaging of thin film cross-sections on the micrometer scale. LPM uses a perpendicular viewing configuration that directly images a source beam propagated through a thin film. Images are formed in dark field contrast, which is highly sensitive to subtle interfacial structures that are invisible to reference methods. The independent focusing of illumination and imaging systems allows multiple registered optical sources to be hosted on a single platform. These features make LPM a powerful multi-contrast (MC) imaging technique, demonstrated in this work with six modes of imaging in a single instrument, based on (1) broad-band elastic scatter; (2) laser excited wideband luminescence; (3) coherent elastic scatter; (4) Raman scatter (three channels with RGB illumination); (5) wavelength resolved luminescence; and (6) spectral broadband scatter, resolved in immediate succession. MC-LPM integrates Raman images with a wider optical and morphological picture of the sample than prior art microprobes. Currently, MC-LPM resolves images at an effective spectral resolution better than 9 cm(-1), at a spatial resolution approaching 1 microm, with optics that operate in air at half the maximum numerical aperture of the prior art microprobes.

Light profile microscopy based on Raman and wavelength resolved luminescence contrast.

Light profile microscopy based on contrast from wavelength resolved Raman and luminescence measurements is demonstrated experimentally for the first time. A Raman/multispectral light profile microscope (RMSLPM) has been constructed based on a line profiling geometry in which the sample is irradiated with a tightly focused laser beam (of ten micrometers radius or less) behind a polished view surface and the resulting line image is dispersed over the wavelength using an imaging spectrograph. The instrumentation developed in this laboratory has a spectral resolution approaching 10 cm(-1) and an (actual) depth independent spatial resolution of 6-8 times the Rayleigh diffraction limit, limited at present by optical aberrations and alignment. The technique has the potential to image at approximately twice the Rayleigh diffraction limit. The spectral signatures reconstructed from a variety of common industrial polymers show excellent agreement with reference spectra from the literature, and may be used to identify individual layers in depth images of unknown materials. RMS-LPM image data based on luminescence contrast have also been used to provide concentration depth profiles of additives and degradation products in injection molded samples of high-density poly(ethylene) (HDPE).

Depth profiling of the optical absorption coefficient in ultraviolet-degraded poly(vinylchloride) films by dual beam light profile microscopy.

Dual beam laser light profile microscopy (LPM) was applied in this work to the depth mapping of the optical absorption coefficient in photo-degraded poly(vinyl chloride) films. Depth profiles followed the absorption coefficient of a conjugated polyene photoproduct at visible wavelengths in photolyzed films of approximately 200 mum thickness. Both continuous and layered (separable laminate) films were studied. The absorption coefficient profiles reconstructed from photo-degraded thin films showed the classic concentration profiles seen in the literature for PVC degraded in the presence of oxygen and nitrogen atmospheres. In the case of single thin layers with continuous properties, the depth profiles were smooth and regular with minimum spatial noise. In the LPM of laminate structures, more optical anomalies were present because of the multiply interfacial structures that appeared in both the images and the reconstructed depth profiles. Notwithstanding, it was possible to profile the optical absorption coefficient at a level of error comparable to standard microtome methods. The latter was determined by comparing the LPM results to a destructive layer-by-layer analysis performed in parallel on the imaged materials. The dual beam LPM method should be generally useful for establishing polyene concentration profiles in industrial materials produced by photochemical, thermal, and chemical degradation mechanisms.

Broadband light profile microscopy: a rapid and direct method for thin film depth imaging.

Light profile microscopy (LPM) is a recently developed technique of optical inspection that is used to record micrometer scale images of thin film cross-sections on a direct basis. This technique uses a novel right-angle imaging geometry that shows outstanding contrast for subtle interface structures and morphologies that are invisible to conventional methods of inspection. When laser sources are used for sample illumination, image contrast is provided by luminescence and elastic and/or inelastic scatter. When a white-light excitation source is used for LPM, primary contrast is obtained from elastic scatter, while secondary contrast results from refraction, secondary transmission, and secondary reflection from material phases. We term this mode of inspection broadband light profile microscopy (BB-LPM). It is implemented with a compact, easily aligned apparatus and minimal sample preparation, and it shows outstanding interface contrast similar to laser LPM. In this work we demonstrate BB-LPM as a method for direct imaging of the layers structures of a variety of thin film samples of industrial and manufacturing interest.

Dual beam light profile microscopy: a new technique for optical absorption depth profilometry.

Light profile microscopy (LPM) is a recently developed technique of optical inspection that is used to record micrometer-scale images of thin-film cross-sections on a direct basis. In single beam mode, LPM provides image contrast based on luminescence, elastic, and/or inelastic scatter. However, LPM may also be used to depth profile the optical absorption coefficient of a thin film based on a method of dual beam irradiation presented in this work. The method uses a pair of collimated laser beams to consecutively irradiate a film from two opposing directions along the depth axis. An average profile of the beam's light intensity variation through the material is recovered for each direction and used to compute a depth-dependent differential absorbance profile. This latter quantity is shown from theory to be related to the film's depth-dependent optical absorption coefficient through a simple linear model that may be inverted by standard methods of numerical linear algebra. The inverse problem is relatively well posed, showing good immunity to data errors. This profilometry method is experimentally applied to a set of well-characterized materials with known absorption properties over a scale of tens of micrometers, and the reconstructed absorption profiles were found to be highly consistent with the reference data.

Electrochemical evidence of H' produced by ultrasound.

Electrochemical evidence of H. produced by cavitation as the result of ultrasonic irradiation of an aqueous solution is presented.

Managing farming systems for nitrate control: a research review from management systems evaluation areas.

The U.S. Department of Agriculture funded the Management Systems Evaluation Area (MSEA) research project in 1990 to evaluate effectiveness of present farming systems in controlling nitrate N in water resources and to develop improved technologies for farming systems. This paper summarizes published research results of a five-year effort. Most research is focused on evaluating the effectiveness of farming system components (fertilizer, tillage, water control, cropping systems, and soil and weather variability). The research results show that current soil nitrate tests reliably predict fertilizer N needed to control environmental and economic risks for crop production. A corn (Zea mays L.)-soybean [Glycine max (L.) Merr.] rotation usually controls risk better than continuous corn, but both may result in unacceptable nitrate leaching. Reduced tillage, especially ridge-till, is better than clean tillage in reducing risk. Tile drainage controls nitrate in ground water, but discharge may increase nitrate in surface waters. Sprinkler irrigation systems provide better water control than furrow irrigation because quantity and spatial variability of applied water is reduced. Present farming systems have two major deficiencies: (i) entire fields are managed uniformly, ignoring inherent soil variability within a field; and (ii) N fertilizer rates and many field practices are selected assuming normal weather for the coming season. Both deficiencies can contribute to nitrate leaching in parts of most fields.

Modelling baculovirus infection of insect cells in culture.

CONCLUSIONS: Infection of insect cells with baculovirus is a potentially attractive means for producing both viral insecticides and recombinant proteins. The continuation of mathematical modelling studies such as those reviewed in this paper are essential in order to realise the full potential of the system. Through mathematical models it is possible to predict complex behaviours such as those observed when infecting cells at low MOI or when propagating virus in a continuous culture system. A purely empirical analysis of the same phenomena is very difficult if not impossible.The present three models are - despite their complexity and the effort that has gone into developing them - all first generation models. They summarise, to a large extent, our present quantitative understanding of the interaction between baculovirus and insect cells, when looked upon as a black box system. The binding and initial infection processes are still quantitatively poorly understood and further work in this area is much needed. On the longer term, a second generation of models is likely to consider interior processes such as viral DNA and RNA accumulation in much more detail using a structured model of the infection cycle.

The kinetics of baculovirus adsorption to insect cells in suspension culture.

The influence of various culture parameters on the attachment of a recombinant baculovirus to suspended insect cells was examined under normal culture conditions. These parameters included cell density, multiplicity of infection, and composition of the cell growth medium. It was found that the fractional rate of virus attachment was independent of the multiplicity of infection but dependent on the cell density. A first order mathematical model was used to simulate the adsorption kinetics and predict the efficiency of virus attachment under the various culture conditions. This calculated efficiency of virus attachment was observed to decrease at high cell densities, which was attributed to cell clumping. It was also observed that virus attachment was more efficient in Sf900II serum free medium than it was in IPL-41 serum-supplemented medium. This effect was attributed to the protein in serum which may coat the cells and so inhibit adsorption. A general discussion relating the observations made in-these experiments to the kinetics of recombinant baculovirus adsorption to suspended insect cells is presented.

Modeling and optimization of the baculovirus expression vector system in batch suspension culture.

A mathematical model has been developed that predicts the cell population dynamics and production of recombinant protein and infective extracellular virus progeny by insect cells after infection with baculovirus in batch suspension culture. Infection in the model is based on the rate of virus attachment to suspended insect cells under culture conditions. The model links the events following infection with the sequence of gene expression in the baculovirus replicative cycle. Substrate depletion is used to account for the decrease in product yield observed when infecting at high cell densities. Model parameters were determined in shaker flasks for two media: serum-supplemented IPL-41 medium and serum free Sf900II medium. There was good agreement between model predictions and the results from an independent series of experiments performed to validate the mode. The model predicted: (1) the optimal time of infection at high multiplicity of infection: (2) the timing and magnitude of recombinant protein production in a 2-L bioreactor; and (3) the timing and magnitude of recombinant protein production at multiplicities of infection from 0.01 to 100 plaque-forming units per cell. Through its ability to predict optimal infection strategies in batch suspension culture, the model has use in the design and optimization of large-scale systems for the production of recombinant products using the baculovirus expression vector system.

Pulsed mode thermal lens effect detection in the near field via thermally induced probe beam spatial phase modulation: a theory.

A Fresnel diffraction model for dual beam pulsed mode laser thermal lens effect detection is described. The model accommodates the effects of aberrations in the lens element introduced by departures in the sample's thermally induced refractive index profile from the ideal parabolic approximation. The model also accommodates probe and irradiation beams of arbitrary complex radius at the sample, and permits the computation of probe beam intensity profiles observed at arbitrary cell-detector distances. The theoretical basis for a new method of thermal lens effect detection is demonstrated in which the radial dimensions of the lens element are much smaller than the probe beam. Detection of the thermal blooming effect is achieved by a Fourier transform method which uses spatial frequency domain detection to measure thermally induced departures in the probe beam's intensity profile from the TEM(0,0) Gaussian mode structure, as the lens element forms. This strategy, combined with near field detection predicts a sensitivity enhancement by a factor of 60 relative to the conventional far field beam center measurement.

Frequency modulation time delay thermal lens effect spectrometry: a new technique of transient photothermal calorimetry.

A new type of laser-induced thermal lens effect measurement is demonstrated in which the thermooptic impulse response of a weakly absorbing sample is recovered in the time delay domain through excitation with a fast linear frequency sweep. The autocorrelation function of the excitation sweep approximates to a Dirac delta function to a time resolution limited by the modulation bandwidth of the sweep, thereby permitting the fast recovery of high quality frequency and impulse response information. Impulse response data recovered in the time delay domain showed good agreement with the results predicted from Fresnel diffraction theory, indicating an equivalence to the response recovered in a typical pulsed measurement. The FM time delay technique, however provides enhanced measurement dynamic range and an overall reduced peak excitation power when compared with the pulsed measurement.

Frequency-modulated impulse response photothermal detection through optical reflectance. 1: Theory.

The 3-D theory of impulse response photothermal detection in opaque (i.e., photothermally saturated) solids through the dependence of the surface temperature optical reflectance on the mathematical equivalent of an optical impulse (the Green's function) is presented. The theory is extended to include the effects of the finite spatial extent of the photothermal laser source. Explicit expressions for the time-dependent temperature field have been obtained in the experimentally important cases of semi-infinite solids and solids of finite thickness in contact with thermally insulating or conducting backings.

Frequency-modulated impulse response photothermal detection through optical reflectance. 2: Experimental.

A fast thermoreflectance impulse response photothermal imager was assembled and tested with several solid materials [quartz, stainless steel, and polyvinylidene difluoride (PVDF)I. The instrument was found to yield quantitative data in agreement with Green's function theoretical models of time domain heat conduction. The FM chirp laser intensity modulation technique used in these experiments gave wide bandwidth photothermal signals and was found to be only limited by the FFT instrumentation frequency response (100 kHz). Thermal diffusivities were calculated, while thermal lensing and thermoelastic effects were further observed. The imager was thus shown to be capable of replacing pulsed laser devices for truly nondestructive applications with materials with low damage threshold to optical pulses.

Nitrification in paleocene shale.

Exchangeable ammonium nitrogen is present in Paleocene (Fort Union) shale below a depth of 10 meters in North Dakota and eastern Montana. Above 10 meters, exchangeable ammonium nitrogen is nitrified in situ. The lack of viable nitrifying organisms and the probable lack of oxygen prevent in situ nitrification below 10 meters. Shale samples incubated at 27 degrees C under nonsterile conditions or shales exposed to atmospheric contamination exhibited active nitrification without additional treatment.