ALBERT

Notes: The kinetics of interaction between proflavine and poly I.poly C at 25°C, neutral pH, and moderate ionic strength have been studied by relaxation methods. The qualitative features of this system resemble those previously reported by Crothers and co-workers for proflavine-DNA and proflavine-poly A·poly U interactions-two relaxations are observed coresponding to a fast bimolecular step followed by a slower isomerization. These results can best be accommodated by a two-step mechanism leading from the free dye through an “outside-bound” complex to the intercalated complex. Quantitative comparison of the various rate constants for proflavine binding to different double-helical polynucleotides shows that the rates are slower for both ribohomopolymer pairs than for DNA. The rates for poly I·poly C are approximately three times faster than these for poly A·poly U.

Notes: The conformational response of calf thymus DNA to solvent conditions altered by varying amounts of ethanol and NaCl has been monitored by circular dichroism (CD). These measurements, which extend over a much greater range of conditions than previously examined, reveal (above critical concentrations of ethanol and salt) a condensed form of the macro-molecule with unusually large positive ellipticity in the 250-300-nm region [the Ψ(+) state]. Mere increase in NaCl concentration at constant 35% (v/v) concentration of ethanol suffices to convert such Ψ(+) samples - via a series of intermediate forms with CD spectra resembling those of A-DNA, then B-DNA - into Ψ(-) states having anomalously large negative ellipticity similar to the well-known Ψ(-) forms produced by above-critical concentrations of poly-(ethylene oxide) and salt. These ethanol/salt-induced transitions are all completely reversible and can occur without formation of any visible precipitates. We suggest that they represent predominantly tertiary structural changes of B-form DNA molecules analogous to the changes which occur in several other systems where Ψ(+) ⇌ Ψ(-) interconversion has been reported. A “skein-of-yarn” model for the condensed tertiary (and quaternary, i.e., aggregated) state of the DNA affords one possible explanation for the inversions of ellipticity in all these cases. Such a model accords well with the accepted description of cholesteric liquid crystals.

Notes: Xanthan gum is an exopolysaccharide secreted by the bacterium Xanthamonas campestris whose ability to make solutions viscous at low concentrations and over a pH and temperature range have generated much interest in both academic and industrial environments. Mutant Xanthamonas strains have been derived that produce xanthan gums with an altered or variant subunit chemical structure and different measured viscosities when compared with the wild type (wt) form of the polymer. Two variant gums were targeted as potentially interesting in this study, these being the nonacetylated tetramer (natct; and the acetylated tetramer (atet), which both lack a side-chain terminal mannose residue and in one case (natet) lacks an acetate group on an internal mannose residue. Solutions of these tetrameric gums possess viscosities higher (natet) and lower (atet) than the wt gum, and therefore we have attempted to determine whether these molecules possess unique conformational preferences when compared with the wt and with each other. In this manner we can initiate an understanding of how a polysaccharide's conformation contributes to its solution properties.The GEGOP software permits a sampling of the static and dynamic equilibrium states of carbohydrate molecules, and this software was employed to calculate equilibrium states of representative oligosaccharides with chemical structures representative of xanthan-like molecules. Energy minimization techniques revealed similar local minima for all three molecules. Some of these minima are comprised of elongate backbone conformations (A type) in which side chains fold onto backbone surfaces. Other minima with A backbones possessed side chains in less intimate backbone contact especially when calculations were performed with a low dielectric constant. This phenomenon was particularly pronounced in the wt molecule where an increased number of negatively charged side-chain residues experience charge repulsion resulting in reduced side-chain-backbone contact.Metropolis Monte Carlo (MMC) dynamic simulations performed with an elevated temperature factor (1000 K) allowed a better qualitative representation of conformational space than 300 K simulations. Employing a nonhierarchical cluster analysis method (population density profile: PDP) coupled with a classification scheme, it was possible to partition resulting MMC data sets into conformational families. This analysis revealed that in simulations performed with different dielectric constant values (10, 25, and ∞) all molecules possessed primarily A-type backbones. Less elongate, more open helical backbone forms (B, C, D, J, and Flat-a) did occur during the simulations but were populated to a lesser extent. In the natet molecule significantly open helical backbones existed (E, F, G, H, and I) that did not occur in the lower viscosity wt and atet molecules. PDP clustering methods and subsequent conformational classification applied to the first residue (mannose) of the side chain permitted a determination of side-chain orientation. Comparison of all three molecules indicated a larger population of side-chain conformational families in less direct backbone contact for the wt molecule than either of the variant molecules (natet/atet) suggesting that the side chains in the wt are more flexible. Thus, a major conformational difference between the high viscosity natet. In addition, the significant difference between the higher viscosity wt and the lower viscosity atet is the increase side-chain flexibility in the wt. We hypothesize that conformational differences of this kind could form a partial explanation of the observed differences in viscosity between these xanthan-like polymers. © 1996 John Wiley & Sons, Inc.

Notes: Circular dichroism spectroscopy has been used to investigate the influence of DNA molecular size, base composition, and the presence of intercalating agents upon the Ψ transition of DNA brought about by high concentrations of poly(ethylene oxide) and salt (Lerman (1971) Proc. Natl. Acad. Sci. (U.S.) 68, 1886-1890). A molecular weight of 0.15-3.0 × 106 daltons yields maximum formation of Ψ-DNA. Both the amplitude of the large negative CD band at 265 nm - a chief characteristic of the Ψ state - and the thermal stability of Ψ-DNA increase linearly with increasing mole fraction of guanine plus cytosine in the DNA sample. Either ethidium or proflavine, at concentrations where approximately one dye is bound per 5-10 nucleotide residues, can prevent the transition completely. Striking similarities between the Ψ-DNA produced by poly(ethylene oxide) + salt and the complexes formed between DNA and lysine-rich histone f1 suggest the presence of similar nucleic acid-nucleic acid interactions in both types of condensed phase.

Notes: Parametric sensitivity of a two-dimensional pulverized-fuel (PF) combustion model is studied extensively for the effect of parametric uncertainty on model predictions. Results show that error in coal devolatilization/oxidation parameters has the dominant effect on predicted burnout, NOx formation, local gas temperature, and coal-gas mixture fraction. Uncertainty in the turbulent particle dispersion parameters appears to have a secondary effect, while error in the particle-gas radiation parameters has little impact on model predictions. Regions of the computational domain exhibiting sensitivity to specific parameters are identified. Specific parameter sensitivity implies the relative importance of various mechanisms in the overall process. Turbulent particle dispersion seems to be important early in the reactor with kinetic processes dominating at and following the predicted ignition point. Radiation appears to be of minor importance. These results indicate the need for a better method of predicting the overall volatiles yield and further understanding of the devolatilization/oxidation mechanism and its role in the overall PF combustion process. The study provides fundamental direction for future comprehensive model development and focuses on experimental work to better quantify critical input parameters.

Notes: A simple and low-cost poultry waste digester (PWD) was constructed to treat the waste from 4000 caged laying hens on University Research Unit No. 2 at North Carolina State University. The system was built basically of a plastic lining with insulation, a heating system, a hot-water tank, and other metering equipment. It was operated at 50°C and pH 7.5-8.0. The initiation of methane production was achieved using the indigenous microflora in the poultry waste. At an optimal loading rate (7.5 kg volatile solids/m3 day), the PWD produced biogas (55% methane) at a rate of 4.0 m3/m3 day. The PWD was biologically stable and able to tolerate temporary overloads and shutdowns. A higher loading rate failed to maintain a high gas production rate and caused drops in methane content and pH value. Under optimal conditions, a positive energy balance was demonstrated with a net surplus of 50.6% of the gross energy. For methane production, the PWD system was proved to be technically feasible. The simple design and inexpensive materials used for this model could significantly reduce the cost of digestion compared to more conventional systems. More studies are needed to determine the durability, the required maintenance of the system, and the most economical method of biogas and solid residue utilization.

Notes: The von Karman analogy between heat transfer and momentum transfer in turbulent fluids is shown to apply to heat transfer through wavy liquid films in horizontal, stratified, gas-liquid flow. Nusselt numbers predicted from the analogy are shown to be in good agreement with experimental data for air-water flows involving three-dimensional wavy films and large-amplitude roll waves. The Nusselt numbers encountered with these turbulent water films are found to be in the same range as those associated with condensation of organics in horizontal tubes under stratified flow conditions.

Notes: A tandem reflectron time-of-flight mass spectrometer has been constructed for the investigation of laser photofragmentation of selected molecular ions. Ions are generated by an ablation laser and attracted by ion optics into the field-free flight region of a reflectron time-of-flight mass spectrometer. Laser photofragmentation of selected molecular ions takes place at the turn-around point of ions in the reflectron. Fragmentation mass calibration, parent ion selection, ion collection effects, reflectron field effects and the mass resolution of this tandem reflectron time-of-flight mass spectrometer are described. Furthermore it is shown that laser parameters may be used to control the fragmentation pattern.