Bayesian Nonparametric Modeling for Comparison of Single-Neuron Firing Intensities

Summary .  We propose a fully inferential model-based approach to the problem of comparing the firing patterns of a neuron recorded under two distinct experimental conditions. The methodology is based on nonhomogeneous Poisson process models for the firing times of each condition with flexible nonparametric mixture prior models for the corresponding intensity functions. We demonstrate posterior inferences from a global analysis, which may be used to compare the two conditions over the entire experimental time window, as well as from a pointwise analysis at selected time points to detect local deviations of firing patterns from one condition to another. We apply our method on two neurons recorded from the primary motor cortex area of a monkey's brain while performing a sequence of reaching tasks.     

THE COMBINED EFFECTS OF LOW TEMPERATURE AND SO2+NO2 POLLUTION ON THE NEW SEASON'S GROWTH AND WATER RELATIONS OF PICEA SITCHENSIS

Picea sitchensis (Bong.) Carr. seedlings were exposed to SO₂, NO₂ and SO₂+ NO₂ during dormancy in controlled environments, and were taken to night temperatures of 4, 0, −5, −10 and −15 °C in a freezer. Conditions in the freezer were carefully monitored during the low–temperature treatments. In two experiments, different photoenvironments and temperature regimes were imposed prior to the cold treatments, and different effects were observed. In the first, only limited frost hardiness was achieved and night temperatures of −15 °C were lethal. Temperatures of −5 and − 10 °C led to poor survival of lateral buds, particularly in plants exposed to 45 ppb SO₂. The poor bud break in plants exposed to SO₂ and to − 5 °C resulted in a loss of the effectiveness of this temperature as a chill requirement. Pressure-volume analysis showed that the shoots of plants exposed to NO₂ had greater elasticity (lower elastic moduli, e), so that loss of turgor occurred at lower relative water contents. In contrast, a hardening period (2 weeks in night/day temperatures of 3/10 °C and 8 h days at 50 μmol m⁻² s⁻¹ PAR) gave decreased elasticity and lower solute potentials of spruce shoots. In the second experiment, exposure to 30 ppb SO₂ and SO₂+ NO₂ led to slight, but consistent, increases in frost injury to the needles of plants frozen to − 5 and − 10 °C. The results suggest that the main interaction of low temperatures and winter pollutants may be on bud survival rather than on needle damage, but that effects are subtle, only occurring with certain combinations of pollutant dose and cold treatment.     

Direct evidence for Ca++-induced lateral phase separation in black membranes of lipid mixtures by the analysis of gramicidin A single-channels

Single-channel conductance fluctuations are analysed for gramicidin A incorporated into binary-mixed black lipid membranes of charged phosphatidic acid and neutral lecithin in different molar ratios. At very low Ca⁺⁺ concentrations in the electrolyte (i.e. in the presence of EDTA) homogeneous lipid mixtures are identified through their conductance and life time probability distributions for integral gramicidin pores. As for the pure lipid components, the conductance histograms each show a single maximum with regular width and for all channels a single mean lifetime is found.For Ca⁺⁺-levels (10^-6–10^-5 M) that are close to the critical demixing concentration (10^-4 M) unusually broad conductance distributions and reduced lifetimes are found provided the PC content, x, of the membrane is close to the critical mixture (x _crit0.5). We interpret this as a first example of the coupling of a membrane function (the transport of ions) to a lipid matrix with locally fluctuating composition close to a critical demixing point.For the conductance histogram of gramicidin A in an equimolar mixture of PA and PC shows two well-separated maxima. A correlation analysis between conductance and lifetime of the single pores shows that the two channel populations also differ significantly in their mean channel lifetime, ^*. This finding is interpreted as being direct evidence for Ca⁺⁺-induced lateral phase separation in black lipid membranes, as has been postulated recently.Abbreviations used HEPES N-2-hydroxyethyl-piperazine-N-2-ethane-sulfonic acid - EDTA ethylenediaminetetraacetic acid     

Nitrogen fertilization effects on dinitrogen fixation as influenced by legume species and proportion in legume-grass mixtures in Uruguay

Grasses grown in mixture with nodulated legumes often are N-limited, but N fertilization may result in reductions of N₂ fixation and legume stands. We studied N-fertilizer effects on N₂ fixation for three binary legume-grass mixtures in Uruguay. Replicated swards of white clover (Trifolium repens L.) (WC), red clover (Trifolium pratense L.) (RC), or birdsfoot trefoil (Lotus corniculatus L.) (BT), each in combination with tall fescue (Festuca arundinacea Schreb) (TF) at two legume proportions were sown in 1983 (Exp. 1) and 1984 (Exp. 2). In the fall of 1984, N treatments at 100 kg ha⁻¹ and controls were randomly assigned to subplots in Exp. 1 (established swards) and in Exp. 2 (at seeding). The soil for both experiments was a fine, montmorillonitic, mesic, Typic Argiudolls. Herbage fixed-N was estimated by ¹⁵N isotope-dilution with pure stands of TF as reference. In both experiments, N fertilization reduced the proportion of legume N derived from air (% Ndfa) and increased herbage yield only during the first 18 to 20 weeks after application. Fertilizer-N reduced annual fixed-N yield from 178 to 148 kg ha⁻¹ in Exp. 1 and from 65 to 29 kg ha⁻¹ in Exp. 2 Fixed-N yield for BT was markedly reduced by N in both experiments (33 to 53%), whereas for the clovers reduction was lesser in Exp. 1 (9 to 13%) than in Exp. 2 (46 to 64%). Negative effects of N on % Ndfa were more evident for the high legume proportion. We conclude that fertilization with 100 kg N ha⁻¹ reduced % Ndfa only for the immediate 18 to 20 weeks after application. Fertilizer-induced reduction of fixed-N yields lasted longer because of a more prolonged depression of legume proportion, especially for BT and for newly seeded swards. Journal Paper no. J.-13327 of the Iowa Agric. and Home Econ. Exp. Stn., Ames, U.S.A. (Project 2281). Supported in part by the Facultad de Agronomía, Montevideo, Uruguay; and the International Atomic Energy Agency, Vienna, Austria (Project URU/5/012). Journal Paper no. J.-13327 of the Iowa Agric. and Home Econ. Exp. Stn., Ames, U.S.A. (Project 2281). Supported in part by the Facultad de Agronomía, Montevideo, Uruguay; and the International Atomic Energy Agency, Vienna, Austria (Project URU/5/012).     

On protein solubility in organic solvent

Solubility of a model protein, hen egg-white lysozyme, was investigated in a wide range of neat nonaqueous solvents and binary mixtures thereof. All solvents that are protic, very hydrophilic, and polar readily dissolve more than 10 mg/mL of lysozyme (lyophilized from aqueous solution of pH 6.0). Only a marginal correlation was found between the lysozyme solubility in a non-aqueous solvent and the letter's dielectric constant or Hildebrand solubility parameter, and no correlation was observed with the dipole moment. Lysozyme dissolved in dimethyl sulfoxide (DMSO) could be precipitated by adding protein nondissolving co-solvents, although the enzyme had a tendency to form supersaturated solutions in such mixtures. The solubility of lysozyme, both in an individual solvent (1,5-pentanediol) and in binary solvent mixtures (DMSO/acetonitrile), markedly increased when the pH of the enzyme aqueous solution prior to lyophilization was moved away from the proteins's isoelectric point. (c) 1994 John Wiley & Sons, Inc.     

Penicillin acylase-catalyzed synthesis of β-lactam antibiotics in water-methanol mixtures: effect of cosolvent content and chemical nature of substrate on reaction rates and yields

The synthesis of four β-lactam antibiotics (penicillin G, pivaloyloxymethyl ester of penicillin G, ampicillin and pivampicillin) catalyzed byEscherichia coli penicillin acylase has been investigated in water-methanol mixtures. The enzyme reactions were either thermodynamically or kinetically controlled at the same conditions using phenylacetic acid andd--phenylglycine methyl ester as acyl donors and 6-aminopenicillanic acid and pivaloyloxymethyl 6-aminopenicillanic acid as acyl acceptors. It has been found that the influences of the cosolvent content on the reaction rates and synthetic yields are significantly different depending on the substrates used in the experiments. On the other hand, within certain ranges of the methanol content (up to ca. 40% (v/v) the residual activities of the enzymes in water-methanol mixtures were only slightly lower than those in aqueous media. To analyze the factors that determine the reaction rate in water-cosolvent mixtures, the effect of methanol on the apparent pK values of the substrates has been investigated, and a mathematical model has been developed on the basis of the assumption that the enzyme binds non-ionized substrates. Model simulation results indicate that the solvent effect on reaction rates is mainly attributed to the kinetic effects of changes in apparent pK values.     

Separating distinct structures of multiple macromolecular assemblies from cryo-EM projections

Single particle analysis for structure determination in cryo-electron microscopy is traditionally applied to samples purified to near homogeneity as current reconstruction algorithms are not designed to handle heterogeneous mixtures of structures from many distinct macromolecular complexes. We extend on long established methods and demonstrate that relating two-dimensional projection images by their common lines in a graphical framework is sufficient for partitioning distinct protein and multiprotein complexes within the same data set. The feasibility of this approach is first demonstrated on a large set of synthetic reprojections from 35 unique macromolecular structures spanning a mass range of hundreds to thousands of kilodaltons. We then apply our algorithm on cryo-EM data collected from a mixture of five protein complexes and use existing methods to solve multiple three-dimensional structures ab initio. Incorporating methods to sort single particle cryo-EM data from extremely heterogeneous mixtures will alleviate the need for stringent purification and pave the way toward investigation of samples containing many unique structures.