Properties of the cured oncogenic strain 37400 ofAgrobacterium tumefaciens

The properties of the 37400 oncogenic strain ofAgrobacterium tumefaciens are described. This strain was derived from the VI lysogenic strain originally isolated by Hamilton from aZinnia elegans tumour. Strain 37400 has a number of properties which render it suitable for quantitative and genetic studies. It is cured of prophages and can serve as a universal sensitive indicator for a number of phages isolated from various lysogenic strains ofAgrobacterium tumefaciens. Its good growth properties in synthetic media and at elevated temperatures enable the isolation of auxotrophic mutants and temperature sensitive phage mutants. Preliminary experiments show that strain 37400 will serve as suitable starting material for conjugation experiments under defined conditions.     

On the superposition of currents from ion channels.

We derive a number of statistical properties of the superposition of several independent channels contributing to a patch-clamp recording. Failure of these properties indicates dependence of the channels and may suggest the nature of interactions. We show how properties such as dwell-time distributions of the individual channels may be determined from those of the superposition in the case that the channels are independent.     

Tritium diagnostics in a fusion reactor

Methods for controlling tritium in a fusion reactor are reviewed. The characteristic features of the interaction of tritium with surfaces are considered, as well as its diffusive properties and its levels and saturation depths for a number of radioactive materials. New properties of boundary layers and new diffusive properties in the polycrystalline structure of metals are revealed. Unique measurements of the diffusive properties of tritium in stainless steel at room temperature are carried out. It is found that the main contribution to the diffusion process comes from the intergranular tritium flux. The capture of tritium by metals in the ITER device is calculated.     

Dependence of Ion Channel Properties Formed by Polyene Antibiotics Molecules on the Lactone Ring Structure

The properties of ion channels formed in membranes by polyene antibiotics of various chemical structure of hydrophilic and hydrophobic chains are investigated. Small differences in a hydrophylic chain with a changed number of hydroxyl and carbonyl groups significantly influence the values of conductivity and selectivity of the polyene channel. The greater number of double bonds in a hydrophobic part of polyene molecules leads to the higher biological activity of antibiotics. Measurement of anion–cationic selectivity of the channels formed by polyenes showed that anionic selectivity, as well as conductivity of channels, decreases among antibiotics: amphotericin B, nystatin, candidin, mycoheptin, and levorin. The study of physical and chemical properties of the single and hybrid ion channels on the bilayer lipid membranes in the presence of polyene antibiotics makes possible to create a theoretically reasonable recommendation for the targeted synthesis of new antibiotics with the desired properties.     

PHYSEAN: PHYsical SEquence ANalysis for the identification of protein domains on the basis of physical and chemical properties of amino acids

MOTIVATION: PHYSEAN predicts protein classes with highly variable sequences on the basis of their physical, chemical and biological characteristics such as diverse hydrophobicity, structural propensity and steric properties. These characteristics, calculated from multiple positions in a sequence, may be conserved even between sequences that fail to produce alignments at any acceptable level of statistical significance. PHYSEAN complements methods that require sequence alignments (BLAST, FASTA, dynamic programming) by adding less residue- and position-specific physicochemical information on the protein or the domain. RESULTS: We predict proteins or their domains like signal peptides using physical, chemical, geometric, and biological properties of the 20 amino acids. This comprehensive set of properties may cover the diagnostic functional and structural aspects of a domain or a protein class. We automatically select and weight a subset of properties so as to discriminate between, e.g., signal peptides and amino-termini of cytosolic proteins with the lowest number of incorrect predictions. This optimal selection of properties and their weights significantly decreases the number of incorrect predictions as compared to any single property or any combination of unweighted properties. Weights have been optimized by high-performance linear programming models that systematically find the optimal solution from among an astronomic number of property/weight combinations. PHYSEAN's performance is demonstrated by highly accurate predictions of signal peptides (the vehicles for protein transport across membranes) and their cleavage sites. The results indicate reliable predictions are possible even in the lack of sequence conservation using an automated physical and chemical analysis of proteins.     

Stobadine: bellwether of a broader view of drug actions

Stobadine was recognized early in its development as having antioxidant properties. A number of laboratories found associations between the antioxidant properties of stobadine and its potential beneficial effects. We found that stobadine acted as an antioxidant in a modification of an oxygen radical absorbance capacity (ORAC) assay. Similar results were observed with other drugs, including tirilazad and pramipexole. We suggest that stobadine and certain other drugs exhibit antioxidant properties in both hydrophilic and hydrophobic environments. Other drugs have been developed for their antioxidant properties and some currently marketed drugs have antioxidant properties. Although they may not have been explicitly sought during development, at least some of the beneficial effects may be related to antioxidant properties and/or scavenging of free radicals. Because stobadine was one of the first drugs for which useful properties were associated with its antioxidant actions, stobadine may be seen as a bellwether of a broader view of pharmacological actions--a view that encompasses antioxidant properties as a useful basis of therapeutic effects.     

Primary astrocyte cultures—a key to astrocyte function

Morphological studies have established the ubiquitous nature of astrocytes in the CNS. Their processes surround capillaries and synapses, form the subpial and subependymal layers, and seemingly invest every neuronal surface not covered by other neuronal surfaces or oligodendroglial membranes. Although such interrelationships have long suggested that astrocytes may play many critical roles, there still remains relatively little experimental information on the functions and properties of these cells. About a decade ago it became evident that primary cultures from neonatal rodent brains can consist predominantly of normal astrocytes. Based on these findings there is now an increasing number of studies in which such primary cultures are being used to help unravel the continuing enigma of the properties and functions of astrocytes. Aspects of this work are reviewed in this article. Such work has already shown that astrocytes in primary culture exhibit the basic electrophysiological characteristics which had been the only functional property well established for these cells in situ. Further studies of the electrophysiological properties of these cells, which can be correlated with ion transport studies, are beginning to show that astrocytes may have more complex electrophysiological properties than had previously been supposed, as well as a number of important electrically silent ion fluxes. In addition, astrocytes in primary culture show uptake of and receptors for a number of transmitters, properties which have wide-ranging implications. Studies in culture also support work in vivo that astroglia may have an important role in neuronal development.     

Virus Deoxyribonucleic Acid Sequences in Subdiploid and Subtetraploid Revertants of Polyoma- Transformed Cells

Polyoma-transformed cells can revert in the properties characteristic of transformation, although they maintain the polyoma-specific T antigen. Transformed cells contain the same number of copies of polyoma virus deoxyribonucleic acid (DNA) per cell (eight) as revertants with a subdiploid or a subtetraploid chromosome number. The results indicate that the duplication of chromosomes in the subtetraploid revertants did not include the chromosomes that carry the viral genome. The virus DNA in both transformed and revertant cells was associated with high-molecular-weight cell DNA. Reversion of the properties of transformed cells was, therefore, not associated either with a decrease in number of virus DNA copies per cell or with a lack of association of the virus DNA with cell DNA.     

Individual Male Calling Pattern and Male Mating Success in the European Treefrog (Hyla arborea): Is there Evidence for Directional or Stabilizing Selection on Male Calling Behaviour?

In anurans, call properties are commonly classified based on within‐male variability as being either static or dynamic. Numerous playback experiments in the laboratory have indicated that female preferences based on dynamic call properties are usually strongly directional, while female preferences based on static call properties are often stabilizing or weakly directional. However, there are only few studies demonstrating that female preferences for high values of dynamic call properties indeed exert directional selection on male calling behaviour in natural populations. Moreover, field studies investigating whether female preferences for values of static call properties around the mean of the population lead to currently operating stabilizing selection on male calling patterns in natural populations are completely lacking. Here I investigate for two consecutive breeding seasons male calling patterns and male mating success in a population of individually marked European treefrogs (Hyla arborea), a hylid frog with prolonged breeding season and a lek mating system. Individual male calling pattern as analysed in terms of seven temporal and spectral call properties did not differ between males that survived from one breeding season to the next and those not surviving. None of the seven call properties investigated differed significantly between mated and unmated males, indicating that there is no strong directional selection on male calling behaviour in the study population. However, in one study season males that produced calls with a number of pulses around the mean of the population were significantly more likely to obtain matings than males that produced calls with a number of pulses at the low or high end of the distribution. Thus, this study provides preliminary evidence for the operation of stabilizing selection on a static call property (i.e. the number of pulses per call) in a natural population of an anuran amphibian.     

Biological properties of clinical staphylococcal strains with a varying number of antibiotic resistance markers]

The study of a number of biological properties of 1881 clinical strains of Staphylococcus showed that in the group of the antibiotic resistant staphylococci there was a tendency for different manifestation of some biological properties depending on the number of the resistance determinants. The staphylococcal strains resistant to 5--7 antibiotics differed from those resistant to a less number of the drugs by greater manifestation of the pathogenicity properties: lecithinase, hyaluronidase and hemolytic activity.     

Gene expression profiling of cranial sensory ganglia that transmit food intake stimuli

Peripheral cranial sensory nerves projecting into the oral cavity receive food intake stimuli and transmit sensory signals to the central nervous system. They are derived from four cranial sensory ganglia, trigeminal, geniculate, petrosal, and nodose ganglia, each of which contains multiple kinds of sensory neurons with different cell morphologies and neuronal properties. We investigated the complex properties of these neurons from the viewpoint of gene expression using DNA microarrays. The 498 genes were selected from a total of 8,740 genes as showing tissue-dependent expression on the microarray by hierarchical cluster analysis, in which several genes known to be differentially expressed in cranial sensory ganglia are included. This suggests that DNA microarray cluster analysis revealed a number of characteristic genes for sensory neurons in these ganglia. Among the selected 498 genes, 44 genes are associated with neurotransmission, such as neuropeptides, their receptors, and vesicle transport, and 26 are ion channels regulating membrane potentials. The identification of a number of genes related directly to neural properties indicates that these sensory ganglia contain heterogeneous types of neurons with different neural properties.     

Ultrastructural ultracytochemical investigation of human gastric carcinomas

We describe the ultrastructure of various types of gastric carcinoma cells as well as their histochemical properties as visualized at the electron-microscope level. The histochemical properties of tumour cells were compared with those of homologous normal epithelial cells. The localization and activity of ATPase, IDPase, acidic phosphatase and alkaline phosphatase as well as of the oxidoreductases (cytochrome oxidase, succinate dehydrogenase and NADH-dehydrogenase) were studied. Our findings demonstrated that, in tumour cells, a complicated process of structural-functional restructuring takes place. It seems that a number of ultracytochemical properties may be preserved or may disappear altogether; also, such properties may become enhanced or weaker. This heterogeneity of the histochemical properties of tumour cells is discussed with regard to the role of the stem (polypotent) cell in the process of the histogenesis (cytogenesis) of human gastric carcinomas.     

An updated algorithm for the generation of neutral landscapes by spectral synthesis

Background

Patterns that arise from an ecological process can be driven as much from the landscape over which the process is run as it is by some intrinsic properties of the process itself. The disentanglement of these effects is aided if it possible to run models of the process over artificial landscapes with controllable spatial properties. A number of different methods for the generation of so-called ‘neutral landscapes’ have been developed to provide just such a tool. Of these methods, a particular class that simulate fractional Brownian motion have shown particular promise. The existing methods of simulating fractional Brownian motion suffer from a number of problems however: they are often not easily generalisable to an arbitrary number of dimensions and produce outputs that can exhibit some undesirable artefacts.

Methodology

We describe here an updated algorithm for the generation of neutral landscapes by fractional Brownian motion that do not display such undesirable properties. Using Monte Carlo simulation we assess the anisotropic properties of landscapes generated using the new algorithm described in this paper and compare it against a popular benchmark algorithm.

Conclusion/Significance

The results show that the existing algorithm creates landscapes with values strongly correlated in the diagonal direction and that the new algorithm presented here corrects this artefact. A number of extensions of the algorithm described here are also highlighted: we describe how the algorithm can be employed to generate landscapes that display different properties in different dimensions and how they can be combined with an environmental gradient to produce landscapes that combine environmental variation at the local and macro scales.     

Ultrastructural and ultracytochemical investigation of human gastric carcinomas

Summary We describe the ultrastructure of various types of gastric carcinoma cells as well as their histochemical properties as visualized at the electron-microscope level. The histochemical properties of tumour cells were compared with those of homologous normal epithelial cells. The localization and activity of ATPase, IDPase, acidic phosphatase and alkaline phosphatase as well as of the oxidoreductases (cytochrome oxidase, succinate dehydrogenase and NADH-dehydrogenase) were studied. Our findings demonstrated that, in tumour cells, a complicated process of structural-functional restructuring takes place. It seems that a number of ultracytochemical properties may be preserved or may disappear altogether, also, such properties may become enhanced or weaker. This heterogeneity of the histochemical properties of tumour cells is discussed with regard to the role of the stem (polypotent) cell in the process of the histogenesis (cytogenesis) of human gastric carcinomas.In honour of Prof. P. van Duijn     

Transport properties of oligomeric subunit structures

The translational friction coefficients, rotational friction coefficient, and intrinsic viscosity of rigid regular structures composed of up to eight identical spherical subunits have been accurately calculated. The aim of this calculation is to interpret the hydrodynamic properties of oligomeric subunit proteins. To avoid the well-known failure of the theory in the evaluation of rotational coefficients and intrinsic viscosities, each subunit is hydrodynamically modeled as a polyhedral array of smaller spheres. The analysis of several alternatives suggests that a cubic array is the best choice. The reliability of this strategy is checked by comparison of the calculated values for all the transport properties of a sphere and the translational friction coefficients of a dimer with their exact values. Finally, the hydrodynamic properties of a number of subunit structures with varying number of subunits and different geometries are tabulated.     

A model of adaptation based on relaxation phenomena in the neural membrane

Summary Adaptation in neural systems is due to a number of phenomena which include characteristic receptor response, delayed inhibition and other network properties, as well as adaptation on the single unit level. The last effect has been isolated and studied extensively by a number of experimenters. We are proposing a model which accounts for this effect. It is assumed that the post-spike hyperpolarizations are cumulative and are caused by two distinct membrane processes of differing relaxation times. The model involves a number of parameters which can be fitted to existing neurophysiological data.     

Shade induced changes in biomechanical petiole properties in the stoloniferous herb <Emphasis Type="Italic">Trifolium repens</Emphasis>

Increased cell number and cell length both contribute to shade induced elongation of petioles which enables stoloniferous plants to place their leaf lamina higher up in the canopy. Although petiole elongation is assumed to be beneficial, it may also imply costs in terms of decreased biomechanical stability. We test the hypothesis that shade induced elongation changes the biomechanical properties of petioles and that the underlying mechanisms, cell division and cell elongation, differentially affect biomechanical properties. This was done by subjecting 14 genotypes differing in the relative contribution of cell size and cell number to shade induced elongation responses to high light conditions and to simulated canopy shade. Developmental traits (cell size and cell number), morphological traits characterizing the petioles, as well as biomechanical characteristics were measured. Our results show that, comparable to stems of non-clonal plants, the rigidity of a petiole’s tissue (the Young’s modulus) increases, leading to increased flexural stiffness of petioles subjected to shading. Increased flexural stiffness proved to be associated with increased performance under shaded conditions. Our results also indicate that cell number affected the material properties and the flexural stiffness of petioles. However, the degree and pattern of the effects differed between light environments. Shade induced increase in cell number translated into shade induced increase of Young’s modulus and flexural stiffness. Genotypes producing relatively larger cells under shaded conditions experienced a decrease in tissue rigidity. In concert our results indicate that the pattern of selection on flexural stiffness, and thereby also on shade induced changes of cell number and cell size differs among light environments. An erratum to this article can be found at     

Effects of isolation,logging and dispersal on woody-species richness of islands

Isolation effects on species richness of woody plants were investigated in a system of islands that were created by the filling of the Clarks Hill Reservoir, Georgia. This reservoir was built between 1946–1954. Some islands were logged and cleared of woody plants prior to the filling of the reservoir and others were not logged. The presence of logged versus unlogged islands in the same system allowed us to test whether and how geographical isolation interacts with island history and species-specific dispersal properties in determining patterns of among-island variation in species number. Thirty-six years after the islands were created, logged islands had significantly fewer species of woody plants than unlogged ones. On logged islands, total number of woody species was negatively correlated with distance to the closest mainland (r=–0.95). On unlogged islands, variation in species number was very low (CV=4.9%) and was not correlated with distance to the mainland. These results indicate that the studied system as a whole has not yet reached equilibrium. However, the mean number of species on unlogged islands was very close to the intercept of the regression obtained for logged islands, suggesting that islands close to the mainland have already reached their equilibrium species richness. This conclusion is consistent with predictions of island biogeography theory. When species representing different dispersal properties were analyzed separately, statistically significant distance effects were obtained for bird-dispersed species (r=0.88) and for species with no adaptations to bird or wind dispersal (r=0.81). Wind-dispersed species did not show a decrease in species number with increasing isolation, but their relative frequency was positively and significantly correlated with distance to the mainland (r=0.94). Historical factors, as well as differences among species in dispersal properties, are important in explaining patterns of among-island variation in species number.     

Tensor products of digraphs and the structure of groups of pairs

The tensor product of two digraphs turns out to be a digraph with certain special properties. Several theorems presenting some of these properties are proved, and a characterization of tensor products having a prime number of lines is obtained. Applications are presented in which tensor products are used as structural models of groups of pairs of individuals formed from two original groups of singles.