A model equation for the gravielectric effect in electrochemical cells

The gravielectric effect model equation for a single-membrane system was elaborated. This model for binary and ternary ionic solutions was verified using a cell with a horizontally mounted membrane. In this cell, the membrane and transition potentials were measured as a function of gravitational configuration. In these experiments, a 0.001 M aqueous solution of sodium chloride was placed on one side of the membrane. The opposite side of the membrane was exposed to either aqueous sodium chloride solutions, with densities greater than that of 0.001 M aqueous NaCl, or ethanol/NaCl/water solutions. On the basis of the experimental results, the influence of constrained release and the gravielectric effect were established. These experimental findings are interpreted in terms of a convective gravitational instability that reduces boundary layer dimensions and increases the permeability coefficient of the complex system: boundary layer/membrane/boundary layer. A concentration-gradient Rayleigh number is used in a mathematical model for gravitationally sensitive membrane potential.     

Optimizing restriction fragment fingerprinting methods for ordering large genomic libraries

We present a statistical analysis of the problem of ordering large genomic cloned libraries through overlap detection based on restriction fingerprinting. Such ordering projects involve a large investment of effort involving many repetitious experiments. Our primary purpose here is to provide methods of maximizing the efficiency of such efforts. To this end, we adopt a statistical approach that uses the likelihood ratio as a statistic to detect overlap. The main advantages of this approach are that (1) it allows the relatively straightforward incorporation of the observed statistical properties of the data; (2) it permits the efficiency of a particular experimental method for detecting overlap to be quantitatively defined so that alternative experimental designs may be compared and optimized; and (3) it yields a direct estimate of the probability that any two library members overlap. This estimate is a critical tool for the accurate, automatic assembly of overlapping sets of fragments into islands called "contigs." These contigs must subsequently be connected by other methods to provide an ordered set of overlapping fragments covering the entire genome.     

A functional gene array for detection of bacterial virulence elements

Emerging known and unknown pathogens create profound threats to public health. Platforms for rapid detection and characterization of microbial agents are critically needed to prevent and respond to disease outbreaks. Available detection technologies cannot provide broad functional information about known or novel organisms. As a step toward developing such a system, we have produced and tested a series of high-density functional gene arrays to detect elements of virulence and antibiotic resistance mechanisms. Our first generation array targets genes from Escherichia coli strains K12 and CFT073, Enterococcus faecalis and Staphylococcus aureus. We determined optimal probe design parameters for gene family detection and discrimination. When tested with organisms at varying phylogenetic distances from the four target strains, the array detected orthologs for the majority of targeted gene families present in bacteria belonging to the same taxonomic family. In combination with whole-genome amplification, the array detects femtogram concentrations of purified DNA, either spiked in to an aerosol sample background, or in combinations from one or more of the four target organisms. This is the first report of a high density NimbleGen microarray system targeting microbial antibiotic resistance and virulence mechanisms. By targeting virulence gene families as well as genes unique to specific biothreat agents, these arrays will provide important data about the pathogenic potential and drug resistance profiles of unknown organisms in environmental samples.     

Volume osmotic flows of non-homogeneous electrolyte solutions through horizontally mounted membrane

Results of an experimental study of volume osmotic flows in a single-membrane osmotic-diffusive cell, which contains a horizontal, microporous, symmetrical polymer membrane separating water and binary or ternary electrolyte solutions are presented. In the experimental set-up, water was placed on one side of the membrane. The opposite side of the membrane was exposed to binary or ternary solutions. As binary solutions, aqueous potassium chloride or ammonia solutions were used, whereas potassium chloride in 0.25 mol x l(-1) aqueous ammonia solution or ammonia in 0.1 mol x l(-1) aqueous potassium chloride solution were used as ternary solutions. Two (A and B) configurations of a single-membrane osmotic-diffusive cell in a gravitational field were studied. In configuration A, water was placed in a compartment above the membrane and the solution below the membrane. In configuration B the position of water and solution was reversed. Furthermore, the effect of amplification of volume osmotic flows of electrolyte solutions in the single-membrane osmotic-diffusive electrochemical cell was demonstrated. The thermodynamic models of the flux graviosmotic and amplification effects were developed, and the volume flux graviosmotic effect for configurations A and B of a single-membrane osmotic-diffusive cell was calculated. The results were interpreted within the conventional instability category, increasing the diffusion permeability coefficient value for the system: concentration boundary layer/membrane/concentration boundary layer.     

Photodynamic antimicrobial therapy

Photodynamic antimicrobial therapy (PACT) involves the utilisation of photosensitizers activated by exposure to visible light in order to eradicate microbes (this method has already been applied in photodynamic therapy of tumours). Photodynamic effect of the particular photosensitive substance (PS) is attributed to its ability to penetrate susceptible microorganisms, to absorb the light of certain wavelength, and to generate reactive cytotoxic oxygen products. The target microorganisms for photoinactivation are bacteria, fungi, viruses and protozoa. Photodynamic antimicrobial therapy is proposed as a potentially topical, non-invasive approach suitable for treatment of locally occurring infection. The fact that bacteria are becoming increasingly resistant to antibiotics and antiseptics has lead to an increased interest in the development of new alternative eradication methods, such as PACT. Research and development of photosensitive substances are aimed at finding effective antimicrobial substances, which would have a broad-spectrum potency.     

Nuclear gene trees and the phylogenetic relationships of the mangabeys (Primates: Papionini)

Phylogenetic relationships of mangabeys within the Old World monkey tribe Papionini are inferred from analyses of nuclear DNA sequences from five unlinked loci. The following conclusions are strongly supported, based on congruence among trees derived for the five separate gene regions: (1) mangabeys are polyphyletic within the Papionini; (2) Cercocebus is the sister taxon to the genus Mandrillus; and (3) Lophocebus belongs to a clade with Papio and Theropithecus, with Papio as its most likely sister taxon. Morphologically based phylogenies positing mangabey monophyly were evaluated by mapping the sequences for each locus on these trees. The data seem to fit these trees poorly in both maximum-parsimony and likelihood analyses. Incongruence among nuclear gene trees occurred in the interrelationships among Lophocebus, Papio, and Theropithecus. Several factors that may account for this incongruence are discussed, including sampling error, random lineage sorting, and introgression.      

PPCMatrix: a PowerPC dotmatrix program to compare large genomic sequences against protein sequences

Summary : An interactive dotmatrix program for the MacOS was designed that allows comparison of DNA to protein sequences using nested 3-frame translations. Availability : Shareware, available at http://copan.bioz.unibas.ch/software/ Contact : burglin@ubaclu. unibas.ch      

The Role of Viral Population Diversity in Adaptation of Bovine Coronavirus to New Host Environments

The high mutation rate of RNA viruses enables a diverse genetic population of viral genotypes to exist within a single infected host. In-host genetic diversity could better position the virus population to respond and adapt to a diverse array of selective pressures such as host-switching events. Multiple new coronaviruses, including SARS, have been identified in human samples just within the last ten years, demonstrating the potential of coronaviruses as emergent human pathogens. Deep sequencing was used to characterize genomic changes in coronavirus quasispecies during simulated host-switching. Three bovine nasal samples infected with bovine coronavirus were used to infect human and bovine macrophage and lung cell lines. The virus reproduced relatively well in macrophages, but the lung cell lines were not infected efficiently enough to allow passage of non lab-adapted samples. Approximately 12 kb of the genome was amplified before and after passage and sequenced at average coverages of nearly 950×(454 sequencing) and 38,000×(Illumina). The consensus sequence of many of the passaged samples had a 12 nucleotide insert in the consensus sequence of the spike gene, and multiple point mutations were associated with the presence of the insert. Deep sequencing revealed that the insert was present but very rare in the unpassaged samples and could quickly shift to dominate the population when placed in a different environment. The insert coded for three arginine residues, occurred in a region associated with fusion entry into host cells, and may allow infection of new cell types via heparin sulfate binding. Analysis of the deep sequencing data indicated that two distinct genotypes circulated at different frequency levels in each sample, and support the hypothesis that the mutations present in passaged strains were “selected” from a pre-existing pool rather than through de novo mutation and subsequent population fixation.