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.     

Cytochemical demonstration of adenylate cyclase in cardiac muscle: effect of dimethyl sulfoxide.

Adenylate cyclase (AC) activity was evaluated after perfusion fixation of rat and dog myocardium with 4% paraformaldehyde (PFA), 2% glutaraldehyde (GA) or a combination of both, in cacodylate buffer. Dimethyl sulfoxide (DMSO) was added to the fixatives and its effect on the preservation of cell organelles and enzyme activity was determined. Adenylate cyclase activity was preserved best after fixation with 4% paraformaldehyde but this fixative did not provide for optimal maintenance of structure. Prefixation with 2% glutaraldehyde and 5% dimethyl sulfoxide provided the most effective preservation of both structural and enzymatic integrity. Precipitation of lead diphosphoimide was the morphologic indicator of sites of adenylate cyclase activity. The most intense precipitate was in the lumen of junctional sarcoplasmic reticulum in close contact with T-tubules and in subsarcolemmal cisternae. Evidence of activity was also seen on the intracellular aspect of the sarcolemmal membrane and in the nexus segment of the intercalated discs. Alloxan was effective as an inhibitor of adenylate cyclase activity only if the concentration of the activating substance sodium fluoride (NaF) was 20 mM or lower.     

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.     

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.     

Effect of the mutation rate and background size on the quality of pathogen identification

MOTIVATION: Genomic-based methods have significant potential for fast and accurate identification of organisms or even genes of interest in complex environmental samples (air, water, soil, food, etc.), especially when isolation of the target organism cannot be performed by a variety of reasons. Despite this potential, the presence of the unknown, variable and usually large quantities of background DNA can cause interference resulting in false positive outcomes. RESULTS: In order to estimate how the genomic diversity of the background (total length of all of the different genomes present in the background), target length and target mutation rate affect the probability of misidentifications, we introduce a mathematical definition for the quality of an individual signature in the presence of a background based on its length and number of mismatches needed to transform the signature into the closest subsequence present in the background. This definition, in conjunction with a probabilistic framework, allows one to predict the minimal signature length required to identify the target in the presence of different sizes of backgrounds and the effect of the target's mutation rate on the quality of its identification. The model assumptions and predictions were validated using both Monte Carlo simulations and real genomic data examples. The proposed model can be used to determine appropriate signature lengths for various combinations of target and background genome sizes. It also predicted that any genomic signatures will be unable to identify target if its mutation rate is >5%. SUPPLEMENTARY INFORMATION: Supplementary data are available at Bioinformatics online.     

Genetic Variability of Yersinia pestis Isolates as Predicted by PCR-Based IS100 Genotyping and Analysis of Structural Genes Encoding Glycerol-3-Phosphate Dehydrogenase (glpD)

A PCR-based genotyping system that detects divergence of IS100 locations within the Yersinia pestis genome was used to characterize a large collection of isolates of different biovars and geographical origins. Using sequences derived from the glycerol-negative biovar orientalis strain CO92, a set of 27 locus-specific primers was designed to amplify fragments between the end of IS100 and its neighboring gene. Geographically diverse members of the orientalis biovar formed a homogeneous group with identical genotype with the exception of strains isolated in Indochina. In contrast, strains belonging to the glycerol-positive biovar antiqua showed a variety of fingerprinting profiles. Moreover, strains of the biovar medievalis (also glycerol positive) clustered together with the antiqua isolates originated from Southeast Asia, suggesting their close phylogenetic relationships. Interestingly, a Manchurian biovar antiqua strain Nicholisk 51 displayed a genotyping pattern typical of biovar orientalis isolates. Analysis of the glycerol pathway in Y. pestis suggested that a 93-bp deletion within the glpD gene encoding aerobic glycerol-3-phosphate dehydrogenase might account for the glycerol-negative phenotype of the orientalis biovar. The glpD gene of strain Nicholisk 51 did not possess this deletion, although it contained two nucleotide substitutions characteristic of the glpD version found exclusively in biovar orientalis strains. To account for this close relationship between biovar orientalis strains and the antiqua Nicholisk 51 isolate, we postulate that the latter represents a variant of this biovar with restored ability to ferment glycerol. The fact that such a genetic lesion might be repaired as part of the natural evolutionary process suggests the existence of genetic exchange between different Yersinia strains in nature. The relevance of this observation on the emergence of epidemic Y. pestis strains is discussed.     

Conserved amino acid markers from past influenza pandemic strains

Background  

Finding the amino acid mutations that affect the severity of influenza infections remains an open and challenging problem. Of special interest is better understanding how current circulating influenza strains could evolve into a new pandemic strain. Influenza proteomes from distinct viral phenotype classes were searched for class specific amino acid mutations conserved in past pandemics, using reverse engineered linear classifiers.