Surface Charge Movements of Purple Membrane During Light-Dark Adaptation

The difference in the surface charge distribution between light-adapted and dark-adapted purple membranes was investigated with electric dichroism measurements from approximately pH 5 to pH 11. Purple membrane sheets in solution are oriented in a weak electric field by their permanent dipole moment, which is due to the charge distribution of the membrane surfaces and/or within the membrane. The degree of orientation of purple membrane sheets was obtained from the measurement of “electrical anisotropy” of retinal chromophore in the membranes. At about pH 7, there was no difference in the “electric anisotropy” between light- and dark-adapted purple membranes. At about pH 9, the electric anisotropy of dark-adapted purple membrane was larger than that of light-adapted purple membrane. But at around pH 6 the difference was opposite. Linear dichroism experiments did not show any change of retinal tilt angle with respect to the membrane normal between the two forms from approximately pH 5 to pH 10. This result indicates that the changes in the “electric anisotropy” are not due to the change of retinal tilt angle, but due to the change in the permanent dipole moment of the membrane. To estimate the change in surface charges from the permanent dipole moment, we investigated the difference of the permanent dipole moment between the native purple membrane and papain-treated purple membrane in which negative charges in the cytoplasmic-terminal part are removed. This estimation suggests that this light-dark difference at around pH 9 can be accounted for by a change of ~0.5 electric charge per bacteriorhodopsin (bR) molecule at either of the two surfaces of the membrane. We also found from pH electrode measurements that at about pH 8 or 9 light adaptation was accompanied by an uptake of ~0.1 protons per bR. A possible movement of protons during light-dark adaptation is discussed. The direction of the permanent dipole moment does not change with papain treatment. The permanent dipole moment in papain-treated purple membrane is estimated to be 27 ±2 debye/bR.     

The effects of heart-cavity blood resistivity and volume on endocardial potentials: theoretical predictions

Theoretical concepts regarding the potential variations within the bloodfilled cavities of the heart caused by excitation of the myocardium are scarce. In an attempt to understand these potential variations, calculations were made of the potentials due to a dipole adjacent to a disk of finite resistivity. The dipole was assumed to be in an infinite two-dimensional medium of higher resistivity. Equations for the potential inside a sphere due to an external source are also given.On the basis of the results, predictions were made on the effects of the intracardiac blood on the endocardial potentials: (1) the potential at the center of the cavity is independent of blood resistivity and equivalent to the free space potential; (2) potentials due to a tangential dipole are uniformly reduced; (3) potentials due to a radial dipole are smaller near the dipole, but greater at the far end of the dipole axis; (4) for a dipole radial to or making an angle with the cavity, potentials are reduced at some points but increased at others; (5) the potential along the transverse axis of the dipole has a constant value depending on conductivity; (6) intracardiac blood tends to smooth out potential variations within the cavity; (7) the potential depends both on dipole distance and direction; and (8) if the cavity volume increases, potentials decrease with distance from the dipole; the potential at the adjacent endocardial wall changes little.     

The Application of Electromagnetic Theory to Electrocardiology: I. Derivation of the Integral Equations

One of the fundamental problems of theoretical electrocardiology is to determine the potential distribution on the surface of the torso due to the time-varying dipolar heart source. In this paper we present a rigorous derivation of the integro-differential equations for the potential, containing, for the first time, the effects of the time dependence of the source and the dielectric properties of the medium. These equations provide a general and rigorous basis from which to attack the problem numerically on a computer and permit the use of a detailed model of the thorax as a multiple region volume of different dielectric and conducting properties.     

An asymptotic estimate for the effective radius of a concentric bipolar electrode.

A concentric bipolar electrode (CBE) (consisting of a central disc and an outer annulus) has been proposed as an approximate method of measuring the surface Laplacian of the body surface electrical potential distribution. The derivation of the surface Laplacian approximation, in terms of the potential difference measured with the bipolar electrode, contained an unspecified parameter which has been dubbed the 'effective radius' of the concentric bipolar electrode. This paper presents an asymptotic analysis to derive an expression for the effective radius in terms of the physical dimensions of the electrode (the radius of the central disc and inner and outer radii of the annulus). Also studied is the way in which the value of the effective radius affects the behaviour of the relative error in the surface Laplacian measurement at various dipole source locations within a conducting medium.     

Isolation of Salmonellae From Food Samples: VI. Comparison of Methods for the Isolation of Salmonella From Egg Products

The recovery of salmonellae from egg products was studied, by use of three different enrichment procedures: (i) selenite broth, (ii) selenite broth containing 10% sterile feces, and (iii) the lactose pre-enrichment procedure. Brilliant Green Agar was used throughout as the recovery medium. Although the lactose pre-enrichment methodology promoted Salmonella recovery from samples containing small numbers of dormant organisms, the efficiency of this enrichment method is adversely affected by unfavorable coliform-Salmonella ratios. Under such conditions, early subculture of lactose broth into selenite broth is indicated. Selenite broth containing 10% sterile feces was more efficient than the lactose pre-enrichment methodology in promoting the growth of “dormant” salmonellae. Albumen adversely affected recovery of salmonellae from selenite broth, whereas whole egg and egg yolk enhanced Salmonella recovery from this medium. The selenite-feces medium presents a solution to the major problems encountered in the detection of salmonellae in egg products and offers an approach to a single medium in which food-borne salmonellae will manifest themselves with a minimum of laboratory manipulation.     

The influence of local tissue conductivity changes on the magnetoencephalogram and the electroencephalogram.

We examined the influence of local tissue conductivity changes in the vicinity of a dipolar source on the neuromagnetic field and the electric scalp potential using a high resolution finite element method model of the human head. We found that the topology of both the electric scalp potential and the neuromagnetic field (and consequently dipole localization) is influenced significantly by conductivity changes only in voxels adjacent to the source. Conductivity changes in these voxels yield a greater change in the amplitude of the magnetic field (and consequently in the dipole strength) than in the amplitude of the electric potential.     

Engineering Bacteria to Search for Specific Concentrations of Molecules by a Systematic Synthetic Biology Design Method

Bacteria navigate environments full of various chemicals to seek favorable places for survival by controlling the flagella’s rotation using a complicated signal transduction pathway. By influencing the pathway, bacteria can be engineered to search for specific molecules, which has great potential for application to biomedicine and bioremediation. In this study, genetic circuits were constructed to make bacteria search for a specific molecule at particular concentrations in their environment through a synthetic biology method. In addition, by replacing the “brake component” in the synthetic circuit with some specific sensitivities, the bacteria can be engineered to locate areas containing specific concentrations of the molecule. Measured by the swarm assay qualitatively and microfluidic techniques quantitatively, the characteristics of each “brake component” were identified and represented by a mathematical model. Furthermore, we established another mathematical model to anticipate the characteristics of the “brake component”. Based on this model, an abundant component library can be established to provide adequate component selection for different searching conditions without identifying all components individually. Finally, a systematic design procedure was proposed. Following this systematic procedure, one can design a genetic circuit for bacteria to rapidly search for and locate different concentrations of particular molecules by selecting the most adequate “brake component” in the library. Moreover, following simple procedures, one can also establish an exclusive component library suitable for other cultivated environments, promoter systems, or bacterial strains.     

Limitations on the Equivalent Cardiac Generator

This paper is a critical summary of the implications of potential theory in electrocardiography with particular attention to the “inverse problem.” It is emphasized that potential measurements on the human torso serve to determine only the multipole coefficients of the heart sources and that no additional information is available. An interpretation of these coefficients with respect to the actual electrophysiological sources is considered further on the basis of distribution theory.     

Defining a Superlens Operating Regime for Imaging Fluorescent Molecules

It has been shown that thin metal-based films can at certain frequencies act as planar near-field lenses for certain polarization components. A desirable property of such “lenses” is that they can also enhance and focus some large transverse spatial frequency components which contain sub-diffraction limit details. Over the last decade there has been much work in optimizing designs to reduce effects (such as material losses and surface roughness) that are detrimental to image reconstruction. One design that can reduce some of these undesirable effects, and which has received a fair amount of attention recently, is the stacked metal-dielectric superlens. Here we theoretically explore the imaging ability of such a design for the specific purpose of imaging a fluorescent dye (the common bio-marker GFP) in the vicinity of the superlens surface. Our calculations take into consideration the interaction (damping) of an oscillating electric dipole with the metallic layers in the superlens. We also assume a Gaussian frequency distribution spectrum for the dipole. We treat the metallic-alloy and dielectric-alloy layers separately using an appropriate effective medium theory. The transmission properties are evaluated via Transfer matrix (-matrix) calculations that were performed in the MatLab and MathCad environments. Our study shows that it is in principle possible to image fluorescent molecules using a simple bilayer planar superlens. We find that optimal parameters for such a superlens occur when the peak dipole emission-frequency is slightly offset from the Surface Plasmon resonance frequency of the metal-dielectric interfaces. The best resolution is obtained when the fluorescent molecules are not too close ( nm) or too far ( nm) from the superlens surface. The realization and application of a superlens with the specified design is possible using current nanofabrication techniques. When combined with e.g. a sub-wavelength grating structure (such as in the far-field superlens design previously proposed [1]) or a fast near-field scanning probe, it could provide a means for fast fluorescent imaging with sub-diffraction limit resolution.     

Could Public Restrooms Be an Environment for Bacterial Resistomes?

Antibiotic resistance in bacteria remains a major problem and environments that help to maintain such resistance, represent a significant problem to infection control in the community. Restrooms have always been regarded as potential sources of infectious diseases and we suggest they have the potential to sustain bacterial “resistomes”. Recent studies have demonstrated the wide range of different bacterial phyla that can be found in non-healthcare restrooms. In our study we focused on the Staphylococci. These species are often skin contaminants on man and have been reported as common restroom isolates in recent molecular studies. We collected samples from 18 toilets sited in 4 different public buildings. Using MALDI-TOF-MS and other techniques, we identified a wide range of antibiotic resistant Staphylococci and other bacteria from our samples. We identified 19 different Staphylococcal species within our isolates and 37.8% of the isolates were drug resistant. We also identified different Staphylococcal species with the same antibiograms inhabiting the same restrooms. Bacterial “resistomes” are communities of bacteria often localised in specific areas and within these environments drug resistance determinants may be freely transferred. Our study shows that non-healthcare restrooms are a source of antibiotic resistant bacteria where a collection of antibiotic resistance genes in pathogenic and non-pathogenic bacteria could form a resistome containing a “nexus of genetic diversity”     

Measurement of the electric field of the heart in a homogeneous volume conductor]

The paper describes a technique and some results of experimental measurements of electrical potentials generated by an isolated dog heart in homogeneous conductor, drawing equipotential maps of the field, and calculating the characteristics of the dipole equivalent generator of the heart. The form of potential distribution on a spherical surface around the heart and its ideal orthogonal vectorcardiograms are discussed.     

Uncovering a Microbial Enigma: Isolation and Characterization of the Streamer-Generating,Iron-Oxidizing,Acidophilic Bacterium “Ferrovum myxofaciens”

A betaproteobacterium, shown by molecular techniques to have widespread global distribution in extremely acidic (pH 2 to 4) ferruginous mine waters and also to be a major component of “acid streamer” growths in mine-impacted water bodies, has proven to be recalcitrant to enrichment and isolation. A modified “overlay” solid medium was devised and used to isolate this bacterium from a number of mine water samples. The physiological and phylogenetic characteristics of a pure culture of an isolate from an abandoned copper mine (“Ferrovum myxofaciens” strain P3G) have been elucidated. “F. myxofaciens” is an extremely acidophilic, psychrotolerant obligate autotroph that appears to use only ferrous iron as an electron donor and oxygen as an electron acceptor. It appears to use the Calvin-Benson-Bassham pathway to fix CO₂ and is diazotrophic. It also produces copious amounts of extracellular polymeric materials that cause cells to attach to each other (and to form small streamer-like growth in vitro) and to different solid surfaces. “F. myxofaciens” can catalyze the oxidative dissolution of pyrite and, like many other acidophiles, is tolerant of many (cationic) transition metals. “F. myxofaciens” and related clone sequences form a monophyletic group within the Betaproteobacteria distantly related to classified orders, with genera of the family Nitrosomonadaceae (lithoautotrophic, ammonium-oxidizing neutrophiles) as the closest relatives. On the basis of the phylogenetic and phenotypic differences of “F. myxofaciens” and other Betaproteobacteria, a new family, “Ferrovaceae,” and order, “Ferrovales,” within the class Betaproteobacteria are proposed. “F. myxofaciens” is the first extreme acidophile to be described in the class Betaproteobacteria.     

Sporulation of Bacillus stearothermophilus

A broth medium containing tryptone and manganese sulfate supported heavy sporulation of Bacillus stearothermophilus ATCC 7953 (NCA 1518) and four isolates identified as B. stearothermophilus. Maximal spore yields were obtained by use of inocula grown anaerobically in a medium containing glucose with aeration of sporulation medium via bubbling. After an extended stationary period, sporulation occurred concurrently with vegetative growth between 6 and 8 hr of incubation at 60 C. Omission of glucose from the inoculum or use of a “young” (2 hr) inoculum abolished the stationary period, but decreased spore yields. A requirement of oxygen for rapid vegetative growth and sporulation was demonstrated. Manganese (15 to 30 ppm) stimulated sporulation but did not enhance cell growth.     

有限元法计算各向异性介质球头模型电位分布

在脑电正问题研究中,脑神经元所产生的电活动可用电流偶极子来模拟.本文提出把大脑看作各向异性介质球,即同时考虑电容效应、电导效应对脑内电流偶极子产生的电位的影响,并用有限元法推导出偶极子在各向异性介质球模型中的电位分布计算公式.结果表明介质的电容效应对电位分布是有影响的,反映了大脑活组织电特性,对外来不同频率的信号刺激有不同的响应.同时有限元法对大脑内某一区域内电位分布求解表明,测量较深层组织的电特性变化敏感的特点,可获得更多的测量信息.     

Isolation of Mesophyll Cells from Sedum telephium Leaves

A technique is described for mechanically isolating metabolically active individual spongy mesophyll cells from the Crassulacean acid metabolism plant, Sedum telephium. Mature leaves are selected at about 2 PM when acidity is low, and three different media are used to reduce the problem of leaf acidity and to maintain isotonic conditions. The upper and lower epidermis is peeled from chilled leaves and the leaves are suspended in a buffered “soaking medium,” then gently ground with a mortar and pestle. Cells and debris are separated using a “washing medium,” with cells being filtered through a 136 micron net and collected on an 80 micron net. Cells then are suspended in a “cell suspension medium” and concentrated by centrifugation. Approximately 2 hours are required for the isolation procedure, and activity in CO₂ fixation is constant for up to 4 hours after isolation. Microscopic examination shows about 65% of the isolated cells appear intact and unplasmolyzed and are similar to leaf msophyll cells. The yield of cells on a leaf chlorophyll basis is about 1%. A light micrograph of the isolated cells is given.     

Model Studies of the Magnetocardiogram

A general expression is developed for the quasi-static magnetic field outside an inhomogeneous nonmagnetic volume conductor containing internal electromotive forces. Multipole expansions for both the electric and magnetic fields are derived. It is shown that the external magnetic field vanishes under conditions of axial symmetry. The magnetic field for a dipole current source in a sphere is derived, and the effect of an eccentric spherical inhomogeneity is analyzed. Finally the magnetic dipole moment is calculated for a current dipole in a conducting prolate spheroid.     

A New Bibliometric Index Based on the Shape of the Citation Distribution

In order to improve the h-index in terms of its accuracy and sensitivity to the form of the citation distribution, we propose the new bibliometric index . The basic idea is to define, for any author with a given number of citations, an “ideal” citation distribution which represents a benchmark in terms of number of papers and number of citations per publication, and to obtain an index which increases its value when the real citation distribution approaches its ideal form. The method is very general because the ideal distribution can be defined differently according to the main objective of the index. In this paper we propose to define it by a “squared-form” distribution: this is consistent with many popular bibliometric indices, which reach their maximum value when the distribution is basically a “square”. This approach generally rewards the more regular and reliable researchers, and it seems to be especially suitable for dealing with common situations such as applications for academic positions. To show the advantages of the -index some mathematical properties are proved and an application to real data is proposed.     

Size Distribution of "Informational" RNA

Previous investigations suggested that the size of “informational” or “messenger” RNA was confined to sedimentation rates lying between 8 and 14S. These involved procedures permitting extended contact of the RNA with enzymatically active extracts. The present study re-examined the size distribution of T2-complementary RNA isolated by a method which minimized enzymatic degradation. A much greater diversity in size distribution (4S to 25S) was observed. Experiments are described indicating that 8 to 12S informational RNA does not readily attach to the 16S and 23S ribosomal components under the conditions used for sedimentation analysis.     

Exploring the Composition of Protein-Ligand Binding Sites on a Large Scale

The residue composition of a ligand binding site determines the interactions available for diffusion-mediated ligand binding, and understanding general composition of these sites is of great importance if we are to gain insight into the functional diversity of the proteome. Many structure-based drug design methods utilize such heuristic information for improving prediction or characterization of ligand-binding sites in proteins of unknown function. The Binding MOAD database if one of the largest curated sets of protein-ligand complexes, and provides a source of diverse, high-quality data for establishing general trends of residue composition from currently available protein structures. We present an analysis of 3,295 non-redundant proteins with 9,114 non-redundant binding sites to identify residues over-represented in binding regions versus the rest of the protein surface. The Binding MOAD database delineates biologically-relevant “valid” ligands from “invalid” small-molecule ligands bound to the protein. Invalids are present in the crystallization medium and serve no known biological function. Contacts are found to differ between these classes of ligands, indicating that residue composition of biologically relevant binding sites is distinct not only from the rest of the protein surface, but also from surface regions capable of opportunistic binding of non-functional small molecules. To confirm these trends, we perform a rigorous analysis of the variation of residue propensity with respect to the size of the dataset and the content bias inherent in structure sets obtained from a large protein structure database. The optimal size of the dataset for establishing general trends of residue propensities, as well as strategies for assessing the significance of such trends, are suggested for future studies of binding-site composition.