Kinetoplastid RNA editing ligases 1 and 2 exhibit different electrostatic properties

Kinetoplastid RNA editing ligases 1 and 2 (KREL1 and KREL2) share a significant degree of sequence homology. However, biochemical experiments have reported that KREL1 and KREL2 differ in their functional roles during the RNA editing process. In this study, we hypothesize that dissimilar roles for KREL1 and KREL2 proteins arise from their different physicochemical characteristics. To test our hypothesis at sequence level, we plotted theoretical titration curves for KREL1, KREL2 and their binding partner proteins. The plots showed a lower isoelectric point for KREL1 compared to that for KREL2 as well as more relative alkalinity and acidity for binding partner proteins of KREL1 and KREL2 at net charge zero, respectively. At structure level, based on the available high resolution structure of KREL1 N-terminal domain and strong sequence similarity between KRELs and other ligases, we built the homology model of KREL2 N-terminal domain. Using Poisson-Boltzmann continuum approach, we calculated the electrostatic potential isosurfaces of KREL1 structure and KREL2 model. KREL1 and KREL2 coordinates differed in their electrostatic isopotential patterns. A wider negative patch on the surface of KREL1 suggests differential affinity for another protein compared to KREL2. In contrast, a larger positive patch on the KREL2 surface predicts its differential affinity and/or specificity for its RNA substrate. Subsequently, we employed in silico mutational scanning and identified the surface-exposed residues contributing to the long-range electrostatic energy of KRELs. We predict that two structurally conserved loops of KRELs, not previously reported in the literature, also recognize their RNA substrates. Our results provide important information about the physicochemical properties of RNA editing ligases that could contribute to the ligation step of RNA editing.     

Reduced Efficiency of Magnetotaxis in Magnetotactic Coccoid Bacteria in Higher than Geomagnetic Fields

Magnetotactic bacteria are microorganisms that orient and migrate along magnetic field lines. The classical model of polar magnetotaxis predicts that the field-parallel migration velocity of magnetotactic bacteria increases monotonically with the strength of an applied magnetic field. We here test this model experimentally on magnetotactic coccoid bacteria that swim along helical trajectories. It turns out that the contribution of the field-parallel migration velocity decreases with increasing field strength from 0.1 to 1.5 mT. This unexpected observation can be explained and reproduced in a mathematical model under the assumption that the magnetosome chain is inclined with respect to the flagellar propulsion axis. The magnetic disadvantage, however, becomes apparent only in stronger than geomagnetic fields, which suggests that magnetotaxis is optimized under geomagnetic field conditions. It is therefore not beneficial for these bacteria to increase their intracellular magnetic dipole moment beyond the value needed to overcome Brownian motion in geomagnetic field conditions.     

Geometric properties of magnetic field lines on toroidal magnetic surfaces in the context of plasma equilibrium

An analysis of plasma equilibrium in a magnetic confinement system includes studies of how the shape of the magnetic surfaces is distorted with varying magnitude and profile of the plasma pressure. Such studies allow one, in particular, to determine the maximum β value consistent with equilibrium, β_eq, i.e., the maximum plasma pressure above which the equilibrium in a confinement system under analysis is impossible. Since the magnetic field lines form magnetic surfaces, their global relationship with equilibrium is obvious. Here, special attention is paid to a local relationship between equilibrium and geometric properties of the magnetic field lines.     

Physical nature of the electric current produced by the asymmetry of particle motion in toroidal magnetic confinement systems

A new type of longitudinal electric current is revealed by analyzing the drift trajectories of charged particles in a tokamak—the current that may be referred to as the asymmetry current because it is associated with the asymmetry of the boundary between trapped and transit particles in phase space. The generation of this current is explained by the fact that the motions of the particles that cross the magnetic surface at a given point in opposite directions are qualitatively different. The asymmetry current results from the toroidal variations of the magnetic field and is maintained by the radial momentum flux of transit particles. The contribution of the particles of different species to the asymmetry current density is proportional to their pressure, is independent of the gradients of the plasma parameters, is maximum at the magnetic axis, and decreases toward the plasma periphery. In contrast to standard neoclassical theory, the asymmetry current can be found only from exact particle trajectories. The asymmetry current is calculated for tokamaks with differently shaped magnetic surfaces and for a model stellarator. By exploiting the newly revealed asymmetry current, together with the bootstrap current, it may be possible to substantially simplify the problem of creating a tokamak reactor.     

Formation of a cylindrical ion beam in the field of an axisymmetric system of ring currents at a low Hall current

A study is made of the structure of an accelerating layer with a closed Hall current and the geometry of an ion beam in an external magnetic field created by an arbitrary axisymmetric system of ring currents under conditions such that the Hall current can be ignored. It is shown that the ion trajectories are perpendicular to the magnetron cutoff surface for electrons and that the cathode plasma boundary coincides with a magnetic field line. A magnetic field configuration is found in which the cutoff surface is a plane surface perpendicular to the axis of the system. It is shown that, for a small ratio of the gyroradius of the electrons (in terms of the maximum energy acquired by them in the layer) to the characteristic size of the structure, such a configuration provides sufficient means to ensure the formation of slightly converging ion beams or those that are essentially parallel to the system axis.     

Propagation of MHD waves in a plasma in a sheared magnetic field with straight field lines

The propagation of MHD plasma waves in a sheared magnetic field is investigated. The problem is solved using a simplified model: a cold plasma is inhomogeneous in one direction, and the magnetic field lines are straight. The waves are assumed to travel in the plane perpendicular to the radial coordinate (i.e., the coordinate along which the plasma and magnetic field are inhomogeneous). It is shown that the character of the singularity at the resonance surface is the same as that in a homogeneous magnetic field. It is found that the shear gives rise to the transverse dispersion of Alfvén waves, i.e., the dependence of the radial component of the wave vector on the wave frequency. In the presence of shear, Alfvén waves are found to propagate across magnetic surfaces. In this case, the transparent region is bounded by two turning points, at one of which, the radial component of the wave vector approaches infinity and, at the other one, it vanishes. At the turning point for magnetosonic waves, the electric and magnetic fields are finite; however, the radial component of the wave vector approaches infinity, rather than vanishes as in the case with a homogeneous field.     

The possible role of contact current in cancer risk associated with residential magnetic fields

Residential electrical wiring safety practices in the US result in the possibility of a small voltage (up to a few tenths of a volt) on appliance surfaces with respect to water pipes or other grounded surfaces. This "open circuit voltage" (V(OC)) will cause "contact current" to flow in a person who touches the appliance and completes an electrical circuit to ground. This paper presents data suggesting that contact current due to V(OC) is an exposure that may explain the reported associations of residential magnetic fields with childhood leukemia. Our analysis is based on a computer model of a 40 house (single-unit, detached dwelling) neighborhood with electrical service that is representative of US grounding practices. The analysis was motivated by recent research suggesting that the physical location of power lines in the backyard, in contrast to the street, may be relevant to a relationship of power lines with childhood leukemia. In the model, the highest magnetic field levels and V(OC)s were both associated with backyard lines, and the highest V(OC)s were also associated with long ground paths in the residence. Across the entire neighborhood, magnetic field exposure was highly correlated with V(OC) (r = 0.93). Dosimetric modeling indicates that, compared to a very high residential level of a uniform horizontal magnetic field (10 mu T) or a vertical electric field (100 V/m), a modest level of contact current (approximately 18 mu A) leads to considerably greater induced electric fields (> 1 mV/m) averaged across tissue, such as bone marrow and heart. The correlation of V(OC) with magnetic fields in the model, combined with the dose estimates, lead us to conclude that V(OC) is a potentially important exposure with respect to childhood leukemia risks associated with residential magnetic fields. These findings, nonetheless, may not apply to residential service used in several European countries or to the Scandinavian studies concerned with populations exposed to magnetic fields from overhead transmission lines.     

Migratory Orientation: Magnetic Compass Orientation of Garden Warblers (Sylvia borin) after a Simulated Crossing of the Magnetic Equator

Since the birds' magnetic compass works as an inclination compass using the axial course of the magnetic field lines and their inclination, transequatorial migrants have to reverse their reaction with respect to the magnetic field after crossing the magnetic equator. Garden Warblers, long distance migrants breeding in Europe and wintering in tropical and southern Africa, were tested during autumn in the local geomagnetic field on the northern hemisphere. The experimental group was exposed to a field with horizontal field lines, simulating equator crossing, at the beginning of October; afterwards the birds were tested in the local geomagnetic field again. While the controls showed southerly tendencies during the entire season, the experimentals reversed their directional tendencies after staying in the horizontal field and now preferred northerly directions. In a field of the southern hemisphere, this preference corresponds to a southern course which would have meant the continuation of their migration flight.     

Residential exposure to magnetic fields generated by 110-400 kV power lines in Finland

In a specific case, the magnetic field generated in a building by a nearby power line is usually easy to calculate, although the accuracy of these calculations is sensitive to the quality of source information. To be able to study public health dimensions of magnetic field exposure (e.g., risk of cancer), it is necessary to evaluate the size and exposure of the population at risk. Relatively little quantitative information on public exposure to power-frequency magnetic fields of high-voltage power lines is available. This report describes residential exposure to magnetic fields from 110 kV, 220 kV, and 400 kV power lines in Finland at the national level, including 90% of the total line length in 1989. A geographical information system (GIS) was used to identify the buildings located near the power lines. After determining the distances between the lines and the buildings, historical data on load currents of these lines were used to calculate the magnetic fields. The residential magnetic field histories were then linked to the residents by means of a computerized central population register. The data obtained on personal exposure have also been utilized in a nationwide epidemiological study on magnetic field exposure of power lines and risk of cancer. The methods of exposure assessment and results of the number of buildings near 110 kV, 220 kV, and 400 kV power lines, their average annual magnetic fields, and personal exposure to magnetic fields from these lines are described. We found that 15,600 residents lived in an average residential magnetic field ≥0.1 μT caused by power lines in 1989. The number of these residents increased fivefold during 1970-1989. We estimated that 0.3% of the population was exposed in their residences to an annual average magnetic flux density from 110 kV, 220 kV, and 400 kV power lines higher than 0.1 μT, the level that the background magnetic flux density in general does not exceed in Finnish homes. Thus, the problem of magnetic field exposure generated by high-voltage lines concerns only a relatively small fraction of the total population in Finland. However, the size and exposure of the population at risk remain somewhat arbitrary in practical multisource situations, as the biological interaction mechanism, the concept of harmful dose, and, in particular, the significance of the duration of exposure are unknown. © 1995 Wiley-Liss, Inc.     

Use of 13C chemical shift surfaces in the study of carbohydrate conformation. Application to cyclomaltooligosaccharides (cyclodextrins) in the solid state and in solution

The anomeric carbon chemical shifts of free cyclomaltohexaose, -heptaose, -octaose, -decaose, and -tetradecaose (alpha-, beta-, gamma-, epsilon-, and eta-cyclodextrin, respectively), and of alpha-cyclodextrin inclusion complexes, both in the solid state and in solution, were computed using ab initio 13C chemical shift surfaces for the D-Glcp-alpha-(1-->4)-D-Glcp linkage as a function of the glycosidic bond dihedral angles. Chemical shift calculations in the solid state used angle pairs measured from cyclodextrin X-ray structures as input. For estimations in the liquid state two different approaches were employed to account for dynamic averaging. In one, the computed solid-state anomeric carbon chemical shifts for each cyclodextrin D-Glcp monomer were simply averaged to obtain an estimate of the 13C shifts in solution. In the other, chemical shifts for the anomeric carbons were determined by averaging back-calculated 13C shift trajectories derived from a series of 5 ns molecular dynamic simulations for the oligosaccharides with explicit representation of water. Good agreement between calculated and experimental 13C shifts was found in all cases. Furthermore, our results show that the ab initio 13C chemical shift surfaces are sufficiently sensitive to reproduce the small variations observed for the anomeric 13C shifts of the different cyclodextrin D-Glcp units in the solid state with excellent accuracy. The use of chemical shift surfaces as tools in conformational studies of oligosaccharides is discussed.     

Analysis of the processes occurring in a submicrosecond discharge with a linear current density of up to 3 MA/cm through a thick-wall stainless-steel electrode

The state of conductors carrying a megampere current from the generator to the load is studied experimentally. It is found that the plasma produced from cylindrical stainless-steel tubes during the passage of a submicrosecond current pulse with a linear density of 3 MA/cm expands with a velocity of 5.5 km/s. Numerical results on the diffusion of the magnetic field induced by a current with a linear density of 1–3MA/cm into metal electrodes agree with the experimental data on the penetration time of the magnetic field. For a linear current density of 3.1 MA/cm, the experimentally determined electric field strength on the inner surface of the tube is 4 kV/cm. The calculated electric field strength on the inner surface of the tube turns out to be two times higher, which can be explained by plasma production on the outer and inner surfaces of the electrode.     

Topology of drift trajectories of charged particles in a tokamak

The topology of drift orbits in a tokamak is analyzed in the entire cross section of the device both near the magnetic axis and at the periphery of the plasma column. The use of invariants of the drift equations (the generalized momentum, magnetic moment, and total energy) as variables for the entire cross section of the plasma column and self-similar variables near the magnetic axis makes it possible to comprehensively classify closed drift orbits in a tokamak. When describing orbits of different types and domains of their existence, discriminant and locus curves obtained by the methods of differential geometry are used to determine the ranges in which the invariants vary. The influence of the nonuniformity of the longitudinal current on the drift trajectories of fast particles is studied. The works in which, together with known types of orbits, trajectories along which particles leave the plasma column and can fall on the chamber wall are analyzed.     

Role of the mean curvature in the geometry of magnetic confinement configurations

Examples are presented of how the geometric notion of the mean curvature is applied to the vector of a general magnetic field and to magnetic surfaces. It is shown that the mean curvature is related to the variation of the absolute value of the magnetic field along its lines. Magnetic surfaces of constant mean curvature are optimum for plasma confinement in multimirror open confinement systems and rippled tori.     

Experimental study of electron vortex structures in an electrostatic plasma lens

Results are presented from experimental studies of electron vortex bunches in a cold ion-beam plasma consisting of strongly magnetized electrons and a beam of almost free positive ions. The existence of electron vortex bunches was detected from local minima of the electric potential on surfaces perpendicular to the magnetic field lines. It is found that the vortices have the form of magnetic-field-aligned filaments, in which electrons rotate with a velocity significantly exceeding both the velocity of the vortex as a whole and the electron velocity in the ambient plasma. It is shown that, in a sufficiently strong magnetic field, the accumulation of electrons in the vortices terminates when the condition for the longitudinal confinement of electrons by the electric field fails to hold.     

Sensitive bondforce measurements of ligand-receptor pairs with magnetic beads

The bondforces between biotinylated surfaces and streptavidin or avidin coated beads are investigated by a magnetic field based manipulation system for magnetic microbeads. The magnetic field is generated by currents through a set of conducting lines, and its gradient exerts a force onto the magnetic beads. The force can be increased until the bond between the bead and the surface breaks. Consistent with other groups we found two conformations for both investigated bonds. The measured bondforces for the two conformations are for Streptavidin-Biotin: 55.9 and 244.7 fN and for Avidin-Biotin: 15.9 and 58.4 fN. These very low bondforces (10-100 times smaller than earlier measurements) match to the extremely low loading rate of about 1 fN/s. This new technique thus allows to investigate biomolecular bonds by extremely low forces.     

Launching of Microwaves into a Dense Plasma in Open Confinement Systems

A study is made of the propagation of microwave beams in a plasma and their passage through the critical surface. It is shown that, in order for microwaves to penetrate deeply into a dense plasma, it is necessary to launch them through a magnetic mirror at a slight angle to the device axis. The characteristic features of ray trajectories are analyzed both ahead of and behind the critical surface. In a dense plasma behind the critical surface, microwaves tend to run out of the axial region toward the plasma periphery. This tendency may be unfavorable for heating plasmas whose radial density profiles are strongly peaked about the system axis. The problems under analysis are particularly important for assessing the prospects for ECR heating of dense plasmas in open confinement systems.     

Switching of Swimming Modes in Magnetospirillium gryphiswaldense

The microaerophilic magnetotactic bacterium Magnetospirillum gryphiswaldense swims along magnetic field lines using a single flagellum at each cell pole. It is believed that this magnetotactic behavior enables cells to seek optimal oxygen concentration with maximal efficiency. We analyze the trajectories of swimming M. gryphiswaldense cells in external magnetic fields larger than the earth’s field, and show that each cell can switch very rapidly (in <0.2 s) between a fast and a slow swimming mode. Close to a glass surface, a variety of trajectories were observed, from straight swimming that systematically deviates from field lines to various helices. A model in which fast (slow) swimming is solely due to the rotation of the trailing (leading) flagellum can account for these observations. We determined the magnetic moment of this bacterium using a to our knowledge new method, and obtained a value of (2.0 ± 0.6) × 10^?16 A · m². This value is found to be consistent with parameters emerging from quantitative fitting of trajectories to our model.     

Calculation and optimization of plasma-optic focusing devices

(i) The focusing of an ion beam by a Morozov lens formed by a current ring in a plasma is calculated using an exact expression for the magnetic field and taking into account the nonparaxial character of the focused beam. The possible ways of optimizing such a lens are considered. (ii) Different versions of extended plasmaoptic devices in which spherical aberrations are minimized are analyzed. It is proposed to optimize extended plasma-optic devices by changing the magnetic field from the entrance end to the exit end of the solenoid in such a way that the boundary magnetic surface always coincides with the boundary surface of the focused beam. It is shown that, under the same conditions, the focusing power of the optimized devices is one to two orders of magnitude higher than that of traditional thin plasma lenses. (iii) The problem of creating a magnetic field whose strength is optimized as a function of the longitudinal coordinate is solved by the Tikhonov regularization method. (iv) An extended plasma-optic device with an optimized solenoid for focusing 1-MeV ion beams is calculated, and the ion trajectories in the device are traced. (v) It is proved expedient to develop special-purpose computer codes aimed at modeling and optimizing the existing and planned experimental plasma-optic focusing devices.     

A theory and a model for interpreting the proton nuclear magnetic resonance spectra of water in plant leaves.

Some plant leaves display complex, orientation-dependent, proton nuclear magnetic resonance (1H NMR) spectra. The spectral patterns vary as the angle between the leaf surface and the applied magnetic field is varied. They also vary with temperature and with the quantity of absorbed manganous ions, but they are independent of magnetic field strength. In this paper, we propose a theory to explain the origin of the spectra and a model from which the patterns can be calculated. The theory shows how heterogeneous magnetic susceptibilities and local dipolar magnetic fields in chloroplasts can shift the water-proton resonance field. The model describes a simplified leaf structure in which the chloroplasts are nonrandomly aligned with respect to the leaf surface. Model calculations are tested by comparison with experimental spectra from hawthorn leaves (Crataegus sp.).