bluuebunny/crossref_metadata_2025 huggingface dataset:
Driven, dissipative, energy-conserving magnetohydrodynamic equilibria. Part 2. The screw pinch
Authors: Goodman Michael L.
Published: March 2009

A cylindrically symmetric, electrically driven, dissipative, energy-conserving magnetohydrodynamic equilibrium model is considered. The high-magneticfield Braginskii ion thermal conductivity perpendicular to the local magnetic field and the complete electron resistivity tensor are included in an energy equation and in Ohm's law. The expressions for the resistivity tensor and thermal conductivity depend on number density, temperature, and the poloidal and axial (z-component) magnetic field, which are functions of radius that are obtained as part of the equilibrium solution. The model has plasma-confining solutions, by which is meant solutions characterized by the separation of the plasma into two concentric regions separated by a transition region that is an internal boundary layer. The inner region is the region of confined plasma, and the outer region is the region of unconfined plasma. The inner region has average values of temperature, pressure, and axial and poloidal current densities that are orders of magnitude larger than in the outer region. The temperature, axial current density and pressure gradient vary rapidly by orders of magnitude in the transition region. The number density, thermal conductivity and Dreicer electric field have a global minimum in the transition region, while the Hall resistivity, Alfvén speed, normalized charge separation, Debye length, (ωλ)ion and the radial electric field have global maxima in the transition region. As a result of the Hall and electron-pressure-gradient effects, the transition region is an electric dipole layer in which the normalized charge separation is localized and in which the radial electric field can be large. The model has an intrinsic value of β, about 13·3%, which must be exceeded in order that a plasma-confining solution exist. The model has an intrinsic length scale that, for plasma-confining solutions, is a measure of the thickness of the boundary-layer transition region. If appropriate boundary conditions are given at R = 0 then the equilibrium is uniquely determined. If appropriate boundary conditions are given at any outer boundary R = a then the equilibrium exhibits a bifurcation into two states, one of which exhibits plasma confinement and carries a larger axial current than the other, which is almost homogeneous and cannot confine a plasma. Exact expressions for the two values of the axial current in the bifurcation are derived. If the boundary conditions are given at R = a then a solution exists if and only if the constant driving electric field exceeds a critical value. An exact expression for this critical electric field is derived. It is conjectured that the bifurcation is associated with an electric-field-driven transition in a real plasma, between states with different rotation rates, energy dissipation rates and confinement properties. Such a transition may serve as a relatively simple example of the L—H mode transition observed in tokamaks.
Models of laser plasma ablation. Part 4. Steadystate theory: collisional absorption flow
Authors: Pert G. J.
Published: March 2009

The clarification of models of laser ablation by plasma heating is examined using a general dimensional argument and introducing a set of universal parameters. The regime of laser-plasma interaction in which collisional absorption and thermal conduction dominate is examined for spherical systems. Detailed scaling relations are derived for uninhibited and flux-limited thermal conduction. The complete set of regimes for steady spherical flow are examined, and it is found that the most important flows are thin collisional and thick local absorption.
Non-diffusive corrections to the long-scale behaviour of ensembles of turbulent magnetic lines: application of the functional method
Authors: Spineanu F. , Vlad M. , Misguich J. H.
Published: March 2009

The transverse spreading of magnetic field lines in a turbulent plasma is investigated analytically in order to obtain a statistical characterization at large spatial scales. We develop a functional-integral method that allows us to calculate in a systematic way statistical averages of physical quantities that depend on the fluctuating field. The known magnetic diffusion coefficient for the shear-free case is corrected with a term arising from the assumption of a finite transverse correlation length. For the case with magnetic shear the functional method provides the appropriate framework for a perturbative approach based on diagram series.
Turbulent transport in magnetic confinement: how to avoid it
Authors: Binderbauer M. W. , Rostoker N.
Published: March 2009

From recent tokamak research, there is considerable experimental evidence that superthermal ions slow down and diffuse classically in the presence of turbulent fluctuations that cause anomalous transport of thermal ions. Further more, research on field-reversed configurations at Los Alamos is consistent with the view that kinetic effects suppress instability growth when the ratio of plasma radius to ion orbital radius is small; turbulence is enhanced and confinement degrades when this ratio increases. Motivated by these experiments, we consider a plasma consisting of large-orbit non-adiabatic ions and adiabatic electrons. For such a plasma, it is possible that the anomalous transport characteristic of tokamaks can be avoided and a compact reactor design becomes viable.
Anomalous transport due to long-lived fluctuations in plasma Part 2. Hydrodynamic contributions to transport in two-dimensional, strongly magnetized systems
Authors: Krommes John A. , Oberman Carl
Published: March 2009

The general formalism for treating two-time fluctuations in magnetized plasma, developed in part 1 of this series, is applied to the case of anomalous cross-field transport in 2-D, strongly magnetized, thermal equilibrium systems. For (where εP is the plasma parameter), classical predictions for the ion shear viscosity and test particle diffusion coefficients are dominated by the anomalous contributions of low frequency, long wavelength hydrodynamic fluctuations (convective cells). The anomalous transport is discussed from the points of view of (a) kinetic theory; (b) the assumption of long-time local thermal equilibrium (Landau-Placzek method); and (c) a renormalized mode-coupling version of the generalized Langevin equation. The results of all these approaches are in agreement, and they predict that the transport coefficients scale with magnetic field B as 1/B for, and as independent of B for

in good agreement with the computer simulations of Okuda & Dawson. The transport is weakly non-Markovian, the Green-Kubo integrands decay non-classically for long times as [t ln (t)]−½, and the test particle ‘;diffusion’ coefficient does not asymptotically approach a constant for t → ∞.
Elements of magnetohydrodynamics with the Hall current. Part 1. Nonlinear phenomena
Authors: Rosenau P. , Tataronis J. A. , Conn G.
Published: March 2009

The elements of magnetohydrodynamics (MHD) with the Hall current are presented. The governing partial differential equations are, like those of ideal MHD, quasi-linear, but unlike ideal MHD, are not hyperbolic. However, they do possess real characteristics which are shown to be associated with the sound wave and the surfaces ø(r, t) = const. determined by B. ∇ø = 0. Properties of weak and strong discontinuities are discussed, and comparisons are made with ideal MHD. It is shown that generalizations of dipole layers appear as a result of discontinuities in the magnetic field.
Structure of shock waves in partially ionized argon
Authors: Shanmugasundaram V. , Murty S. S. R.
Published: March 2009

A unified picture of the structure of steady, one-dimensional shock waves in partially ionized argon, in the absence of external electric or magnetic field, is presented. The investigation is based on a two-temperature, three-fluid continuum approach, using the Navier–Stokes equations as a model and including non-equilibrium ionization. Quasi charge neutrality and zero velocity slip are assumed. The analysis of the governing equations is based on the method of matched asymptotic expansions and results in the following three layers: (1) a broad thermal layer dominated by electron thermal conduction, (2) an atom-ion (A-I) shock structured by the heavy particle (atoms and ions) collisional dissipative mechanisms and (3) an ionization relaxation layer (IRL) wherein electron- atom inelastic collisions dominate. Solutions have been obtained for the first two orders with respect to a small parameter, which is the ratio of energy fluxes due to heavy particle viscous dissipation and electron thermal conduction. Whereas only electron temperature and electric potential show any marked variation in the thermal layer, the changes in all the variables in both the A-I shock and the IRL are significant.

Inclusion of electron thermal conduction terms in the governing equations has been observed to introduce numerical instabilities in the analysis of the IRL. They are circumvented by adopting a regular perturbation scheme with respect to a local small parameter, which has been identified to be the ratio of the freestream degree of ionization to the nondimensional characteristic temperature for first ionization. Numerical results show that the effect of electron thermal conduction on the IRL profiles is significant. Results in the form of tables and figures are presented for five sets of equilibrium free-stream conditions.
The Zakharov–Kuznetsov equation for nonlinear ion-acoustic waves
Authors: Murawski K. , Edwin P. M.
Published: March 2009

The Zakharov-Kuznetsov equation is used to describe ion-acoustic wave propagation in a magnetic environment. An initial-value problem is solved for this equation on the basis of a numerical method that uses the fast-Fourier-transform technique for calculating space derivatives and a fourth-order Runge-Kutta method for the time scheme. Numerical simulations show that the disturbed flat (planar) solitary waves can break up into more robust cylindrical ones. Interactions between these two types of wave, and recurrence phenomena, are also studied.
Ion–acoustic instability of the positive column
Authors: Ilić D. B. , Wheeler G. M. , Crawford F. W. , Self S. A.
Published: March 2009

The excitation characteristics of the current-driven ion acoustic instability are studied, using a linearized kinetic model for a weakly ionized, unmagnetized plasma. Convective instability is predicted for typical low-pressure positive column conditions. The calculated spatial growth rates show a variation with frequency, which is similar to that of the amplitude variation with frequency of the self-excited instability measured in our positive column experiments in helium and argon. The comparison between theory and experiment indicates that ion Landau damping is significant for typical experimental conditions.
Electric fields parallel to the magnetic field in a laboratory plasma in a magnetic mirror field
Authors: Geller R. , Hopfgarten N. , Jacquot B. , Jacquot C.
Published: March 2009

With electrostatic probes, the electric field component E∥ along the magnetic field B was comprehensively investigated in a collisionless plasma, the density of which was of the order of 1010 cm-3. The plasma in the experiment has several properties in common with the plasma of the ionosphere/magnetosphere scaled to laboratory dimensions. It is produced by means of electron cyclotron resonance in a microwave cavity located in the magnetic field gradient in one half of a magnetic mirror field. The magnetic field strength is 3600G in the resonance zone and 1800G in the middle of the mirror field. The measurements show that a stationary E∥ exists everywhere in the plasma, where the magnetic field gradient grad11 B in the direction of the field is different from zero. The direction of E‖ is opposite to that of grad‖B. The total potential drop along B between the resonance zone and the midplane of the mirror field is of the order of kilovolts. E‖ accelerates ions along B to energies of the order of kilo electron volts. Experimental parameters of importance for the production of E‖ are the neutral gas pressure p (normally a few times 10− Torr), the microwave power (usually about 2kW), and the mirror ratio γ in the mirror region opposite to the cavity side, γ was normally <2. For γ>2·3, an instability develops and no stationary E‖ remains. As p is increased, E‖ decreases successively. In terms of the mean free path λ, it is found that λ>5−10L is a necessary condition for the existence of E‖. L is twice the distance between the cavity and the midplane of the mirror field. In the experiment, the ion and electron pitch angle distributions are forced to be different; the ion velocity is mainly parallel to B, and the electron velocity essentially perpendicular to JB, and as consequence E‖ is created. In this way an experimental demonstration is presented of the theoretically predicted relation between E‖ and the pitch angle distributions. When imposing sufficiently strong radial electric fields Er (fields perpendicular to B), the distribution of the potential along B is deformed, probably due to changes in the particle distributions caused by E‖. We think that our results strongly support the idea that Et is produced in the magnetosphere, and is at least sometimes an important mechanism for the acceleration and precipitation of auroral particles.
The expansion of a plasma into a vacuum
Authors: Crow J. E. , Auer P. L. , Allen J. E.
Published: March 2009

This paper reports calculations of the collision-free expansion of a semi-infinite plasma. It is shown that the ion front is accelerated to velocities comparable with the thermal velocity of the electrons.
The totality of waves in a homogeneous Vlasov plasma
Authors: Puri S. , Leuterer F. , Tutter M.
Published: March 2009

An attempt is made to trace the physical origin of the complex roots of the dispersion relation for a Maxwellian, non-relativistic, homogeneous, magnetized Vlasov plasma. For simplicity, the identification process is performed for the case of propagation perpendicular to the magnetic field. For a given real ω, there are infinitely many complex roots, in addition to a finite number of propagating solutions. The propagating waves correspond (in addition to the cold-plasma waves) to either the extraordinary Gross— Bernstein mode propagating just above the harmonics, or the pair of Dnestrovskij— Kostomarov modes (one ordinary and the other extraordinary) propagating just below the harmonics. The hot-plasma solutions asymptotically approach the harmonic frequencies as k‖→∞, and analytically continue across the harmonics as complex waves. These complex waves, originating in groups of three from each cyclotron harmonic, apparently remain distinct, giving rise to an infinity of complex roots for a given frequency (since there are an infinite number of cyclotron harmonics). Detailed analysis reveals that, for the ordinary and the extraordinary Dnestrovskij-Kostomarov modes, electric displacement and magnetic induction, respectively, are the dominant field components.
Construction of electron distribution functions from laser scattering spectra
Authors: Williamson J. H. , Clarke M. E.
Published: March 2009

The Thomson scattering spectrum, for laser light scattered by a low density plasma, is determined by the Doppler shifts from the moving electrons. It is shown how the full three-dimensional distribution function may be constructed if spectra are observed in several directions. Calculations using a model loss-cone distribution show that four spectra are sufficient for a faithful reconstruction of f(v). Most of the complications that arise at relativistic electron velocities can be avoided by placing a diffraction grating in the scattered laser beam.
Kinetic equations for plasmas subjected to a strong time-dependent external field: Part 3. Stochastic equations for plasma turbulence
Authors: Balescu R. , Misguich J. H.
Published: March 2009

The kinetic equation obtained in parts 1 and 2 is treated stochastically: the external field is stochastic, with an average and a fluctuating part. The turbulence of the system is described by the induced fluctuations in the plasma, and a general equation is derived for the average distribution function. As a particular case, the stochastic Vlasov equation is treated explicitly, and compared with the descriptions of Dupree, Weinstock and Benford & Thomson.
On the temporal development of a plasma sheath
Authors: Cipolla J. W. , Silevitch M. B.
Published: March 2009

In this work we study a one-dimensional model for the time-dependent behaviour caused by placing an uncharged conducting surface in contact with a uniform equilibrium plasma. Both the probe potential and plasma response are unknown a priori but are specified through a set of self-consistent model equations and boundary conditions. We investigate some numerical and analytical consequences of this model. In particular, we consider such issues as (i) the formation and expansion of a quasi-neutral region connecting the non-neutral sheath to the distant undisturbed plasma; (ii) the validity of assuming the existence of a sheath edge; and (iii) the role of both static and dynamic Bohm criteria in the theory of unsteady sheath development.
A theory for Langmuir solitons
Authors: Rao N. Nagesha , Varma Ram K.
Published: March 2009

A systematic and self-consistent analysis of the problem of Langmuir solitons in the entire range of Mach numbers (0 < M < 1) has been presented. A coupled set of nonlinear equations for the amplitude of the modulated, high-frequency Langmuir waves and the associated low-frequency ion waves is derived without using the charge neutrality condition or any a priori ordering schemes. A technique has been developed for obtaining analytic solutions of these equations where any arbitrary degree of ion nonlinearity consistent with the nonlinearity retained in the Langmuir field can be taken into account self-consistently. A class of solutions with non-zero Langmuir field intensity at the centre (ξ = 0) are found for intermediate values of the Mach number. Using these solutions, a smooth transition from single-hump solitons to the double-hump solitons with respect to the Mach number has been established through the definitions of critical and cut-off Mach numbers. Further, under appropriate limiting conditions, various solutions discussed by other authors are obtained. Sagdeev potential analyses of the solutions for the Langmuir field as well as the ion field are carried out. These analyses confirm the transition from single-hump solitons to the double-hump solitons with respect to the Mach number. The existence of many-hump solitons for higher-order nonlinearities in the low-frequency ion wave potential has been conjectured. The method of solution developed here can be applied to similar equations in other fields.
Coding of sounds in lower levels of the auditory system
Authors: Møller Aage R.
Published: March 2009

The great number of investigations and advanced developments in neurophysiology and psychoacoustics during recent years have extensively increased our knowledge about the frequency analysis of simple sounds in the peripheral auditory system.

New methods have facilitated quantitative measurements of the amplitude of the submicroscopic vibration of a narrow segment of the basilar membrane in anaesthetized animals at physiological sound intensities. The results of these studies have quantitatively confirmed the results of past studies by showing that the basilar membrane has a selectivity with regard to tone frequency. In addition to this, the recent studies have increased our knowledge about the finer details of vibration of the basilar membrane. At the lowest levels used in the recent investigations, i.e. about 70 dB SPL, the selectivity in the 7 kHz region of the basilar membrane was found to be greater than expected on the basis of extrapolation of older data. Moreover, the high frequency slope of the tuning curves of the basilar membrane was found to be particularly steep. The results of these recent studies, furthermore, showed that the basilar membrane vibrates in a non-linear way at intensities within the physiological range. This non-linearity results in a broadening of the selectivity curves of a narrow segment of the basilar membrane when the sound intensity is increased.

Little is known as to how the motion of the basilar membrane is transformed to excitation of the cochlear sensory cells, i.e. the haircells. The excitation may be related to displacement, spatial differentiation or other transformations of the basilar membrane motion. Recording from the interior of mammalian haircells has so far been unsuccessful, and the neural excitatory process within the haircells in the cochlea is as yet practically unknown. Studies of the haircells in the lateral line organ of fish have provided fundamental knowledge about their excitation; since they in many respects resemble those in the mammalian cochlea, the results very probably can be applied to the excitatory process in the mammalian cochlea.
Fluorescence relaxation spectroscopy in the analysis of macromolecular structure and motion
Authors: Rigler Rudolf , Ehrenberg Måns
Published: March 2009

Fluorescence spectroscopy offers particularly sensitive tools for the investigation of physical properties of macromolecules in solution. Differences in molecular structure under varying experimental conditions are often reflected in quantum yield and lifetime of natural or synthetically inserted fluorescent probes. inserted fluorescent probes. Energy transfer between fluorescent groups at known places of a primary sequence can be used to measure distances between the label sites (Eisinger, 1976) as well as to investigate their relative motion, e.g. measurements of the kinetics of variations in the end to end distance of a polymer (E. Haas & I. Steinberg, personal communication).
Structure and function of the constant regions of immunoglobulins
Authors: Beale D. , Feinstein A.
Published: March 2009

Immunoglobulins are somewhat unusual in that they are biologically active proteins capable of carrying out several different functions. Thus, they can bind specifically with antigen, activate the complement system, mediate many cytotropic reactions, and act as antigen receptors on lymphocyte membranes.
Magnetic field effects on photosynthetic reactions
Authors: Hoff A. J.
Published: March 2009

When light impinges on photosynthetic material – a plant leaf, an alga or a photosynthetic bacterium – it is absorbed by an array of lightcollecting pigments. Through resonant energy transfer the absorbed quantum of light is transported to a trap, the reaction centre. Within such a trap, a specialized (bacterio)chlorophyll complex is able to eject from its excited state an electron. This electron is ‘captured’ by an adjacent acceptor, which in turn donates the electron to a second acceptor, and so on. Thus, light energy is converted into chemical energy which is ultimately used in the metabolic processes of the cell.
Physical models for the analysis of acoustical systems in biology
Authors: Fletcher N. H. , Thwaites Suszanne
Published: March 2009

One of the important problems of biophysics is to understand in detail the mechanisms by which animals produce acoustic signals, and the ways in which other animals, of the same or different species, detect and process these signals, through the masking effects of ambient noise, to extract their information content. At a primitive level this information relates simply to the presence of the other animal and perhaps to its proximity and direction. At the next level we find some sort of coding in the acoustic signal which identifies the species and perhaps the sex, and finally there is the whole range of information content and emotional overtone contained in a complex sound like human speech or music.
Progress in high resolution atomic force microscopy in biology
Authors: Shao Zhifeng , Yang Jie
Published: March 2009

The atomic force microscope (AFM) was invented by Binnig, Quate and Gerber less than 10 years ago (Binniget al. 1986). In their first prototype, a piece of goldfoil was used as the cantilever, with a crushed diamond tip mounted at the end. On the back of the cantilever, a tunnelling junction was used to monitor the deflection of the cantilever (the gold-foil) when the specimen was scanned with the tip in contact with the surface. Thus, the surface topography of the specimen was obtained with a resolution critically dependent on the sharpness of the tip provided the deformation of the specimen was not serious. Even with such a crude set-up, they managed to obtain a lateral resolution of ˜ 30 Å and a vertical resolution of better than 1 Å on an amorphous A12O3surface. The operating principle of such an instrument is deceptively simple. However, such an arrangement was inconvenient for routine operations and unsuitable for imaging hydrated specimens, because the tunnelling junction is easily contaminated in air and works poorly in aqueous solutions (Alexanderet al. 1989). As a result, the application of this type of AFM to biological samples was rare (Engel, 1991).
Origin of the homochirality of biomolecules
Authors: Keszthelyi L.
Published: March 2009

Molecules built up from a given set of atoms may differ in their three-dimensional structure. They may have one or more asymmetric centres that serve as reference points for the steric distribution of the atoms. Carbon atoms, common to all biomolecules, are often such centres. For example, the Cα atom between the carboxyl and amino groups in amino acids is an asymmetric centre: looking ON ward (i.e. from the carbOxyl to the amiNo group, with the Cα oriented so that it is above the carboxyl and amino groups) the radical characterizing the amino acid may be to the right (D-molecules) or to the left (L-molecules). Nineteen of the 20 amino acids occurring in proteins have such a structure (the exception is glycine, where the radical is a hydrogen atom). These pairs of molecules cannot be brought into coincidence with their own mirror image, as is the situation with our hands. The phenomenon has therefore been named handedness, or chirality, from the Greek word cheir, meaning hand. The two forms of the chiral molecules are called enantiomers or antipodes. They differ in rotating the plane of the polarized light either to the right or to the left. The sense of rotation depends on the wavelength of the measuring light, but at a given wavelength it is always opposite for a pair of enantiomers. Chirality may also occur when achiral molecules form chiral substances during crystallization (for example, quartz forms D-quartz or Lquartz). A detailed theoretical treatment of molecular chirality is given by Barron (1991).
Problems and prospects in the theory of gel electrophoresis of DNA
Authors: Zimm Bruno H. , Levene Stephen D.
Published: March 2009

Electrophoresis of DNA through gels of agarose or polyacrylamide (PA) has been one of the most widely used techniques of molecular biology during the past decade, serving both analytical and preparative purposes. The molecular theory of this process has been developing slowly over the same period of time as the result of the efforts of a small but expanding group of people. Initially simple, the theory has grown in ways that no one anticipated at the beginning, partly in response to unexpected experimental discoveries. In this review we describe its current state, including both solved and unsolved problems.
Regional air‐sea fluxes of anthropogenic carbon inferred with an Ensemble Kalman Filter
Authors: Gerber M. , Joos F. , Vázquez‐Rodríguez M. , Touratier F. , Goyet C.
Published: March 2009

Regional air‐sea fluxes, ocean transport, and storage of anthropogenic carbon () are quantified. Observation‐based data from the ocean interior are assimilated into the Bern3D dynamic ocean model using an Ensemble Kalman Filter. Global uptake of is estimated to be 131 ± 18 GtC over the period 1770 to 2000. Uncertainties from systematic biases in the reconstruction of are assessed by assimilating data from four global and six Atlantic reconstructions and found to be comparable or larger than uncertainties from ocean transport. Aggregated fluxes for the southern high‐latitude, tropical and midlatitude, and northern high‐latitude ocean agree within 0.11 GtC a−1 for the two reconstructions with the highest skill score, whereas regional uptake rates are up to a factor of three different. Results indicate that uptake and regional partitioning of anthropogenic carbon in the Southern Ocean remains uncertain.
Sympathetic nervous system control of anti-influenza CD8+T cell responses
Authors: Grebe Kristie M. , Hickman Heather D. , Irvine Kari R. , Takeda Kazuyo , Bennink Jack R. , Yewdell Jonathan W.
Published: March 2009

Despite the longstanding appreciation of communication between the nervous and the immune systems, the nature and significance of these interactions to immunity remain enigmatic. Here, we show that 6-hydroxydopamine-mediated ablation of the mouse peripheral sympathetic nervous system increases primary CD8+T cell responses to viral and cellular antigens presented by direct priming or cross-priming. The sympathetic nervous system also suppresses antiviral CD4+T cell responses, but this is not required for suppressing CD8+T cell responses. Adoptive transfer experiments indicate that enhanced CD8+responses do not result from permanent alterations in CD8+T cell function in sympathectomized mice. Rather, additional findings suggest that the sympathetic nervous system tempers the capacity of antigen-presenting cells to activate naïve CD8+T cells. We also show that antiviral CD8+T cell responses are enhanced by administration of a β2(but not β1or α) adrenergic antagonist. These findings demonstrate a critical role for the sympathetic nervous system in limiting CD8+T cell responses and indicate that CD8+T cell responses may be altered in patients using β-blockers, one of the most widely prescribed classes of drugs.
Characterization of
Drosophila melanogaster
cytochrome P450 genes
Authors: Chung Henry , Sztal Tamar , Pasricha Shivani , Sridhar Mohan , Batterham Philip , Daborn Phillip J.
Published: March 2009

Cytochrome P450s form a large and diverse family of heme-containing proteins capable of carrying out many different enzymatic reactions. In both mammals and plants, some P450s are known to carry out reactions essential for processes such as hormone synthesis, while other P450s are involved in the detoxification of environmental compounds. In general, functions of insect P450s are less well understood. We characterized
Drosophila melanogaster
P450 expression patterns in embryos and 2 stages of third instar larvae. We identified numerous P450s expressed in the fat body, Malpighian (renal) tubules, and in distinct regions of the midgut, consistent with hypothesized roles in detoxification processes, and other P450s expressed in organs such as the gonads, corpora allata, oenocytes, hindgut, and brain. Combining expression pattern data with an RNA interference lethality screen of individual P450s, we identify candidate P450s essential for developmental processes and distinguish them from P450s with potential functions in detoxification.
Bilirubin and glutathione have complementary antioxidant and cytoprotective roles
Authors: Sedlak Thomas W. , Saleh Masoumeh , Higginson Daniel S. , Paul Bindu D. , Juluri Krishna R. , Snyder Solomon H.
Published: March 2009

Glutathione (GSH) and bilirubin are prominent endogenous antioxidant cytoprotectants. Despite tissue levels that are thousands of times lower than GSH, bilirubin is effective because of the biosynthetic cycle wherein it is generated from biliverdin by biliverdin reductase (BVR). When bilirubin acts as an antioxidant, it is oxidized to biliverdin, which is immediately reduced by BVR to bilirubin. Why does the body employ both of these 2 distinct antioxidant systems? We show that the water-soluble GSH primarily protects water soluble proteins, whereas the lipophilic bilirubin protects lipids from oxidation. Mice with deletion of heme oxygenase-2, which generates biliverdin, display greater lipid than protein oxidation, while the reverse holds for GSH depletion. RNA interference depletion of BVR increases oxidation of lipids more than protein. Depletion of BVR or GSH augments cell death in an oxidant-specific fashion.
Young Children's Interpretations of Page Breaks in Contemporary Picture Storybooks
Authors: Sipe Lawrence R. , Brightman Anne E.
Published: March 2009

This article reports on a study of the responses of a second-grade class to the page breaks in contemporary picturebooks. In a picturebook, the text and accompanying illustrations are divided into a series of facing pages called openings, and the divisions between the openings are called page breaks or turns. Unlike a novel, in which the page breaks are arbitrary, a picturebook's page breaks have been carefully considered by authors, illustrators, editors, and designers, and thus possess complex semiotic significance. No research exists on children's interpretations of what might have happened from one opening to next, yet this activity is important because children must fill in the natural gaps created by the page breaks to make meaning and to construct a continuous narrative. During a series of readalouds of five picturebooks, the classroom teacher asked the students to speculate on what might have happened “between” the pages. Findings based on qualitative content analysis suggest that, with relatively little teacher direction, there were at least seven ways young children responded to the question of what happens in this liminal space: (1) speculating on actions the characters might have performed; (2) creating imaginary dialogue that might have occurred among characters; (3) creating possible thoughts and feelings of characters; (4) talking about likely changes of setting between page breaks; (5) speculating on the amount of time that might have elapsed between one page opening and the next; (6) hypothesizing about the changes in the reader's perspective from one opening to the next; and (7) observations about the change from one literary genre to another during the page breaks. Findings also suggest that children began to speculate on their own about page breaks, without the stimulus of the teacher's question. More research is clearly indicated in this area for various ages of children and books of differing literary genres in order to build on, refine, and extend our knowledge of the ways children interpret the “space between” the openings of picturebooks. Encouraging children to speculate about page breaks develops inference-making and positions them as co-authors, adding another element to their literary repertoires.
A novel parallel approach to the likelihood-based estimation of admixture in population genetics
Authors: Giovannini Ambra , Zanghirati Gaetano , Beaumont Mark A. , Chikhi Lounès , Barbujani Guido
Published: March 2009

Summary: Inferring population admixture from genetic data and quantifying it is a difficult but crucial task in evolutionary and conservation biology. Unfortunately state-of-the-art probabilistic approaches are computationally demanding. Effectively exploiting the computational power of modern multiprocessor systems can thus have a positive impact to Monte Carlo-based simulation of admixture modeling. A novel parallel approach is briefly described and promising results on its message passing interface (MPI)-based C++ implementation are reported.

Availability: The software package parLEA is freely available at http://dm.unife.it/parlea.

Contact:  ambra.giovannini@unife.it

Supplementary information: Additional information, including instructions for installation/use the original sequential LEA code and the data used in this paper, are also available in the web site.
Site of metabolism prediction for six biotransformations mediated by cytochromes P450
Authors: Zheng Mingyue , Luo Xiaomin , Shen Qiancheng , Wang Yong , Du Yun , Zhu Weiliang , Jiang Hualiang
Published: March 2009

Motivation: One goal of metabolomics is to define and monitor the entire metabolite complement of a cell, while it is still far from reach since systematic and rapid approaches for determining the biotransformations of newly discovered metabolites are lacking. For drug development, such metabolic biotransformation of a new chemical entity (NCE) is of more interest because it may profoundly affect its bioavailability, activity and toxicity profile. The use of in silico methods to predict the site of metabolism (SOM) in phase I cytochromes P450-mediated reactions is usually a starting point of metabolic pathway studies, which may also assist in the process of drug/lead optimization.

Results: This article reports the Cytochromes P450 (CYP450)-mediated SOM prediction for the six most important metabolic reactions by incorporating the use of machine learning and semi-empirical quantum chemical calculations. Non-local models were developed on the basis of a large dataset comprising 1858 metabolic reactions extracted from 1034 heterogeneous chemicals. For validation, the overall accuracies of all six reaction types are higher than 0.81, four of which exceed 0.90. In further receiver operating characteristic (ROC) analyses, each of the SOM model gave a significant area under curve (AUC) value over 0.86, indicating a good predicting power. An external test was made on a previously published dataset, of which 80% of the experimentally observed SOMs can be correctly identified by applying the full set of our SOM models.

Availability: The program package SOME_v1.0 (Site Of Metabolism Estimator) developed based on our models is available at http://www.dddc.ac.cn/adme/myzheng/SOME_1_0.tar.gz.

Contact:  xmluo@mail.shcnc.ac.cn; hljiang@mail.shcnc.ac.cn
Evolutionary construction of multiple graph alignments for the structural analysis of biomolecules
Authors: Fober Thomas , Mernberger Marco , Klebe Gerhard , Hüllermeier Eyke
Published: March 2009

The concept of multiple graph alignment (MGA) has recently been introduced as a novel method for the structural analysis of biomolecules. Using approximate graph matching techniques, this method enables the robust identification of approximately conserved patterns in biologically related structures. In particular, MGA enables the characterization of functional protein families independent of sequence or fold homology. This article first recalls the concept of MGA and then addresses the problem of computing optimal alignments from an algorithmic point of view. In this regard, a method from the field of evolutionary algorithms is proposed and empirically compared with a hitherto existing heuristic approach. Empirically, it is shown that the former yields significantly better results than the latter, albeit at the cost of an increased runtime.

Contact:  eyke@mathematik.uni-marburg.de

Supplementary information:  Supplementary data are available at Bioinformatics online.
SimMLST: simulation of multi-locus sequence typing data under a neutral model
Authors: Didelot Xavier , Lawson Daniel , Falush Daniel
Published: March 2009

Summary: Multi-locus sequence typing (MLST) is a widely used method of characterization of bacterial isolates. It has been applied to over 50 000 isolates in over 50 different species. Here, we present a coalescent method to jointly simulate MLST data and the clonal genealogy that gave rise to the sample.

Availability and Implementation: SimMLST was implemented in C++and Qt4 for the graphical user interface. It is distributed under the terms of the GNU General Public License. Source code and binaries for Windows and Linux are available from http://go.warwick.ac.uk/SimMLST. A user guide and a technical description of the algorithm are provided with the program.

Contact:  X.Didelot@warwick.ac.uk
The evaluation of two management strategies for the Gulf of Alaska walleye pollock fishery under climate change
Authors: A’mar Z. Teresa , Punt André E. , Dorn Martin W.
Published: March 2009

A’mar, Z. T., Punt, A. E., and Dorn, M. W. 2009. The evaluation of two management strategies for the Gulf of Alaska walleye pollock fishery under climate change. – ICES Journal of Marine Science, 66: 1614–1632. Management strategy evaluation (MSE) is the process of using simulation testing with feedback to examine the robustness of candidate management strategies to error and uncertainty. The structure of the management strategy can be selected to attempt to satisfy desired (but conflicting) management objectives. MSE was used to assess the performance of the current management strategy and an alternative management strategy (the “dynamic B0” strategy) for the fishery for walleye pollock (Theragra chalcogramma) in the Gulf of Alaska (GOA), when age-1 recruitment was driven by climate. The relationships between age-1 abundance and climate indices (and the uncertainties associated with these relationships) were characterized within an age-structured operating model that was fitted to the data for GOA walleye pollock. Projections into the future were based on the fitted relationships and predictions of those indices from the Intergovernmental Panel on Climate Change (IPCC) models, using the current or the alternative management strategy to determine catch limits. Management performance (the ability to leave the stock close to the management reference level and achieve high and stable catches) deteriorated when age-1 recruitment was forced by climate, although stocks were kept near the reference level on average. In addition, the ability to estimate management-related quantities, such as spawning biomass, deteriorated markedly when recruitment was forced by climate. Performance was sensitive to the choice of IPCC dataset and, in particular, estimation and management performance was poorest (outcomes most variable) for the IPCC datasets that led to the greatest variation in recruitment to the fishery. Although basing management on a “dynamic B0” management strategy led to improved management and estimation performance, the magnitude of the improvement was slight.
Suppression of a Phospholipase D Gene,OsPLDβ1, Activates Defense Responses and Increases Disease Resistance in Rice
Authors: Yamaguchi Takeshi , Kuroda Masaharu , Yamakawa Hiromoto , Ashizawa Taketo , Hirayae Kazuyuki , Kurimoto Leona , Shinya Tomonori , Shibuya Naoto
Published: March 2009

Phospholipase D (PLD) plays an important role in plants, including responses to abiotic as well as biotic stresses. A survey of the rice (Oryza  sativa) genome database indicated the presence of 17 PLD genes in the genome, among which OsPLDα1, OsPLDα5, and OsPLDβ1 were highly expressed in most tissues studied. To examine the physiological function of PLD in rice, we made knockdown plants for each PLD isoform by introducing gene-specific RNA interference constructs. One of them, OsPLDβ1-knockdown plants, showed the accumulation of reactive oxygen species in the absence of pathogen infection. Reverse transcription-polymerase chain reaction and DNA microarray analyses revealed that the knockdown of OsPLDβ1 resulted in the up-/down-regulation of more than 1,400 genes, including the induction of defense-related genes such as pathogenesis-related protein genes and WRKY/ERF family transcription factor genes. Hypersensitive response-like cell death and phytoalexin production were also observed at a later phase of growth in the OsPLDβ1-knockdown plants. These results indicated that the OsPLDβ1-knockdown plants spontaneously activated the defense responses in the absence of pathogen infection. Furthermore, the OsPLDβ1-knockdown plants exhibited increased resistance to the infection of major pathogens of rice, Pyricularia grisea and Xanthomonas oryzae pv oryzae. These results suggested that OsPLDβ1 functions as a negative regulator of defense responses and disease resistance in rice.
The Arabidopsis RING Finger E3 Ligase RHA2a Is a Novel Positive Regulator of Abscisic Acid Signaling during Seed Germination and Early Seedling Development
Authors: Bu Qingyun , Li Hongmei , Zhao Qingzhen , Jiang Hongling , Zhai Qingzhe , Zhang Jie , Wu Xiaoyan , Sun Jiaqiang , Xie Qi , Wang Daowen , Li Chuanyou
Published: March 2009

The phytohormone abscisic acid (ABA) is well known for its regulatory roles in integrating environmental constraints with the developmental programs of plants. Here, we characterize the biological function of the Arabidopsis (Arabidopsis thaliana) RING-H2 protein RHA2a in ABA signaling. The rha2a mutant is less sensitive to ABA than the wild type during seed germination and early seedling development, whereas transgenic plants overexpressing RHA2a are hypersensitive, indicating that RHA2a positively regulates ABA-mediated control of seed germination and early seedling development. Double mutant analyses of rha2a with several known ABA-insensitive mutants suggest that the action of RHA2a in ABA signaling is independent of that of the transcription factors ABI3, ABI4, and ABI5. We provide evidence showing that RHA2a also positively regulates plant responses to salt and osmotic stresses during seed germination and early seedling development. RHA2a is a functional E3 ubiquitin ligase, and its conserved RING domain is likely important for the biological function of RHA2a in ABA signaling. Together, these results suggest that the E3 ligase RHA2a is an important regulator of ABA signaling during seed germination and early seedling development.
Polymorphism of CaTeO3 and solid solutions Ca
x
Sr1 − x
TeO3
Authors: Stöger Berthold , Weil Matthias , Zobetz Erich , Giester Gerald
Published: March 2009

Single crystals and microcrystalline samples of the calcium tellurate(IV) phases α-, β-, β′- and γ-CaTeO3 as well as of two solid solutions Ca
x
Sr1 − x
TeO3 (x = 0.55 and 0.77) have been synthesized and characterized by X-ray diffraction and thermal analysis. A comparative description of the structures and the relations between the polymorphs is given. The main building units of the hitherto unknown structures are isolated [TeIVO3]2− units and [(Ca,Sr)O
x
] (x = 6–8) polyhedra. All structures exhibit channels in which the TeIV electron lone pairs protrude. The low-temperature phase α-CaTeO3 is stable up to 1168 K. It exhibits nearly cylindrical channels (diameter ∼ 4 Å) and differs structurally from the other phases, whereas the metastable high-temperature phases are closely related to each other. They feature oval channels (shortest and longest diameter ∼ 2 and 8 Å). γ-CaTeO3 can be described as an order–disorder (OD) structure of two non-polar layers with layer groups p121/m1 and p1211. The γ-CaTeO3 crystal under investigation consists of two polytypes with a maximum degree of order. The two phases Ca
x
Sr1 − x
TeO3 (x = 0.55 and 0.77) are isostructural to the MDO1 polytype of γ-CaTeO3. β-CaTeO3 shows a distinct reversible phase transition at ∼ 293 K. The low-temperature modification β′-CaTeO3 as well as its high-temperature modification β-CaTeO3 can be considered as threefold superstructures along [100] based on the MDO1 polytype of γ-CaTeO3.