Signature proteins for the major clades of Cyanobacteria

<p>Abstract</p> <p>Background</p> <p>The phylogeny and taxonomy of cyanobacteria is currently poorly understood due to paucity of reliable markers for identification and circumscription of its major clades.</p> <p>Results</p> <p>A combination of phylogenomic and protein signature based approaches was used to characterize the major clades of cyanobacteria. Phylogenetic trees were constructed for 44 cyanobacteria based on 44 conserved proteins. In parallel, Blastp searches were carried out on each ORF in the genomes of <it>Synechococcus WH8102, Synechocystis PCC6803, Nostoc PCC7120, Synechococcus JA-3-3Ab, Prochlorococcus MIT9215 </it>and <it>Prochlor. marinus subsp. marinus CCMP1375 </it>to identify proteins that are specific for various main clades of cyanobacteria. These studies have identified 39 proteins that are specific for all (or most) cyanobacteria and large numbers of proteins for other cyanobacterial clades. The identified signature proteins include: (i) 14 proteins for a deep branching clade (Clade A) of <it>Gloebacter violaceus </it>and two diazotrophic <it>Synechococcus </it>strains (JA-3-3Ab and JA2-3-B'a); (ii) 5 proteins that are present in all other cyanobacteria except those from Clade A; (iii) 60 proteins that are specific for a clade (Clade C) consisting of various marine unicellular cyanobacteria (viz. <it>Synechococcus </it>and <it>Prochlorococcus</it>); (iv) 14 and 19 signature proteins that are specific for the Clade C <it>Synechococcus </it>and <it>Prochlorococcus </it>strains, respectively; (v) 67 proteins that are specific for the Low B/A ecotype <it>Prochlorococcus </it>strains, containing lower ratio of <it>chl b/a</it>₂and adapted to growth at high light intensities; (vi) 65 and 8 proteins that are specific for the <it>Nostocales </it>and <it>Chroococcales </it>orders, respectively; and (vii) 22 and 9 proteins that are uniquely shared by various <it>Nostocales </it>and <it>Oscillatoriales </it>orders, or by these two orders and the <it>Chroococcales</it>, respectively. We also describe 3 conserved indels in flavoprotein, heme oxygenase and protochlorophyllide oxidoreductase proteins that are specific for either Clade C cyanobacteria or for various subclades of <it>Prochlorococcus</it>. Many other conserved indels for cyanobacterial clades have been described recently.</p> <p>Conclusions</p> <p>These signature proteins and indels provide novel means for circumscription of various cyanobacterial clades in clear molecular terms. Their functional studies should lead to discovery of novel properties that are unique to these groups of cyanobacteria.</p

Extra dimensions and Strong Neutrino-Nucleon interactions above 101910^{19} eV : Breaking the GZK Barrier

Cosmic ray events above $10^{20}$ eV are on the verge of confronting fundamental particle physics. The neutrino is the only candidate primary among established particles capable of crossing 100 Mpc intergalactic distances unimpeded. The magnitude of $\nu N$ cross sections indicated by events, plus consistency with the Standard Model at low-energy, point to new physics of massive spin-2 exchange. In models based on extra dimensions, we find that the $\nu N$ cross section rises to typical hadronic values of between 1 and 100 mb at energies above $10^{20}$ eV. Our calculations take into account constraints of unitarity. We conclude that air-showers observed with energies above $10^{19}$ eV are consistent with neutrino primaries and extra-dimension models. An {\it upper bound} of 1-10 TeV on the mass scale at which graviton exchange becomes strong in current Kaluza-Klein models follows.Comment: 14 pages, 2 figures, minor change

Data-Optimized Coronal Field Model: I. Proof of Concept

Deriving the strength and direction of the three-dimensional (3D) magnetic field in the solar atmosphere is fundamental for understanding its dynamics. Volume information on the magnetic field mostly relies on coupling 3D reconstruction methods with photospheric and/or chromospheric surface vector magnetic fields. Infrared coronal polarimetry could provide additional information to better constrain magnetic field reconstructions. However, combining such data with reconstruction methods is challenging, e.g., because of the optical-thinness of the solar corona and the lack and limitations of stereoscopic polarimetry. To address these issues, we introduce the Data-Optimized Coronal Field Model (DOCFM) framework, a model-data fitting approach that combines a parametrized 3D generative model, e.g., a magnetic field extrapolation or a magnetohydrodynamic model, with forward modeling of coronal data. We test it with a parametrized flux rope insertion method and infrared coronal polarimetry where synthetic observations are created from a known "ground truth" physical state. We show that this framework allows us to accurately retrieve the ground truth 3D magnetic field of a set of force-free field solutions from the flux rope insertion method. In observational studies, the DOCFM will provide a means to force the solutions derived with different reconstruction methods to satisfy additional, common, coronal constraints. The DOCFM framework therefore opens new perspectives for the exploitation of coronal polarimetry in magnetic field reconstructions and for developing new techniques to more reliably infer the 3D magnetic fields that trigger solar flares and coronal mass ejections.Comment: 14 pages, 6 figures; Accepted for publication in Ap

Semi-analytical Solution of Dirac equation in Schwarzschild Geometry

Separation of the Dirac equation in the spacetime around a Kerr black hole into radial and angular coordinates was done by Chandrasekhar in 1976. In the present paper, we solve the radial equations in a Schwarzschild geometry semi-analytically using Wentzel-Kramers-Brillouin approximation (in short WKB) method. Among other things, we present analytical expression of the instantaneous reflection and transmission coefficients and the radial wave functions of the Dirac particles. Complete physical parameter space was divided into two parts depending on the height of the potential well and energy of the incoming waves. We show the general solution for these two regions. We also solve the equations by a Quantum Mechanical approach, in which the potential is approximated by a series of steps and found that these two solutions agree. We compare solutions of different initial parameters and show how the properties of the scattered wave depend on these parameters.Comment: RevTex, 11 Latex pages and 12 Figures ; Classical and Quantum Gravity (in Press) (1999

Revised Relativistic Hydrodynamical Model for Neutron-Star Binaries

We report on numerical results from a revised hydrodynamic simulation of binary neutron-star orbits near merger. We find that the correction recently identified by Flanagan significantly reduces but does not eliminate the neutron-star compression effect. Although results of the revised simulations show that the compression is reduced for a given total orbital angular momentum, the inner most stable circular orbit moves to closer separation distances. At these closer orbits significant compression and even collapse is still possible prior to merger for a sufficiently soft EOS. The reduced compression in the corrected simulation is consistent with other recent studies of rigid irrotational binaries in quasiequilibrium in which the compression effect is observed to be small. Another significant effect of this correction is that the derived binary orbital frequencies are now in closer agreement with post-Newtonian expectations.Comment: Submitted to Phys. Rev.

Relativistic Charged Spheres II: Regularity and Stability

We present new results concerning the existence of static, electrically charged, perfect fluid spheres that have a regular interior and are arbitrarily close to a maximally charged black-hole state. These configurations are described by exact solutions of Einstein's field equations. A family of these solutions had already be found (de Felice et al., 1995) but here we generalize that result to cases with different charge distribution within the spheres and show, in an appropriate parameter space, that the set of such physically reasonable solutions has a non zero measure. We also perform a perturbation analysis and identify the solutions which are stable against adiabatic radial perturbations. We then suggest that the stable configurations can be considered as classic models of charged particles. Finally our results are used to show that a conjecture of Kristiansson et al. (1998) is incorrect.Comment: revtex, 13 pages. five EPS figures. Accepted by CQ

Possible explanation for star-crushing effect in binary neutron star simulations

A possible explanation is suggested for the controversial star-crushing effect seen in numerical simulations of inspiraling neutron star binaries by Wilson, Mathews and Marronetti (WMM). An apparently incorrect definition of momentum density in the momentum constraint equation used by WMM gives rise to a post-1-Newtonian error in the approximation scheme. We show by means of an analytic, post-1-Newtonian calculation that this error causes an increase of the stars' central densities which is of the order of several percent when the stars are separated by a few stellar radii, in agreement with what is seen in the simulations.Comment: 4 pages, 1 figure, uses revetx macros, minor revision

Analytic structure and power-series expansion of the Jost function for the two-dimensional problem

For a two-dimensional quantum mechanical problem, we obtain a generalized power-series expansion of the S-matrix that can be done near an arbitrary point on the Riemann surface of the energy, similarly to the standard effective range expansion. In order to do this, we consider the Jost-function and analytically factorize its momentum dependence that causes the Jost function to be a multi-valued function. The remaining single-valued function of the energy is then expanded in the power-series near an arbitrary point in the complex energy plane. A systematic and accurate procedure has been developed for calculating the expansion coefficients. This makes it possible to obtain a semi-analytic expression for the Jost-function (and therefore for the S-matrix) near an arbitrary point on the Riemann surface and use it, for example, to locate the spectral points (bound and resonant states) as the S-matrix poles. The method is applied to a model simlar to those used in the theory of quantum dots.Comment: 42 pages, 9 figures, submitted to J.Phys.