A large-scale proteogenomics study of apicomplexan pathogens-Toxoplasma gondii and Neospora caninum

Proteomics data can supplement genome annotation efforts, for example being used to confirm gene models or correct gene annotation errors. Here, we present a large‐scale proteogenomics study of two important apicomplexan pathogens: Toxoplasma gondii and Neospora caninum. We queried proteomics data against a panel of official and alternate gene models generated directly from RNASeq data, using several newly generated and some previously published MS datasets for this meta‐analysis. We identified a total of 201 996 and 39 953 peptide‐spectrum matches for T. gondii and N. caninum, respectively, at a 1% peptide FDR threshold. This equated to the identification of 30 494 distinct peptide sequences and 2921 proteins (matches to official gene models) for T. gondii, and 8911 peptides/1273 proteins for N. caninum following stringent protein‐level thresholding. We have also identified 289 and 140 loci for T. gondii and N. caninum, respectively, which mapped to RNA‐Seq‐derived gene models used in our analysis and apparently absent from the official annotation (release 10 from EuPathDB) of these species. We present several examples in our study where the RNA‐Seq evidence can help in correction of the current gene model and can help in discovery of potential new genes

There are No Causality Problems for Fermi's Two Atom System

A repeatedly discussed gedanken experiment, proposed by Fermi to check Einstein causality, is reconsidered. It is shown that, contrary to a recent statement made by Hegerfeldt, there appears no causality paradoxon in a proper theoretical description of the experiment.Comment: 6 pages, latex, DESY 94-02

Dilaton-Axion hair for slowly rotating Kerr black holes

Campbell et al. demonstrated the existence of axion ``hair'' for Kerr black holes due to the non-trivial Lorentz Chern-Simons term and calculated it explicitly for the case of slow rotation. Here we consider the dilaton coupling to the axion field strength, consistent with low energy string theory and calculate the dilaton ``hair'' arising from this specific axion source.Comment: 13 pages + 1 fi

The quadrupole moment of slowly rotating fluid balls

In this paper we use the second order formalism of Hartle to study slowly and rigidly rotating stars with focus on the quadrupole moment of the object. The second order field equations for the interior fluid are solved numerically for different classes of possible equations of state and these solutions are then matched to a vacuum solution that includes the general asymptotically flat axisymmetric metric to second order, using the Darmois-Israel procedure. For these solutions we find that the quadrupole moment differs from that of the Kerr metric, as has also been found for some equations of state in other studies. Further we consider the post-Minkowskian limit analytically. In the paper we also illustrate how the relativistic multipole moments can be calculated from a complex gravitational potential.Comment: 13 pages, 5 figure

Local magnetic structure due to inhomogeneity of interaction in S=1/2 antiferromagnetic chain

We study the magnetic properties of $S=1/2$ antiferromagnetic Heisenberg chains with inhomogeneity of interaction. Using a quantum Monte Carlo method and an exact diagonalization method, we study bond-impurity effect in the uniform $S=1/2$ chain and also in the bond-alternating chain. Here `bond impurity' means a bond with strength different from those in the bulk or a defect in the alternating order. Local magnetic structures induced by bond impurities are investigated both in the ground state and at finite temperatures, calculating the local magnetization, the local susceptibility and the local field susceptibility. We also investigate the force acting between bond impurities and find the force generally attractive.Comment: 15pages, 34figure

Experiments towards quantum information with trapped Calcium ions

Ground state cooling and coherent manipulation of ions in an rf-(Paul) trap is the prerequisite for quantum information experiments with trapped ions. With resolved sideband cooling on the optical S1/2 - D5/2 quadrupole transition we have cooled one and two 40Ca+ ions to the ground state of vibration with up to 99.9% probability. With a novel cooling scheme utilizing electromagnetically induced transparency on the S1/2 - P1/2 manifold we have achieved simultaneous ground state cooling of two motional sidebands 1.7 MHz apart. Starting from the motional ground state we have demonstrated coherent quantum state manipulation on the S1/2 - D5/2 quadrupole transition at 729 nm. Up to 30 Rabi oscillations within 1.4 ms have been observed in the motional ground state and in the n=1 Fock state. In the linear quadrupole rf-trap with 700 kHz trap frequency along the symmetry axis (2 MHz in radial direction) the minimum ion spacing is more than 5 micron for up to 4 ions. We are able to cool two ions to the ground state in the trap and individually address the ions with laser pulses through a special optical addressing channel.Comment: Proceedings of the ICAP 2000, Firenz

Experimental demonstration of ground state laser cooling with electromagnetically induced transparency

Ground state laser cooling of a single trapped ion is achieved using a technique which tailors the absorption profile for the cooling laser by exploiting electromagnetically induced transparency in the Zeeman structure of a dipole transition. This new method is robust, easy to implement and proves particularly useful for cooling several motional degrees of freedom simultaneously, which is of great practical importance for the implementation of quantum logic schemes with trapped ions.Comment: 4 pages, 4 figure