An ancestral secretory apparatus in the protozoan parasite Giardia intestinalis

The protozoan parasite Giardia intestinalis belongs to one of the earliest diverged eukaryotic lineages. This is also reflected in a simple intracellular organization, as Giardia lacks common subcellular compartments such as mitochondria, peroxisomes, and apparently also a Golgi apparatus. During encystation, developmentally regulated formation of large secretory compartments containing cyst wall material occurs. Despite the lack of any morphological similarities, these encystation-specific vesicles (ESVs) show several biochemical characteristics of maturing Golgi cisternae. Previous studies suggested that Golgi structure and function are induced only during encystation in Giardia, giving rise to the hypothesis that ESVs, as a Giardia Golgi equivalent, are generated de novo. Alternatively, ESV compartments could be built on the template structure of a cryptic Golgi in trophozoites in response to ER export of cyst wall material during encystation. We addressed this question by defining the molecular framework of the Giardia secretory apparatus using a comparative genomic approach. Analysis of the corresponding transcriptome during growth and encystation revealed surprisingly little stage-specific regulation. A panel of antibodies was generated against selected marker proteins to investigate the developmental dynamics of the endomembrane system. We show evidence that Giardia accommodates the export of large amounts of cyst wall material through re-organization of membrane compartment(s) in trophozoites with biochemical similarities to ESVs. This suggests that ESVs are selectively stabilized Golgi-like compartments in a unique and archetypical secretory system, which arise from a structural template in trophozoites rather than being generated de novo

Linear theory and velocity correlations of clusters

Linear theory provides a reasonable description of the velocity correlations of biased tracers both perpendicular and parallel to the line of separation, provided one accounts for the fact that the measurement is almost always made using pair-weighted statistics. This introduces an additional term which, for sufficiently biased tracers, may be large. Previous work suggesting that linear theory was grossly in error for the components parallel to the line of separation ignored this term.Comment: 5 pages, 2 figures, MNRAS accepte

The Inverse Redshift-Space Operator: Reconstructing Cosmological Density and Velocity Fields

We present the linear inverse redshift space operator which maps the galaxy density field derived from redshift surveys from redshift space to real space. Expressions are presented for observers in both the CMBR and Local Group rest frames. We show how these results can be generalised to flux--limited galaxy redshift surveys. These results allow the straightforward reconstruction of real space density and velocity fields without resort to iterative or numerically intensive inverse methods. As a corollary to the inversion of the density in the Local Group rest frame we present an expression for estimating the real space velocity dipole from redshift space, allowing one to estimate the Local Group dipole without full reconstruction of the redshift survey. We test these results on some simple models and find the reconstruction is very accurate. A new spherical harmonic representation of the redshift distortion and its inverse is developed, which simplifies the reconstruction and allows analytic calculation of the properties of the reconstructed redshift survey. We use this representation to analyse the uncertainties in the reconstruction of the density and velocity fields from redshift space, due to only a finite volume being available. Both sampling and shot-noise variance terms are derived and we discuss the limits of reconstruction analysis. We compare the reconstructed velocity field with the true velocity field and show that reconstruction in the Local Group rest frame is preferable, since this eliminates the major source of uncertainty from the dipole mode. These results can be used to transform redshift surveys to real space and may be used as part of a full likelihood analysis to extract cosmological parameters.Comment: 13 pages (Latex), 6 postscript figures included, accepted for publication in MNRA

The velocity-density relation in the spherical model

We study the cosmic velocity-density relation using the spherical collapse model (SCM) as a proxy to non-linear dynamics. Although the dependence of this relation on cosmological parameters is known to be weak, we retain the density parameter Omega_m in SCM equations, in order to study the limit Omega_m -> 0. We show that in this regime the considered relation is strictly linear, for arbitrary values of the density contrast, on the contrary to some claims in the literature. On the other hand, we confirm that for realistic values of Omega_m the exact relation in the SCM is well approximated by the classic formula of Bernardeau (1992), both for voids (delta<0) and for overdensities up to delta ~ 3. Inspired by this fact, we find further analytic approximations to the relation for the whole range delta from -1 to infinity. Our formula for voids accounts for the weak Omega_m-dependence of their maximal rate of expansion, which for Omega_m < 1 is slightly smaller that 3/2. For positive density contrasts, we find a simple relation div v = 3 H_0 (Omega_m)^(0.6) [ (1+delta)^(1/6) - (1+delta)^(1/2) ], that works very well up to the turn-around (i.e. up to delta ~ 13.5 for Omega_m = 0.25 and neglected Omega_Lambda). Having the same second-order expansion as the formula of Bernardeau, it can be regarded as an extension of the latter for higher density contrasts. Moreover, it gives a better fit to results of cosmological numerical simulations.Comment: 11 pages, 6 figures. Accepted for publication in MNRA

Mass transfer in eccentric binaries: the new Oil-on-Water SPH technique

To measure the onset of mass transfer in eccentric binaries we have developed a two-phase SPH technique. Mass transfer is important in the evolution of close binaries, and a key issue is to determine the separation at which mass transfer begins. The circular case is well understood and can be treated through the use of the Roche formalism. To treat the eccentric case we use a newly-developed two phase system. The body of the donor star is made up from high-mass "water" particles, whilst the atmosphere is modelled with low-mass "oil" particles. Both sets of particles take part fully in SPH interactions. To test the technique we model circular mass-transfer binaries containing a 0.6 Msun donor star and a 1 Msun white dwarf; such binaries are thought to form cataclysmic variable (CV) systems. We find that we can reproduce a reasonable CV mass-transfer rate, and that our extended atmosphere gives a separation that is too large by aproximately 16%, although its pressure scale height is considerably exaggerated. We use the technique to measure the semi-major axis required for the onset of mass transfer in binaries with a mass ratio of q=0.6 and a range of eccentricities. Comparing to the value obtained by considering the instantaneous Roche lobe at pericentre we find that the radius of the star required for mass transfer to begin decreases systematically with increasing eccentricity.Comment: 9 pages, 8 figures, accepted by MNRA

The Dynamics and Stability of Circumbinary Orbits

We numerically investigate the dynamics of orbits in 3D circumbinary phase-space as a function of binary eccentricity and mass fraction. We find that inclined circumbinary orbits in the elliptically-restricted three-body problem display a nodal libration mechanism in the longitude of the ascending node and in the inclination to the plane of the binary. We (i) analyse and quantify the behaviour of these orbits with reference to analytical work performed by Farago & Laskar (2010) and (ii) investigate the stability of these orbits over time. This work is the first dynamically aware analysis of the stability of circumbinary orbits across both binary mass fraction and binary eccentricity. This work also has implications for exoplanetary astronomy in the existence and determination of stable orbits around binary systems.Comment: Monthly Notices of the Royal Astronomical Society. in pres

Rotation of the cluster of galaxies A2107

We present indications of rotation in the galaxy cluster A2107 by a method that searches for the maximum gradient in the velocity field in a flat disk-like model of a cluster. Galaxies from cumulative sub-samples containing more and more distant members from the cluster centre, are projected onto an axis passing through the centre and we apply a linear regression model on the projected distances $x$ and the line-of-sight velocities $V$. The axis with the maximum linear correlation coefficient $r_{max} = \max [ r(V,x) ]$ defines the direction of the maximum velocity gradient, and consequently it presents the major axis of the apparently elliptical cluster. Because the effects of rotation are subtle, we put strong emphasis on the estimation of the uncertainties of the results by implementing different bootstrap techniques. We have found the rotational effects are more strongly expressed from distances $0.26 \div 0.54$ Mpc from the cluster centre. The total virial mass of the cluster is (3.2\pm0.6)\times10^{14} {\cal M}_{\sun}, while the virial mass, corrected for the rotation, is (2.8\pm0.5) \times 10^{14}{\cal M}_{\sun}.Comment: 7 pages, 9 figures gzipped tar file. to be published in MNRA

Measuring the escape velocity and mass profiles of galaxy clusters beyond their virial radius

The caustic technique uses galaxy redshifts alone to measure the escape velocity and mass profiles of galaxy clusters to clustrocentric distances well beyond the virial radius, where dynamical equilibrium does not necessarily hold. We provide a detailed description of this technique and analyse its possible systematic errors. We apply the caustic technique to clusters with mass M_200>=10^{14}h^{-1} M_sun extracted from a cosmological hydrodynamic simulation of a LambdaCDM universe. With a few tens of redshifts per squared comoving megaparsec within the cluster, the caustic technique, on average, recovers the profile of the escape velocity from the cluster with better than 10 percent accuracy up to r~4 r_200. The caustic technique also recovers the mass profile with better than 10 percent accuracy in the range (0.6-4) r_200, but it overestimates the mass up to 70 percent at smaller radii. This overestimate is a consequence of neglecting the radial dependence of the filling function F_beta(r). The 1-sigma uncertainty on individual escape velocity profiles increases from ~20 to ~50 percent when the radius increases from r~0.1 r_200 to ~4 r_200. Individual mass profiles have 1-sigma uncertainty between 40 and 80 percent within the radial range (0.6-4) r_200. We show that the amplitude of these uncertainties is completely due to the assumption of spherical symmetry, which is difficult to drop. Alternatively, we can apply the technique to synthetic clusters obtained by stacking individual clusters: in this case, the 1-sigma uncertainty on the escape velocity profile is smaller than 20 percent out to 4 r_200. The caustic technique thus provides reliable average profiles which extend to regions difficult or impossible to probe with other techniques.Comment: MNRAS accepted, 20 page

Redshift space correlations and scale-dependent stochastic biasing of density peaks

We calculate the redshift space correlation function and the power spectrum of density peaks of a Gaussian random field. In the linear regime k < 0.1 h/Mpc, the redshift space power spectrum is P^s_{pk}(k,u) = exp(-f^2 s_{vel}^2 k^2 u^2) * [b_{pk}(k) + b_{vel}(k) f u^2]^2 * P_m(k), where u is the angle with respect to the line of sight, s_{vel} is the one-dimensional velocity dispersion, f is the growth rate, and b_{pk}(k) and b_{vel}(k) are k-dependent linear spatial and velocity bias factors. For peaks, the value of s_{vel} depends upon the functional form of b_{vel}. The peaks model is remarkable because it has unbiased velocities -- peak motions are driven by dark matter flows -- but, in order to achieve this, b_{vel} is k-dependent. We speculate that this is true in general: k-dependence of the spatial bias will lead to k-dependence of b_{vel} even if the biased tracers flow with the dark matter. Because of the k-dependence of the linear bias parameters, standard manipulations applied to the peak model will lead to k-dependent estimates of the growth factor that could erroneously be interpreted as a signature of modified dark energy or gravity. We use the Fisher formalism to show that the constraint on the growth rate f is degraded by a factor of two if one allows for a k-dependent velocity bias of the peak type. We discuss a simple estimate of nonlinear evolution and illustrate the effect of the peak bias on the redshift space multipoles. For k < 0.1 h/Mpc, the peak bias is deterministic but k-dependent, so the configuration space bias is stochastic and scale dependent, both in real and redshift space. We provide expressions for this stochasticity and its evolution (abridged).Comment: 24 pages, 7 figures (v3): references added (v4): added figure+appendix. In press in PR

Modeling scale-dependent bias on the baryonic acoustic scale with the statistics of peaks of Gaussian random fields

Models of galaxy and halo clustering commonly assume that the tracers can be treated as a continuous field locally biased with respect to the underlying mass distribution. In the peak model pioneered by BBKS, one considers instead density maxima of the initial, Gaussian mass density field as an approximation to the formation site of virialized objects. In this paper, the peak model is extended in two ways to improve its predictive accuracy. Firstly, we derive the two-point correlation function of initial density peaks up to second order and demonstrate that a peak-background split approach can be applied to obtain the k-independent and k-dependent peak bias factors at all orders. Secondly, we explore the gravitational evolution of the peak correlation function within the Zel'dovich approximation. We show that the local (Lagrangian) bias approach emerges as a special case of the peak model, in which all bias parameters are scale-independent and there is no statistical velocity bias. We apply our formulae to study how the Lagrangian peak biasing, the diffusion due to large scale flows and the mode-coupling due to nonlocal interactions affect the scale dependence of bias from small separations up to the baryon acoustic oscillation (BAO) scale. For 2-sigma density peaks collapsing at z=0.3, our model predicts a ~ 5% residual scale-dependent bias around the acoustic scale that arises mostly from first-order Lagrangian peak biasing (as opposed to second-order gravity mode-coupling). We also search for a scale dependence of bias in the large scale auto-correlation of massive halos extracted from a very large N-body simulation provided by the MICE collaboration. For halos with mass M>10^{14}Msun/h, our measurements demonstrate a scale-dependent bias across the BAO feature which is very well reproduced by a prediction based on the peak model.Comment: (v1): 23 pages text, 8 figures + appendix (v2): typos fixed, references added, accepted for publication in PR