Chromatin Preparation and Chromatin Immuno-precipitation from Drosophila Embryos

This protocol provides specific details on how to perform Chromatin immunoprecipitation (ChIP) from Drosophila embryos. ChIP allows the matching of proteins or histone modifications to specific genomic regions. Formaldehyde-cross-linked chromatin is isolated and antibodies against the target of interest are used to determine whether the target is associated with a specific DNA sequence. This can be performed in spatial and temporal manner and it can provide information about the genome-wide localization of a given protein or histone modification if coupled with deep sequencing technology (ChIP-Seq)

Southern Sky Redshift Survey: Clustering of Local Galaxies

We use the two-point correlation function to calculate the clustering properties of the recently completed SSRS2 survey. The redshift space correlation function for the magnitude-limited SSRS2 is given by xi(s)=(s/5.85 h-1 Mpc)^{-1.60} for separations between 2 < s < 11 h-1 Mpc, while our best estimate for the real space correlation function is xi(r) = (r/5.36 h-1 Mpc)^{-1.86}. Both are comparable to previous measurements using surveys of optical galaxies over much larger and independent volumes. By comparing the correlation function calculated in redshift and real space we find that the redshift distortion on intermediate scales is small. This result implies that the observed redshift-space distribution of galaxies is close to that in real space, and that beta = Omega^{0.6}/b < 1, where Omega is the cosmological density parameter and b is the linear biasing factor for optical galaxies. We also use the SSRS2 to study the dependence of xi on the internal properties of galaxies. We confirm earlier results that luminous galaxies (L>L*) are more clustered than sub-L* galaxies and that the luminosity segregation is scale-independent. We find that early types are more clustered than late types, but that in the absence of rich clusters, the relative bias between early and late types in real space, is not as strong as previously estimated. Furthermore, both morphologies present a luminosity-dependent bias, with the early types showing a slightly stronger dependence on luminosity. We also find that red galaxies are significantly more clustered than blue ones, with a mean relative bias stronger than that seen for morphology. Finally, we find that the relative bias between optical and iras galaxies in real space is b_o/b_I $\sim$ 1.4.Comment: 43 pages, uses AASTeX 4.0 macros. Includes 8 tables and 16 Postscript figures, updated reference

Depopulation of dense α-synuclein aggregates is associated with rescue of dopamine neuron dysfunction and death in a new Parkinson's disease model.

Parkinson's disease (PD) is characterized by the presence of α-synuclein aggregates known as Lewy bodies and Lewy neurites, whose formation is linked to disease development. The causal relation between α-synuclein aggregates and PD is not well understood. We generated a new transgenic mouse line (MI2) expressing human, aggregation-prone truncated 1-120 α-synuclein under the control of the tyrosine hydroxylase promoter. MI2 mice exhibit progressive aggregation of α-synuclein in dopaminergic neurons of the substantia nigra pars compacta and their striatal terminals. This is associated with a progressive reduction of striatal dopamine release, reduced striatal innervation and significant nigral dopaminergic nerve cell death starting from 6 and 12 months of age, respectively. In the MI2 mice, alterations in gait impairment can be detected by the DigiGait test from 9 months of age, while gross motor deficit was detected by rotarod test at 20 months of age when 50% of dopaminergic neurons in the substantia nigra pars compacta are lost. These changes were associated with an increase in the number and density of 20-500 nm α-synuclein species as shown by dSTORM. Treatment with the oligomer modulator anle138b, from 9 to 12 months of age, restored striatal dopamine release, prevented dopaminergic cell death and gait impairment. These effects were associated with a reduction of the inner density of large α-synuclein aggregates and an increase in dispersed small α-synuclein species as revealed by dSTORM. The MI2 mouse model recapitulates the progressive dopaminergic deficit observed in PD, showing that early synaptic dysfunction is associated to fine behavioral motor alterations, precedes dopaminergic axonal loss and neuronal death that become associated with a more consistent motor deficit upon reaching a certain threshold. Our data also provide new mechanistic insight for the effect of anle138b's function in vivo supporting that targeting α-synuclein aggregation is a promising therapeutic approach for PD

Studying the evolution of large-scale structure with the VIMOS-VLT Deep Survey

The VIMOS-VLT Deep Survey (VVDS) currently offers a unique combination of depth, angular size and number of measured galaxies among surveys of the distant Universe: ~ 11,000 spectra over 0.5 deg2 to I_{AB}=24 (VVDS-Deep), 35,000 spectra over ~ 7 deg2 to I_{AB}=22.5 (VVDS-Wide). The current ``First Epoch'' data from VVDS-Deep already allow investigations of galaxy clustering and its dependence on galaxy properties to be extended to redshifts ~1.2-1.5, in addition to measuring accurately evolution in the properties of galaxies up to z~4. This paper concentrates on the main results obtained so far on galaxy clustering. Overall, L* galaxies at z~ 1.5 show a correlation length r_0=3.6\pm 0.7. As a consequence, the linear galaxy bias at fixed luminosity rises over the same range from the value b~1 measured locally, to b=1.5 +/- 0.1. The interplay of galaxy and structure evolution in producing this observation is discussed in some detail. Galaxy clustering is found to depend on galaxy luminosity also at z~ 1, but luminous galaxies at this redshift show a significantly steeper small-scale correlation function than their z=0 counterparts. Finally, red galaxies remain more clustered than blue galaxies out to similar redshifts, with a nearly constant relative bias among the two classes, b_{rel}~1.4, despite the rather dramatic evolution of the color-density relation over the same redshift range.Comment: 14 pages. Extended, combined version of two invited review papers presented at: 1) XXVIth Astrophysics Moriond Meeting: "From Dark Halos to Light", March 2006, proc. edited by L.Tresse, S. Maurogordato and J. Tran Thanh Van (Editions Frontieres); 2) Vulcano Workshop 2006 "Frontier Objects in Astrophysics and Particle Physics", May 2006, proc. edited by F. Giovannelli & G. Mannocchi, Italian Physical Society (Editrice Compositori, Bologna

Seeking the Local Convergence Depth. V. Tully-Fisher Peculiar Velocities for 52 Abell Clusters

We have obtained I band Tully-Fisher (TF) measurements for 522 late-type galaxies in the fields of 52 rich Abell clusters distributed throughout the sky between 50 and 200\h Mpc. Here we estimate corrections to the data for various forms of observational bias, most notably Malmquist and cluster population incompleteness bias. The bias-corrected data are applied to the construction of an I band TF template, resulting in a relation with a dispersion of 0.38 magnitudes and a kinematical zero-point accurate to 0.02 magnitudes. This represents the most accurate TF template relation currently available. Individual cluster TF relations are referred to the average template relation to compute cluster peculiar motions. The line-of-sight dispersion in the peculiar motions is 341+/-93 km/s, in general agreement with that found for the cluster sample of Giovanelli and coworkers.Comment: 31 pages, 14 figures, uses AAS LaTeX; to appear in the Astronomical Journa

The redshift-space two-point correlation functions of galaxies and groups in the Nearby Optical Galaxy sample

We use the two-point correlation function in redshift space, $\xi(s)$, to study the clustering of the galaxies and groups of the Nearby Optical Galaxy (NOG) sample, which is a nearly all-sky, complete, magnitude-limited sample of $\sim$7000 bright and nearby optical galaxies. The correlation function of galaxies is well described by a power law, $\xi(s)=(s/s_0)^{-\gamma}$, with slope $\gamma\sim1.5$ and $s_0\sim6.4 h^{-1}$Mpc (on scales $2.7 - 12 h^{-1}$Mpc), in agreement with previous results of several redshift surveys of optical galaxies. We confirm the existence of morphological segregation between early- and late-type galaxies and, in particular, we find a gradual decreasing of the strength of clustering from the S0 galaxies to the late-type spirals, on intermediate scales. Furthermore, luminous galaxies turn out to be more clustered than dim galaxies. The luminosity segregation, which is significant for both early- and late-type objects, starts to become appreciable only for galaxies brighter than $M_B\sim -19.5 + 5 \log h$ ($\sim 0.6 L^*$) and is independent on scale. The NOG group correlation functions are characterized by $s_0$-values ranging from $\sim 8 h^{-1}$ Mpc (for groups with at least three members) to $\sim10 h^{-1}$ Mpc (for groups with at least five members). The degree of group clustering depends on the physical properties of groups. Specifically, groups with greater velocity dispersions, sizes and masses tend to be more clustered than those with lower values of these quantities.Comment: Astrophysical Journal, in press, 72 pages, 16 eps figure

The VIMOS Public Extragalactic Redshift Survey (VIPERS). Never mind the gaps: comparing techniques to restore homogeneous sky coverage

[Abridged] Non-uniform sampling and gaps in sky coverage are common in galaxy redshift surveys, but these effects can degrade galaxy counts-in-cells and density estimates. We carry out a comparison of methods that aim to fill the gaps to correct for the systematic effects. Our study is motivated by the analysis of the VIMOS Extragalactic Redshift Survey (VIPERS), a flux-limited survey (i<22.5) based on one-pass observations with VIMOS, with gaps covering 25% of the surveyed area and a mean sampling rate of 35%. Our findings are applicable to other surveys with similar observing strategies. We compare 1) two algorithms based on photometric redshift, that assign redshifts to galaxies based on the spectroscopic redshifts of the nearest neighbours, 2) two Bayesian methods, the Wiener filter and the Poisson-Lognormal filter. Using galaxy mock catalogues we quantify the accuracy of the counts-in-cells measurements on scales of R=5 and 8 Mpc/h after applying each of these methods. We also study how they perform to account for spectroscopic redshift error and inhomogeneous and sparse sampling rate. We find that in VIPERS the errors in counts-in-cells measurements on R<10 Mpc/h scales are dominated by the sparseness of the sample. All methods underpredict by 20-35% the counts at high densities. This systematic bias is of the same order as random errors. No method outperforms the others. Random and systematic errors decrease for larger cells. We show that it is possible to separate the lowest and highest densities on scales of 5 Mpc/h at redshifts 0.5<z<1.1, over a large volume such as in VIPERS survey. This is vital for the characterisation of cosmic variance and rare populations (e.g, brightest galaxies) in environmental studies at these redshifts.Comment: 17 pages, 13 figures, accepted for publication in A&A (revised version after minor revision and language editing

Physical properties of galaxies and their evolution in the VIMOS VLT Deep Survey. II. Extending the mass-metallicity relation to the range z=0.89-1.24

Aims. We present a continuation of our study about the relation between stellar mass and gas-phase metallicity in the VIMOS VLT Deep Survey (VVDS). In this work we extend the determination of metallicities up to redshift = 1.24 for a sample of 42 star-forming galaxies with a mean redshift value of 0.99. Methods. For a selected sample of emission-line galaxies, we use both diagnostic diagrams and empirical calibrations based on [OII] emission lines along with the empirical relation between the intensities of the [OIII] and [NeIII] emission lines and the theoretical ratios between Balmer recombination emission lines to identify star-forming galaxies and to derive their metallicities. We derive stellar masses by fitting the whole spectral energy distribution with a set of stellar population synthesis models. Results. These new methods allow us to extend the mass-metallicity relation to higher redshift. We show that the metallicity determinations are consistent with more established strong-line methods. Taken together this allows us to study the evolution of the mass-metallicity relation up to z = 1.24 with good control of systematic uncertainties. We find an evolution with redshift of the average metallicity of galaxies very similar to those reported in the literature: for a given stellar mass, galaxies at z = 1 have, on average, a metallicity = 0.3 dex lower than galaxies in the local universe. However we do not see any significant metallicity evolution between redshifts z = 0.7 (Paper I) and z = 1.0 (this paper). We find also the same flattening of the mass-metallicity relation for the most massive galaxies as reported in Paper I at lower redshifts, but again no apparent evolution of the slope is seen between z = 0.7 and z = 1.0.Comment: 9 pages and 8 figures. In press in Astronomy & Astrophysic