491 research outputs found
Rolling ES cells down the Waddington landscape with Oct4 and Sox2
Embryonic stem cell (ESC) pluripotency is maintained by core transcriptional circuits whereby critical factors sustain their own expression while preventing the expression of genes required for differentiation. Thomson et al. (2011) now show that two core components of the pluripotency circuit, Oct4 and Sox2, are also critical for germ layer fate choice
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)
Trithorax group proteins: switching genes on and keeping them active
Cellular memory is provided by two counteracting groups of chromatin proteins termed Trithorax group (TrxG) and Polycomb group (PcG) proteins. TrxG proteins activate transcription and are perhaps best known because of the involvement of the TrxG protein MLL in leukaemia. However, in terms of molecular analysis, they have lived in the shadow of their more famous counterparts, the PcG proteins. Recent advances have improved our understanding of TrxG protein function and demonstrated that the heterogeneous group of TrxG proteins is of critical importance in the epigenetic regulation of the cell cycle, senescence, DNA damage and stem cell biology
Redshift-Space Distortions and the Real-Space Clustering of Different Galaxy Types
We study the distortions induced by peculiar velocities on the redshift-space
correlation function of galaxies of different morphological types in the
Pisces-Perseus redshift survey. Redshift-space distortions affect early- and
late-type galaxies in different ways. In particular, at small separations, the
dominant effect comes from virialized cluster cores, where ellipticals are the
dominant population. The net result is that a meaningful comparison of the
clustering strength of different morphological types can be performed only in
real space, i.e., after projecting out the redshift distortions on the
two-point correlation function xi(r_p,pi). A power-law fit to the projected
function w_p(r_p) on scales smaller than 10/h Mpc gives r_o =
8.35_{-0.76}^{+0.75} /h Mpc, \gamma = 2.05_{-0.08}^{+0.10} for the early-type
population, and r_o = 5.55_{-0.45}^{+0.40} /h Mpc, \gamma =
1.73_{-0.08}^{+0.07} for spirals and irregulars. These values are derived for a
sample luminosity brighter than M_{Zw} = -19.5. We detect a 25% increase of r_o
with luminosity for all types combined, from M_{Zw} = -19 to -20. In the
framework of a simple stable-clustering model for the mean streaming of pairs,
we estimate sigma_12(1), the one-dimensional pairwise velocity dispersion
between 0 and 1 /h Mpc, to be 865^{+250}_{-165} km/s for early-type galaxies
and 345^{+95}_{-65} km/s for late types. This latter value should be a fair
estimate of the pairwise dispersion for ``field'' galaxies; it is stable with
respect to the presence or absence of clusters in the sample, and is consistent
with the values found for non-cluster galaxies and IRAS galaxies at similar
separations.Comment: 17 LaTeX pages including 3 tables, plus 11 PS figures. Uses AASTeX
macro package (aaspp4.sty) and epsf.sty. To appear on ApJ, 489, Nov 199
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
1.4.Comment: 43 pages, uses AASTeX 4.0 macros. Includes 8 tables and 16 Postscript
figures, updated reference
The XXL Survey VIII: MUSE characterisation of intracluster light in a z0.53 cluster of galaxies
Within a cluster, gravitational effects can lead to the removal of stars from
their parent galaxies. Gas hydrodynamical effects can additionally strip gas
and dust from galaxies. The properties of the ICL can therefore help constrain
the physical processes at work in clusters by serving as a fossil record of the
interaction history. The present study is designed to characterise this ICL in
a ~10^14 M_odot and z~0.53 cluster of galaxies from imaging and spectroscopic
points of view. By applying a wavelet-based method to CFHT Megacam and WIRCAM
images, we detect significant quantities of diffuse light. These sources were
then spectroscopically characterised with MUSE. MUSE data were also used to
compute redshifts of 24 cluster galaxies and search for cluster substructures.
An atypically large amount of ICL has been detected in this cluster. Part of
the detected diffuse light has a very weak optical stellar component and
apparently consists mainly of gas emission, while other diffuse light sources
are clearly dominated by old stars. Furthermore, emission lines were detected
in several places of diffuse light. Our spectral analysis shows that this
emission likely originates from low-excitation parameter gas. The stellar
contribution to the ICL is about 2.3x10^9 yrs old even though the ICL is not
currently forming a large number of stars. On the other hand, the contribution
of the gas emission to the ICL in the optical is much greater than the stellar
contribution in some regions, but the gas density is likely too low to form
stars. These observations favour ram pressure stripping, turbulent viscous
stripping, or supernovae winds as the origin of the large amount of
intracluster light. Since the cluster appears not to be in a major merging
phase, we conclude that ram pressure stripping is the most plausible process
that generates the observed ICL sources.Comment: Accepted in A&A, english enhanced, figure location different than in
the A&A version due to different style files, shortened abstrac
HP1 drives de novo 3D genome reorganization in early Drosophila embryos
Fundamental features of 3D genome organization are established de novo in the early embryo, including clustering of pericentromeric regions, the folding of chromosome arms and the segregation of chromosomes into active (A-) and inactive (B-) compartments. However, the molecular mechanisms that drive de novo organization remain unknown. Here, by combining chromosome conformation capture (Hi-C), chromatin immunoprecipitation with high-throughput sequencing (ChIP–seq), 3D DNA fluorescence in situ hybridization (3D DNA FISH) and polymer simulations, we show that heterochromatin protein 1a (HP1a) is essential for de novo 3D genome organization during Drosophila early development. The binding of HP1a at pericentromeric heterochromatin is required to establish clustering of pericentromeric regions. Moreover, HP1a binding within chromosome arms is responsible for overall chromosome folding and has an important role in the formation of B-compartment regions. However, depletion of HP1a does not affect the A-compartment, which suggests that a different molecular mechanism segregates active chromosome regions. Our work identifies HP1a as an epigenetic regulator that is involved in establishing the global structure of the genome in the early embryo
Cactus pear pruning residue in agriculture: Unveiling soil-specific responses to enhance water retention
This study examines the effects of incorporating powdered cactus pear pruning waste (PCPPW) on the hydraulic properties of benchmark soils, in line with circular economy principles. The cultivation of cactus pear generates substantial amounts of pruning residues, which offer the potential for nutrient recovery and reuse. Our findings reveal that amending soils with this material has a positive impact on water retention, but it requires a substantial volume, exceeding 20%, which may not be practical for open-field applications. However, this presents promise for the horticultural and floricultural sectors. These results challenge previous assumptions about soil density, plant-available water capacity, and swelling potential, contributing to our understanding of agronomic applications. Notably, the enhancement of drainable water capacity is most significant in less clayey soils, while highly clayey soils experience fewer benefits. These results highlight the importance of considering specific soil conditions when implementing circular economy principles, particularly in soil amendment practices
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