392 research outputs found
Initial conditions, Discreteness and non-linear structure formation in cosmology
In this lecture we address three different but related aspects of the initial
continuous fluctuation field in standard cosmological models. Firstly we
discuss the properties of the so-called Harrison-Zeldovich like spectra. This
power spectrum is a fundamental feature of all current standard cosmological
models. In a simple classification of all stationary stochastic processes into
three categories, we highlight with the name ``super-homogeneous'' the
properties of the class to which models like this, with , belong. In
statistical physics language they are well described as glass-like. Secondly,
the initial continuous density field with such small amplitude correlated
Gaussian fluctuations must be discretised in order to set up the initial
particle distribution used in gravitational N-body simulations. We discuss the
main issues related to the effects of discretisation, particularly concerning
the effect of particle induced fluctuations on the statistical properties of
the initial conditions and on the dynamical evolution of gravitational
clustering.Comment: 28 pages, 1 figure, to appear in Proceedings of 9th Course on
Astrofundamental Physics, International School D. Chalonge, Kluwer, eds N.G.
Sanchez and Y.M. Pariiski, uses crckapb.st pages, 3 figure, ro appear in
Proceedings of 9th Course on Astrofundamental Physics, International School
D. Chalonge, Kluwer, Eds. N.G. Sanchez and Y.M. Pariiski, uses crckapb.st
Insights into the role of DNA methylation in diatoms by genome-wide profiling in Phaeodactylum tricornutum
DNA cytosine methylation is a widely conserved epigenetic mark in eukaryotes that appears to have critical roles in the regulation of genome structure and transcription. Genome-wide methylation maps have so far only been established from the supergroups Archaeplastida and Unikont. Here we report the first whole-genome methylome from a stramenopile, the marine model diatom Phaeodactylum tricornutum. Around 6% of the genome is intermittently methylated in a mosaic pattern. We find extensive methylation in transposable elements. We also detect methylation in over 320 genes. Extensive gene methylation correlates strongly with transcriptional silencing and differential expression under specific conditions. By contrast, we find that genes with partial methylation tend to be constitutively expressed. These patterns contrast with those found previously in other eukaryotes. By going beyond plants, animals and fungi, this stramenopile methylome adds significantly to our understanding of the evolution of DNA methylation in eukaryotes.Fil: Veluchamy, Alaguraj. Institut de Biologie de l'École Normale Supérieure; FranciaFil: Lin, Xin. Institut de Biologie de l'École Normale Supérieure; Francia. Xiamen University; ChinaFil: Maumus, Florian.Fil: Rivarola, Maximo Lisandro.Fil: Bhavsar, Jaysheel.Fil: Creasy, Todd.Fil: O'Brien, Kimberly.Fil: Sengamalay, Naomi A..Fil: Tallon, Luke J..Fil: Smith, Andrew D..Fil: Rayko, Edda.Fil: Ahmed, Ikhlak.Fil: Crom, Stéphane Le.Fil: Farrant, Gregory K..Fil: Sgro, Jean-Yves.Fil: Olson, Sue A..Fil: Bondurant, Sandra Splinter.Fil: Allen, Andrew.Fil: Rabinowicz, Pablo D..Fil: Sussman, Michael R..Fil: Bowler, Chris.Fil: Tirichine, Leïla
CTCF-mediated transcriptional regulation through cell type-specific chromosome organization in the {\beta}-globin locus
The principles underlying the architectural landscape of chromatin beyond the
nucleosome level in living cells remains largely unknown despite its potential
to play a role in mammalian gene regulation. We investigated the 3-dimensional
folding of a 1 Mbp region of human chromosome 11 containing the {\beta}-globin
genes by integrating looping interactions of the insulator protein CTCF
determined comprehensively by chromosome conformation capture (3C) into a
polymer model of chromatin. We find that CTCF-mediated cell type specific
interactions in erythroid cells are organized to favor contacts known to occur
in vivo between the {\beta}-globin locus control region (LCR) and genes. In
these cells, the modeled {\beta}-globin domain folds into a globule with the
LCR and the active globin genes on the periphery. By contrast, in non-erythroid
cells, the globule is less compact with few but dominant CTCF interactions
driving the genes away from the LCR. This leads to a decrease in contact
frequencies that can exceed 1000-fold depending on the stiffness of the
chromatin and the exact positioning of the genes. Our findings show that an
ensemble of CTCF contacts functionally affects spatial distances between
control elements and target genes contributing to chromosomal organization
required for transcription.Comment: Full article, including Supp. Mat., is available at Nucleic Acids
Research, doi: 10.1093/nar/gks53
Modelling Cross-Shore Shoreline Change on Multiple Timescales and Their Interactions
In this paper, a new approach to model wave-driven, cross-shore shoreline change incorporating multiple timescales is introduced. As a base, we use the equilibrium shoreline prediction model ShoreFor that accounts for a single timescale only. High-resolution shoreline data collected at three distinctly different study sites is used to train the new data-driven model. In addition to the direct forcing approach used in most models, here two additional terms are introduced: a time-upscaling and a time-downscaling term. The upscaling term accounts for the persistent effect of short-term events, such as storms, on the shoreline position. The downscaling term accounts for the effect of long-term shoreline modulations, caused by, for example, climate variability, on shorter event impacts. The multi-timescale model shows improvement compared to the original ShoreFor model (a normalized mean square error improvement during validation of 18 to 59%) at the three contrasted sandy beaches. Moreover, it gains insight in the various timescales (storms to inter-annual) and reveals their interactions that cause shoreline change. We find that extreme forcing events have a persistent shoreline impact and cause 57–73% of the shoreline variability at the three sites. Moreover, long-term shoreline trends affect short-term forcing event impacts and determine 20–27% of the shoreline variability.</jats:p
Quantitative analysis of chromatin interaction changes upon a 4.3 Mb deletion at mouse 4E2
BACKGROUND: Circular chromosome conformation capture (4C) has provided important insights into three dimensional (3D) genome organization and its critical impact on the regulation of gene expression. We developed a new quantitative framework based on polymer physics for the analysis of paired-end sequencing 4C (PE-4Cseq) data. We applied this strategy to the study of chromatin interaction changes upon a 4.3 Mb DNA deletion in mouse region 4E2. RESULTS: A significant number of differentially interacting regions (DIRs) and chromatin compaction changes were detected in the deletion chromosome compared to a wild-type (WT) control. Selected DIRs were validated by 3D DNA FISH experiments, demonstrating the robustness of our pipeline. Interestingly, significant overlaps of DIRs with CTCF/Smc1 binding sites and differentially expressed genes were observed. CONCLUSIONS: Altogether, our PE-4Cseq analysis pipeline provides a comprehensive characterization of DNA deletion effects on chromatin structure and function
Heatshield for Extreme Entry Environment Technology (HEEET) for Missions to Saturn and Beyond
This poster provides an overview of the requirements, design, development and testing of the 3D Woven TPS being developed under NASAs Heatshield for Extreme Entry Environment Technology (HEEET) project. Under this current program, NASA is working to develop a Thermal Protection System (TPS) capable of surviving entry into Saturn. A primary goal of the project is to build and test an Engineering Test Unit (ETU) to establish a Technical Readiness Level (TRL) of 6 for this technology by 2017
Constraints on the shapes of galaxy dark matter haloes from weak gravitational lensing
We study the shapes of galaxy dark matter haloes by measuring the anisotropy
of the weak gravitational lensing signal around galaxies in the second
Red-sequence Cluster Survey (RCS2). We determine the average shear anisotropy
within the virial radius for three lens samples: all galaxies with
19<m_r'<21.5, and the `red' and `blue' samples, whose lensing signals are
dominated by massive low-redshift early-type and late-type galaxies,
respectively. To study the environmental dependence of the lensing signal, we
separate each lens sample into an isolated and clustered part and analyse them
separately. We also measure the azimuthal dependence of the distribution of
physically associated galaxies around the lens samples. We find that these
satellites preferentially reside near the major axis of the lenses, and
constrain the angle between the major axis of the lens and the average location
of the satellites to =43.7 deg +/- 0.3 deg for the `all' lenses,
=41.7 deg +/- 0.5 deg for the `red' lenses and =42.0 deg +/- 1.4
deg for the `blue' lenses. For the `all' sample, we find that the anisotropy of
the galaxy-mass cross-correlation function =0.23 +/- 0.12, providing
weak support for the view that the average galaxy is embedded in, and
preferentially aligned with, a triaxial dark matter halo. Assuming an
elliptical Navarro-Frenk-White (NFW) profile, we find that the ratio of the
dark matter halo ellipticity and the galaxy ellipticity
f_h=e_h/e_g=1.50+1.03-1.01, which for a mean lens ellipticity of 0.25
corresponds to a projected halo ellipticity of e_h=0.38+0.26-0.25 if the halo
and the lens are perfectly aligned. For isolated galaxies of the `all' sample,
the average shear anisotropy increases to =0.51+0.26-0.25 and
f_h=4.73+2.17-2.05, whilst for clustered galaxies the signal is consistent with
zero. (abridged)Comment: 28 pages, 23 figues, accepted for publication in A&
Heatshield for Extreme Entry Environment Technology (HEEET) Enabling Missions Beyond Heritage Carbon Phenolic
This poster provides an overview of the requirements, design, development and testing of the 3D Woven TPS being developed under NASAs Heatshield for Extreme Entry Environment Technology (HEEET) project. Under this current program, NASA is working to develop a Thermal Protection System (TPS) capable of surviving entry into Venus or Saturn. A primary goal of the project is to build and test an Engineering Test Unit (ETU) to establish a Technical Readiness Level (TRL) of 6 for this technology by 2017
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