Altered intra-nuclear organisation of heterochromatin and genes in ICF syndrome.

The ICF syndrome is a rare autosomal recessive disorder, the most common symptoms of which are immunodeficiency, facial anomalies and cytogenetic defects involving decondensation and instability of chromosome 1, 9 and 16 centromeric regions. ICF is also characterised by significant hypomethylation of the classical satellite DNA, the major constituent of the juxtacentromeric heterochromatin. Here we report the first attempt at analysing some of the defining genetic and epigenetic changes of this syndrome from a nuclear architecture perspective. In particular, we have compared in ICF (Type 1 and Type 2) and controls the large-scale organisation of chromosome 1 and 16 juxtacentromeric heterochromatic regions, their intra-nuclear positioning, and co-localisation with five specific genes (BTG2, CNN3, ID3, RGS1, F13A1), on which we have concurrently conducted expression and methylation analysis. Our investigations, carried out by a combination of molecular and cytological techniques, demonstrate the existence of specific and quantifiable differences in the genomic and nuclear organisation of the juxtacentromeric heterochromatin in ICF. DNA hypomethylation, previously reported to correlate with the decondensation of centromeric regions in metaphase described in these patients, appears also to correlate with the heterochromatin spatial configuration in interphase. Finally, our findings on the relative positioning of hypomethylated satellite sequences and abnormally expressed genes suggest a connection between disruption of long-range gene-heterochromatin associations and some of the changes in gene expression in ICF. Beyond its relevance to the ICF syndrome, by addressing fundamental principles of chromosome functional organisation within the cell nucleus, this work aims to contribute to the current debate on the epigenetic impact of nuclear architecture in development and disease

Three-dimensional structure of Serratia marcescens nuclease at 1.7 Å resolution and mechanism of its action

AbstractThe three-dimensional crystal structure of Serratia marcescens (Sm) nuclease has been refined at 1.7 Å resolution to the R-factor of 17.3% and R-free of 22.2%. The final model consists of 3678 non-hydrogen atoms and 443 water molecules. The analysis of the secondary and the tertiary structures of the Sm nuclease suggests a topology which reveals essential inner symmetry in all the three layers forming the monomer. We propose the plausible mechanism of its action based on a concerted participation of the catalytically important amino acid residues of the enzyme active site

Parity Invariance and Effective Light-Front Hamiltonians

In the light-front form of field theory, boost invariance is a manifest symmetry. On the downside, parity and rotational invariance are not manifest, leaving the possibility that approximations or incorrect renormalization might lead to violations of these symmetries for physical observables. In this paper, it is discussed how one can turn this deficiency into an advantage and utilize parity violations (or the absence thereof) in practice for constraining effective light-front Hamiltonians. More precisely, we will identify observables that are both sensitive to parity violations and easily calculable numerically in a non-perturbative framework and we will use these observables to constrain the finite part of non-covariant counter-terms in effective light-front Hamiltonians.Comment: REVTEX, 9 page

Canonical Formulation of the Light-Front Gluodynamics and Quantization of the Non-Abelian Plane Waves

Without a gauge fixing, canonical variables for the light-front SU(2) gluodynamics are determined. The Gauss law is written in terms of the canonical variables. The system is qualified as a generalized dynamical system with first class constraints. Abeliazation is a specific feature of the formulation (most of the canonical variables transform nontrivially only under the action of an Abelian subgroup of the gauge transformations). At finite volume, a discrete spectrum of the light-front Hamiltonian $P_+$ is obtained in the sector of vanishing $P_-$. We obtain, therefore, a quantized form of the classical solutions previously known as non-Abelian plane waves. Then, considering the infinite volume limit, we find that the presence of the mass gap depends on the way the infinite volume limit is taken, which may suggest the presence of different ``phases'' of the infinite volume theory. We also check that the formulation obtained is in accord with the standard perturbation theory if the latter is taken in the covariant gauges.Comment: REVTEX, 18 pages, version to appear in Phys. Rev.

The Thermodynamics of Quarks and Gluons

This is an introduction to the study of strongly interacting matter. We survey its different possible states and discuss the transition from hadronic matter to a plasma of deconfined quarks and gluons. Following this, we summarize the results provided by lattice QCD finite temperature and density, and then investigate the nature of the deconfinement transition. Finally we give a schematic overview of possible ways to study the properties of the quark-gluon plasma.Comment: 19 pages, 21 figures; lecture given at the QGP Winter School, Jaipur/India, Feb.1-3, 2008; to appear in Springer Lecture Notes in Physic

Constraining the dark energy dynamics with the cosmic microwave background bispectrum

We consider the influence of the dark energy dynamics at the onset of cosmic acceleration on the Cosmic Microwave Background (CMB) bispectrum, through the weak lensing effect induced by structure formation. We study the line of sight behavior of the contribution to the bispectrum signal at a given angular multipole $l$: we show that it is non-zero in a narrow interval centered at a redshift $z$ satisfying the relation $l/r(z)\simeq k_{NL}(z)$, where the wavenumber corresponds to the scale entering the non-linear phase, and $r$ is the cosmological comoving distance. The relevant redshift interval is in the range 0.1\lsim z\lsim 2 for multipoles 1000\gsim\ell\gsim 100; the signal amplitude, reflecting the perturbation dynamics, is a function of the cosmological expansion rate at those epochs, probing the dark energy equation of state redshift dependence independently on its present value. We provide a worked example by considering tracking inverse power law and SUGRA Quintessence scenarios, having sensibly different redshift dynamics and respecting all the present observational constraints. For scenarios having the same present equation of state, we find that the effect described above induces a projection feature which makes the bispectra shifted by several tens of multipoles, about 10 times more than the corresponding effect on the ordinary CMB angular power spectrum.Comment: 15 pages, 7 figures, matching version accepted by Physical Review D, one figure improve

Weak lensing, dark matter and dark energy

Weak gravitational lensing is rapidly becoming one of the principal probes of dark matter and dark energy in the universe. In this brief review we outline how weak lensing helps determine the structure of dark matter halos, measure the expansion rate of the universe, and distinguish between modified gravity and dark energy explanations for the acceleration of the universe. We also discuss requirements on the control of systematic errors so that the systematics do not appreciably degrade the power of weak lensing as a cosmological probe.Comment: Invited review article for the GRG special issue on gravitational lensing (P. Jetzer, Y. Mellier and V. Perlick Eds.). V3: subsection on three-point function and some references added. Matches the published versio

Small-scale solar magnetic fields

As we resolve ever smaller structures in the solar atmosphere, it has become clear that magnetism is an important component of those small structures. Small-scale magnetism holds the key to many poorly understood facets of solar magnetism on all scales, such as the existence of a local dynamo, chromospheric heating, and flux emergence, to name a few. Here, we review our knowledge of small-scale photospheric fields, with particular emphasis on quiet-sun field, and discuss the implications of several results obtained recently using new instruments, as well as future prospects in this field of research.Comment: 43 pages, 18 figure

Deep Inelastic Structure Functions in Light-Front QCD: Radiative Corrections

Recently, we have introduced a unified theory to deal with perturbative and non-perturbative QCD contributions to hadronic structure functions in deep inelastic scattering. This formulation is realized by combining the coordinate space approach based on light-front current algebra techniques and the momentum space approach based on Fock space expansion methods in the Hamiltonian formalism of light-front field theory. In this work we show how a perturbative analysis in the light-front Hamiltonian formalism leads to the factorization scheme we have proposed recently. The analysis also shows that the scaling violations due to perturbative QCD corrections can be rather easily addressed in this framework by simply replacing the hadron target by dressed parton target and then carrying out a systematic expansion in the coupling constant $\alpha_s$ based on the perturbative QCD expansion of the dressed parton target. The tools employed for this calculation are those available from light-front old-fashioned perturbation theory. We present the complete set of calculations of unpolarized and polarized deep inelastic structure functions to order $\alpha_s$. We extract the relevant splitting functions in all the cases. We explicitly verify all the sum rules to order $\alpha_s$. We demonstrate the validity of approximations made in the derivation of the new factorization scheme. This is achieved with the help of detailed calculations of the evolution of structure function of a composite system carried out using multi-parton wavefunctions.Comment: Revtex, 26 pages and no figur

Confining QCD Strings, Casimir Scaling, and a Euclidean Approach to High-Energy Scattering

We compute the chromo-field distributions of static color-dipoles in the fundamental and adjoint representation of SU(Nc) in the loop-loop correlation model and find Casimir scaling in agreement with recent lattice results. Our model combines perturbative gluon exchange with the non-perturbative stochastic vacuum model which leads to confinement of the color-charges in the dipole via a string of color-fields. We compute the energy stored in the confining string and use low-energy theorems to show consistency with the static quark-antiquark potential. We generalize Meggiolaro's analytic continuation from parton-parton to gauge-invariant dipole-dipole scattering and obtain a Euclidean approach to high-energy scattering that allows us in principle to calculate S-matrix elements directly in lattice simulations of QCD. We apply this approach and compute the S-matrix element for high-energy dipole-dipole scattering with the presented Euclidean loop-loop correlation model. The result confirms the analytic continuation of the gluon field strength correlator used in all earlier applications of the stochastic vacuum model to high-energy scattering.Comment: 65 pages, 13 figures, extended and revised version to be published in Phys. Rev. D (results unchanged, 2 new figures, 1 new table, additional discussions in Sec.2.3 and Sec.5, new appendix on the non-Abelian Stokes theorem, old Appendix A -> Sec.3, several references added