New analysis method of the halo phenomenon in finite many-fermion systems. First applications to medium-mass atomic nuclei

A new analysis method to investigate halos in finite many-fermion systems is designed, as existing characterization methods are proven to be incomplete/inaccurate. A decomposition of the internal wave-function of the {$N$-body} system in terms of overlap functions allows a model-independent analysis of medium-range and asymptotic properties of the internal one-body density. The existence of a spatially decorrelated region in the density profile is related to the existence of three typical energy scales in the excitation spectrum of the {$(N-1)$-body} system. A series of model-independent measures, taking the internal density as the only input, are introduced. The new measures allow a quantification of the potential halo in terms of the average number of fermions participating to it and of its impact on the system extension. Those new "halo factors" are validated through simulations and applied to results obtained through energy density functional calculations of medium-mass nuclei. Performing spherical Hartree-Fock-Bogoliubov calculations with state-of-the-art Skyrme plus pairing functionals, a collective halo is predicted in drip-line Cr isotopes, whereas no such effect is seen in Sn isotopes.Comment: 27 Pages, 29 Figures. Accepted for publication in Phys. Rev. C back-to-back with second part (arXiv:0711.1275

Halo phenomenon in finite many-fermion systems. Atom-positron complexes and large-scale study of atomic nuclei

The analysis method proposed in Ref. \cite{rotival07a} is applied to characterize halo properties in finite many-fermion systems. First, the versatility of the method is highlighted by applying it to light and medium-mass nuclei as well as to atom-positron and ion-positronium complexes. Second, the dependence of nuclear halo properties on the characteristics of the energy density functional used in self-consistent Hartree-Fock-Bogoliubov calculations is studied. It is found that (a) the low-density behavior of the pairing functional and the regularization/renormalization scheme must be chosen coherently and with care to provide meaningful predictions, (b) the impact of pairing correlations on halo properties is significant and is the result of two competing effects, (c) the detailed characteristics of the pairing functional has however only little importance, (d) halo properties depend significantly on any ingredient of the energy density functional that influences the location of single-particle levels; i.e. the effective mass, the tensor terms and the saturation density of nuclear matter. The latter dependencies give insights to how experimental data on medium-mass drip-line nuclei can be used in the distant future to constrain some characteristics of the nuclear energy density functional. Last but not least, large scale predictions of halos among all spherical even-even nuclei are performed using specific sets of particle-hole and particle-particle energy functionals. It is shown that halos in the ground state of medium-mass nuclei will only be found at the very limit of neutron stability and for a limited number of elements.Comment: 24 Pages, 32 Figures. Accepted for publication in Phys. Rev. C back-to back with first part (nucl-th/0702050

JAG1 (jagged 1 (Alagille syndrome))

Review on JAG1 (jagged 1 (Alagille syndrome)), with data on DNA, on the protein encoded, and where the gene is implicated

Integrating Phosphoproteome and Transcriptome Reveals New Determinants of Macrophage Multinucleation

This research was originally published in Molecular and Cellular Proteomics. Rotival M, Ko JH, Srivastava PK, Kerloc'h A, Montoya A, Mauro C, Faull P, Cutillas PR, Petretto E, Behmoaras J. Integrating phosphoproteome and transcriptome reveals new determinants of macrophage multinucleation. Molecular and Cellular Proteomics. 2014. Vol:pp-pp. © the American Society for Biochemistry and Molecular Biology.File embargoed until 22 Dec 2015

Identification of Ceruloplasmin as a Gene that Affects Susceptibility to Glomerulonephritis Through Macrophage Function

Crescentic glomerulonephritis (Crgn) is a complex disorder where macrophage activity and infiltration are significant effector causes. In previous linkage studies using the uniquely susceptible Wistar Kyoto (WKY) rat strain, we have identified multiple crescentic glomerulonephritis QTL (Crgn) and positionally cloned genes underlying Crgn1 and Crgn2, which accounted for 40% of total variance in glomerular inflammation. Here, we have generated a backcross (BC) population (n = 166) where Crgn1 and Crgn2 were genetically fixed and found significant linkage to glomerular crescents on chromosome 2 (Crgn8, LOD = 3.8). Fine mapping analysis by integration with genome-wide expression QTLs (eQTLs) from the same BC population identified ceruloplasmin (Cp) as a positional eQTL in macrophages but not in serum. Liquid chromatography-tandem mass spectrometry confirmed Cp as a protein QTL in rat macrophages. WKY macrophages overexpress Cp and its downregulation by RNA interference decreases markers of glomerular proinflammatory macrophage activation. Similarly, short incubation with Cp results in a strain-dependent macrophage polarization in the rat. These results suggest that genetically determined Cp levels can alter susceptibility to Crgn through macrophage function and propose a new role for Cp in early macrophage activation

The nuclear energy density functional formalism

The present document focuses on the theoretical foundations of the nuclear energy density functional (EDF) method. As such, it does not aim at reviewing the status of the field, at covering all possible ramifications of the approach or at presenting recent achievements and applications. The objective is to provide a modern account of the nuclear EDF formalism that is at variance with traditional presentations that rely, at one point or another, on a {\it Hamiltonian-based} picture. The latter is not general enough to encompass what the nuclear EDF method represents as of today. Specifically, the traditional Hamiltonian-based picture does not allow one to grasp the difficulties associated with the fact that currently available parametrizations of the energy kernel $E[g',g]$ at play in the method do not derive from a genuine Hamilton operator, would the latter be effective. The method is formulated from the outset through the most general multi-reference, i.e. beyond mean-field, implementation such that the single-reference, i.e. "mean-field", derives as a particular case. As such, a key point of the presentation provided here is to demonstrate that the multi-reference EDF method can indeed be formulated in a {\it mathematically} meaningful fashion even if $E[g',g]$ does {\it not} derive from a genuine Hamilton operator. In particular, the restoration of symmetries can be entirely formulated without making {\it any} reference to a projected state, i.e. within a genuine EDF framework. However, and as is illustrated in the present document, a mathematically meaningful formulation does not guarantee that the formalism is sound from a {\it physical} standpoint. The price at which the latter can be enforced as well in the future is eventually alluded to.Comment: 64 pages, 8 figures, submitted to Euroschool Lecture Notes in Physics Vol.IV, Christoph Scheidenberger and Marek Pfutzner editor

Genetics and beyond - the transcriptome of human monocytes and disease susceptibility

BACKGROUND: Variability of gene expression in human may link gene sequence variability and phenotypes; however, non-genetic variations, alone or in combination with genetics, may also influence expression traits and have a critical role in physiological and disease processes. METHODOLOGY/PRINCIPAL FINDINGS: To get better insight into the overall variability of gene expression, we assessed the transcriptome of circulating monocytes, a key cell involved in immunity-related diseases and atherosclerosis, in 1,490 unrelated individuals and investigated its association with >675,000 SNPs and 10 common cardiovascular risk factors. Out of 12,808 expressed genes, 2,745 expression quantitative trait loci were detected (P<5.78x10(-12)), most of them (90%) being cis-modulated. Extensive analyses showed that associations identified by genome-wide association studies of lipids, body mass index or blood pressure were rarely compatible with a mediation by monocyte expression level at the locus. At a study-wide level (P<3.9x10(-7)), 1,662 expression traits (13.0%) were significantly associated with at least one risk factor. Genome-wide interaction analyses suggested that genetic variability and risk factors mostly acted additively on gene expression. Because of the structure of correlation among expression traits, the variability of risk factors could be characterized by a limited set of independent gene expressions which may have biological and clinical relevance. For example expression traits associated with cigarette smoking were more strongly associated with carotid atherosclerosis than smoking itself. CONCLUSIONS/SIGNIFICANCE: This study demonstrates that the monocyte transcriptome is a potent integrator of genetic and non-genetic influences of relevance for disease pathophysiology and risk assessment

The epigenomic landscape of African rainforest hunter-gatherers and farmers

International audienceThe genetic history of African populations is increasingly well documented, yet their patterns of epigenomic variation remain uncharacterized. Moreover, the relative impacts of DNA sequence variation and temporal changes in lifestyle and habitat on the human epigenome remain unknown. Here we generate genome-wide genotype and DNA methylation profiles for 362 rainforest hunter-gatherers and sedentary farmers. We find that the current habitat and historical lifestyle of a population have similarly critical impacts on the methylome, but the biological functions affected strongly differ. Specifically, methylation variation associated with recent changes in habitat mostly concerns immune and cellular functions, whereas that associated with historical lifestyle affects developmental processes. Furthermore, methylation variation—particularly that correlated with historical lifestyle—shows strong associations with nearby genetic variants that, moreover, are enriched in signals of natural selection. Our work provides new insight into the genetic and environmental factors affecting the epigenomic landscape of human populations over time

Systems genetics identifies Sestrin 3 as a regulator of a proconvulsant gene network in human epileptic hippocampus

Gene-regulatory network analysis is a powerful approach to elucidate the molecular processes and pathways underlying complex disease. Here we employ systems genetics approaches to characterize the genetic regulation of pathophysiological pathways in human temporal lobe epilepsy (TLE). Using surgically acquired hippocampi from 129 TLE patients, we identify a gene-regulatory network genetically associated with epilepsy that contains a specialized, highly expressed transcriptional module encoding proconvulsive cytokines and Toll-like receptor signalling genes. RNA sequencing analysis in a mouse model of TLE using 100 epileptic and 100 control hippocampi shows the proconvulsive module is preserved across-species, specific to the epileptic hippocampus and upregulated in chronic epilepsy. In the TLE patients, we map the trans-acting genetic control of this proconvulsive module to Sestrin 3 (SESN3), and demonstrate that SESN3 positively regulates the module in macrophages, microglia and neurons. Morpholino-mediated Sesn3 knockdown in zebrafish confirms the regulation of the transcriptional module, and attenuates chemically induced behavioural seizures in vivo