Genome-Wide Survey of MicroRNA - Transcription Factor Feed-Forward Regulatory Circuits in Human

In this work, we describe a computational framework for the genome-wide identification and characterization of mixed transcriptional/post-transcriptional regulatory circuits in humans. We concentrated in particular on feed-forward loops (FFL), in which a master transcription factor regulates a microRNA, and together with it, a set of joint target protein coding genes. The circuits were assembled with a two step procedure. We first constructed separately the transcriptional and post-transcriptional components of the human regulatory network by looking for conserved over-represented motifs in human and mouse promoters, and 3'-UTRs. Then, we combined the two subnetworks looking for mixed feed-forward regulatory interactions, finding a total of 638 putative (merged) FFLs. In order to investigate their biological relevance, we filtered these circuits using three selection criteria: (I) GeneOntology enrichment among the joint targets of the FFL, (II) independent computational evidence for the regulatory interactions of the FFL, extracted from external databases, and (III) relevance of the FFL in cancer. Most of the selected FFLs seem to be involved in various aspects of organism development and differentiation. We finally discuss a few of the most interesting cases in detail.Comment: 51 pages, 5 figures, 4 tables. Supporting information included. Accepted for publication in Molecular BioSystem

Counterterms vs. Dualities

We investigate and clarify the mutual compatibility of the higher order corrections arising in supergravity and string theory effective actions and the non-linear duality symmetries of these theories. Starting from a conventional tree level action leading to duality invariant equations of motion, we show how to accommodate duality invariant counterterms given as functionals of both electric and magnetic fields in a perturbative expansion, and to deduce from them a non-polynomial bona fide action satisfying the Gaillard-Zumino constraint. There exists a corresponding consistency constraint in the non-covariant Henneaux-Teitelboim formalism which ensures that one can always restore diffeomorphism invariance by perturbatively solving this functional identity. We illustrate how this procedure works for the R^2 \nabla F \nabla F and F^4 counterterms in Maxwell theory.Comment: 15 page

Crossings, Motzkin paths and Moments

Kasraoui, Stanton and Zeng, and Kim, Stanton and Zeng introduced certain $q$-analogues of Laguerre and Charlier polynomials. The moments of these orthogonal polynomials have combinatorial models in terms of crossings in permutations and set partitions. The aim of this article is to prove simple formulas for the moments of the $q$-Laguerre and the $q$-Charlier polynomials, in the style of the Touchard-Riordan formula (which gives the moments of some $q$-Hermite polynomials, and also the distribution of crossings in matchings). Our method mainly consists in the enumeration of weighted Motzkin paths, which are naturally associated with the moments. Some steps are bijective, in particular we describe a decomposition of paths which generalises a previous construction of Penaud for the case of the Touchard-Riordan formula. There are also some non-bijective steps using basic hypergeometric series, and continued fractions or, alternatively, functional equations.Comment: 21 page

Kinetic modelling of competition and depletion of shared miRNAs by competing endogenous RNAs

Non-conding RNAs play a key role in the post-transcriptional regulation of mRNA translation and turnover in eukaryotes. miRNAs, in particular, interact with their target RNAs through protein-mediated, sequence-specific binding, giving rise to extended and highly heterogeneous miRNA-RNA interaction networks. Within such networks, competition to bind miRNAs can generate an effective positive coupling between their targets. Competing endogenous RNAs (ceRNAs) can in turn regulate each other through miRNA-mediated crosstalk. Albeit potentially weak, ceRNA interactions can occur both dynamically, affecting e.g. the regulatory clock, and at stationarity, in which case ceRNA networks as a whole can be implicated in the composition of the cell's proteome. Many features of ceRNA interactions, including the conditions under which they become significant, can be unraveled by mathematical and in silico models. We review the understanding of the ceRNA effect obtained within such frameworks, focusing on the methods employed to quantify it, its role in the processing of gene expression noise, and how network topology can determine its reach.Comment: review article, 29 pages, 7 figure

The SEGUE Stellar Parameter Pipeline. III. Comparison with High-Resolution Spectroscopy of SDSS/SEGUE Field Stars

We report high-resolution spectroscopy of 125 field stars previously observed as part of the Sloan Digital Sky Survey and its program for Galactic studies, the Sloan Extension for Galactic Understanding and Exploration (SEGUE). These spectra are used to measure radial velocities and to derive atmospheric parameters, which we compare with those reported by the SEGUE Stellar Parameter Pipeline (SSPP). The SSPP obtains estimates of these quantities based on SDSS ugriz photometry and low-resolution (R = 2000) spectroscopy. For F- and G-type stars observed with high signal-to-noise ratios (S/N), we empirically determine the typical random uncertainties in the radial velocities, effective temperatures, surface gravities, and metallicities delivered by the SSPP to be 2.4 km/s, 130 K (2.2%), 0.21 dex, and 0.11 dex, respectively, with systematic uncertainties of a similar magnitude in the effective temperatures and metallicities. We estimate random errors for lower S/N spectra based on numerical simulations.Comment: 37 pages, 6 tables, 6 figures, submitted to the Astronomical Journa

Small but crucial : the novel small heat shock protein Hsp21 mediates stress adaptation and virulence in Candida albicans

Peer reviewedPublisher PD

Study of B0(s)→K0Sh+h′− decays with first observation of B0s→K0SK±π∓ and B0s→K0Sπ+π−

A search for charmless three-body decays of B 0 and B0s mesons with a K0S meson in the final state is performed using the pp collision data, corresponding to an integrated luminosity of 1.0 fb−1, collected at a centre-of-mass energy of 7 TeV recorded by the LHCb experiment. Branching fractions of the B0(s)→K0Sh+h′− decay modes (h (′) = π, K), relative to the well measured B0→K0Sπ+π− decay, are obtained. First observation of the decay modes B0s→K0SK±π∓ and B0s→K0Sπ+π− and confirmation of the decay B0→K0SK±π∓ are reported. The following relative branching fraction measurements or limits are obtained B(B0→K0SK±π∓)B(B0→K0Sπ+π−)=0.128±0.017(stat.)±0.009(syst.), B(B0→K0SK+K−)B(B0→K0Sπ+π−)=0.385±0.031(stat.)±0.023(syst.), B(B0s→K0Sπ+π−)B(B0→K0Sπ+π−)=0.29±0.06(stat.)±0.03(syst.)±0.02(fs/fd), B(B0s→K0SK±π∓)B(B0→K0Sπ+π−)=1.48±0.12(stat.)±0.08(syst.)±0.12(fs/fd)B(B0s→K0SK+K−)B(B0→K0Sπ+π−)∈[0.004;0.068]at90%CL