Elucidation of the chondrogenic gene regulatory network controlling embryonic skeletal development.

More than 90% of the skeleton in the developing mammalian embryo is formed via endochondral ossification which requires an obligatory cartilage intermediate as a template for bone formation, making chondrogenesis an essential pathway during development. Sox5, Sox6, and Sox9 were uncovered via classical genetic analyses of human diseases and mouse models to be the key transcription factors controlling chondrogenesis. The knowledge behind the regulation of the Sox proteins and the genes they regulate in vivo is still in its infancy. In this study by merging classical mouse genetics with advanced technology, transcriptome profiling and chromatin immunoprecipitation sequencing for the Sox trio were carried out in the mouse at E13.5 for the first time to gain insight to what is happening in the context of a developing embryo. From the analysis of the data generated, a novel high-confident chondrogenic gene regulatory network at E13.5 was built.​Doctor of Philosophy (SBS

Endogenous tagging of the murine transcription factor Sox5 with hemaglutinin for functional studies

Gene expression is usually studied at the transcript level rather than at the protein level due to the lack of a specific and sensitive antibody. A way to overcome this is to fuse to the protein of interest an immunoreactive tag that has well-characterized antibodies. This epitope tagging approach is often used for in vitro experiments but for in vivo studies, the success rate of protein tagging has not been extensively analyzed and our study seeks to cover the void. A small epitope, hemaglutinin derived from the influenza virus was used to tag a transcription factor, Sox5 at the N-terminal via homologous recombination in the mouse. Sox5 is part of the Sry-related high-mobility-group box gene family and plays multiple roles in essential biological processes. Understanding of its molecular function in relation to its biological roles remains incomplete. In our study, we show that the longer isoform of Sox5 can be tagged endogenously with hemaglutinin without affecting its biological function in vivo. The tagged protein is easily and specifically detected with an anti-hemaglutinin antibody using immunohistochemistry with its expression matching the endogenous expression of Sox5. Immunoprecipitation of Sox5 was also carried out successfully using an anti-hemaglutinin antibody. The transgenic line generated from this study is predicted to be useful for future experiments such as co-immunoprecipitation and chromatin immunoprecipitation, allowing the further understanding of Sox5. Lastly, this approach can be easily employed for the investigation of other transcription factors and proteins in vivo to overcome technical limitations such as antibody cross-reactivity and to perform isoform-specific studies

An Integrative Developmental Genomics and Systems Biology Approach to Identify an In Vivo Sox Trio-Mediated Gene Regulatory Network in Murine Embryos.

Embryogenesis is an intricate process involving multiple genes and pathways. Some of the key transcription factors controlling specific cell types are the Sox trio, namely, Sox5, Sox6, and Sox9, which play crucial roles in organogenesis working in a concerted manner. Much however still needs to be learned about their combinatorial roles during this process. A developmental genomics and systems biology approach offers to complement the reductionist methodology of current developmental biology and provide a more comprehensive and integrated view of the interrelationships of complex regulatory networks that occur during organogenesis. By combining cell type-specific transcriptome analysis and in vivo ChIP-Seq of the Sox trio using mouse embryos, we provide evidence for the direct control of Sox5 and Sox6 by the transcriptional trio in the murine model and by Morpholino knockdown in zebrafish and demonstrate the novel role of Tgfb2, Fbxl18, and Tle3 in formation of Sox5, Sox6, and Sox9 dependent tissues. Concurrently, a complete embryonic gene regulatory network has been generated, identifying a wide repertoire of genes involved and controlled by the Sox trio in the intricate process of normal embryogenesis

Performance of the ALICE Electromagnetic Calorimeter

International audienceThe performance of the electromagnetic calorimeter of theALICE experiment during operation in 2010–2018 at the Large HadronCollider is presented. After a short introduction into the design,readout, and trigger capabilities of the detector, the proceduresfor data taking, reconstruction, and validation are explained. Themethods used for the calibration and various derived corrections arepresented in detail. Subsequently, the capabilities of thecalorimeter to reconstruct and measure photons, light mesons,electrons and jets are discussed. The performance of thecalorimeter is illustrated mainly with data obtained with test beamsat the Proton Synchrotron and Super Proton Synchrotron or inproton-proton collisions at √s = 13 TeV, and compared tosimulations

Forward rapidity J/ψ production as a function of charged-particle multiplicity in pp collisions at s \sqrt{s} = 5.02 and 13 TeV

International audienceThe production of J/ψ is measured as a function of charged-particle multiplicity at forward rapidity in proton-proton (pp) collisions at center-of-mass energies $\sqrt{s}$ = 5.02 and 13 TeV. The J/ψ mesons are reconstructed via their decay into dimuons in the rapidity interval (2.5 < y < 4.0), whereas the charged-particle multiplicity density (dN$_{ch}$/dη) is measured at midrapidity (|η| < 1). The production rate as a function of multiplicity is reported as the ratio of the yield in a given multiplicity interval to the multiplicity-integrated one. This observable shows a linear increase with charged-particle multiplicity normalized to the corresponding average value for inelastic events (dN$_{ch}$/dη/〈dN$_{ch}$/dη〉), at both the colliding energies. Measurements are compared with available ALICE results at midrapidity and theoretical model calculations. First measurement of the mean transverse momentum (〈p$_{T}$〉) of J/ψ in pp collisions exhibits an increasing trend as a function of dN$_{ch}$/dη/〈dN$_{ch}$/dη〉 showing a saturation towards high charged-particle multiplicities.[graphic not available: see fulltext

Neutral to charged kaon yield fluctuations in Pb – Pb collisions at sNN\sqrt{s_{\rm NN}} = 2.76 TeV

We present the first measurement of event-by-event fluctuations in the kaon sector in Pb – Pb collisions at $\sqrt{s_{\rm NN}}$ = 2.76 TeV with the ALICE detector at the LHC. The robust fluctuation correlator ν$_{dyn}$ is used to evaluate the magnitude of fluctuations of the relative yields of neutral and charged kaons, as well as the relative yields of charged kaons, as a function of collision centrality and selected kinematic ranges. While the correlator ν$_{dyn}$[K$^+$,K$^−$] exhibits a scaling approximately in inverse proportion of the charged particle multiplicity, ν$_{dyn}$[K$_S^0$,K$^\pm$] features a significant deviation from such scaling. Within uncertainties, the value of ν$_{dyn}$[K$_S^0$,K$^\pm$] is independent of the selected transverse momentum interval, while it exhibits a pseudorapidity dependence. The results are compared with HIJING, AMPT and EPOS–LHC predictions, and are further discussed in the context of the possible production of disoriented chiral condensates in central Pb – Pb collisions

First study of the two-body scattering involving charm hadrons

This article presents the first measurement of the interaction between charm hadrons and nucleons. The two-particle momentum correlations of $pD^-$ and $\bar{p}D^+$ pairs are measured by the ALICE Collaboration in high-multiplicity pp collisions at $\sqrt{s}$ = 13 TeV. The data are compatible with the Coulomb-only interaction hypothesis within (1.1–1.5)σ. The level of agreement slightly improves if an attractive nucleon $(N)\bar{D}$ strong interaction is considered, in contrast to most model predictions which suggest an overall repulsive interaction. This measurement allows for the first time an estimation of the 68% confidence level interval for the isospin I=0 inverse scattering length of the $N\bar{D}$ state $f_{0,I=0}^{-1}$∈[-0.4,0.9] fm$^{-1}$, assuming negligible interaction for the isospin I=1 channel