Comparative transcriptomics of early dipteran development.

Published onlineJournal ArticleResearch Support, Non-U.S. Gov'tThis is the final version of the article. Available from BioMed Central via the DOI in this record.BACKGROUND: Modern sequencing technologies have massively increased the amount of data available for comparative genomics. Whole-transcriptome shotgun sequencing (RNA-seq) provides a powerful basis for comparative studies. In particular, this approach holds great promise for emerging model species in fields such as evolutionary developmental biology (evo-devo). RESULTS: We have sequenced early embryonic transcriptomes of two non-drosophilid dipteran species: the moth midge Clogmia albipunctata, and the scuttle fly Megaselia abdita. Our analysis includes a third, published, transcriptome for the hoverfly Episyrphus balteatus. These emerging models for comparative developmental studies close an important phylogenetic gap between Drosophila melanogaster and other insect model systems. In this paper, we provide a comparative analysis of early embryonic transcriptomes across species, and use our data for a phylogenomic re-evaluation of dipteran phylogenetic relationships. CONCLUSIONS: We show how comparative transcriptomics can be used to create useful resources for evo-devo, and to investigate phylogenetic relationships. Our results demonstrate that de novo assembly of short (Illumina) reads yields high-quality, high-coverage transcriptomic data sets. We use these data to investigate deep dipteran phylogenetic relationships. Our results, based on a concatenation of 160 orthologous genes, provide support for the traditional view of Clogmia being the sister group of Brachycera (Megaselia, Episyrphus, Drosophila), rather than that of Culicomorpha (which includes mosquitoes and blackflies).Toni Hermoso Pulido from the CRG Bioinformatics Core provided help and support with the diptex database. We thank Debayan Datta, Maik Zehnsdorf, and Anna Menoyo (CRG Genomics Unit) for technical help. We gratefully acknowledge Urs Schmidt-Ott, for providing fly cultures, for sharing Episyrphus balteatus transcriptome data, for crucial advice on sequencing strategy, fly husbandry, and other experimental protocols, as well as for useful comments on the manuscript. Victor Jiménez-Guri drew the embryo pictures in Figure 1. This research was funded by the MEC/EMBL agreement for the EMBL/CRG Research Unit in Systems Biology, by AGAUR SGR grant 406, and by Grants BFU2009-10184 and BFU2009-09168 from the Spanish Ministry of Science and Innovation (MICINN). EJG is supported by ERASysBio+ Grant P#161 (MODHEART). LC was supported by grant PTA2011-6729-I from the Spanish Ministry of Science and Innovation (MICINN). JHC is supported by a Juan de la Cierva postdoctoral fellowship from the Spanish Ministry of Science and Innovation (JCI2010-07614). HK was supported by GABI-FUTURE grant BeetSeq (0315069A) by the German Federal Ministry of Education and Research

Runx1 orchestrates sphingolipid metabolism and glucocorticoid resistance in lymphomagenesis

The three-membered RUNX gene family includes RUNX1, a major mutational target in human leukemias, and displays hallmarks of both tumour suppressors and oncogenes. In mouse models the Runx genes appear to act as conditional oncogenes, as ectopic expression is growth suppressive in normal cells but drives lymphoma development potently when combined with over-expressed Myc or loss of p53. Clues to underlying mechanisms emerged previously from murine fibroblasts where ectopic expression of any of the Runx genes promotes survival through direct and indirect regulation of key enzymes in sphingolipid metabolism associated with a shift in the ‘sphingolipid rheostat’ from ceramide to sphingosine-1-phosphate (S1P). Testing of this relationship in lymphoma cells was therefore a high priority. We find that ectopic expression of Runx1 in lymphoma cells consistently perturbs the sphingolipid rheostat, while an essential physiological role for Runx1 is revealed by reduced S1P levels in normal spleen after partial Cre-mediated excision. Furthermore we show that ectopic Runx1 expression confers increased resistance of lymphoma cells to glucocorticoid-mediated apoptosis, and elucidate the mechanism of cross-talk between glucocorticoid and sphingolipid metabolism through Sgpp1. Dexamethasone potently induces expression of Sgpp1 in T-lymphoma cells and drives cell death which is reduced by partial knockdown of Sgpp1 with shRNA or direct transcriptional repression of Sgpp1 by ectopic Runx1. Together these data show that Runx1 plays a role in regulating the sphingolipid rheostat in normal development and that perturbation of this cell fate regulator contributes to Runx-driven lymphomagenesis

Test of the photon detection system for the LHCb RICH Upgrade in a charged particle beam

The LHCb detector will be upgraded to make more efficient use of the available luminosity at the LHC in Run III and extend its potential for discovery. The Ring Imaging Cherenkov detectors are key components of the LHCb detector for particle identification. In this paper we describe the setup and the results of tests in a charged particle beam, carried out to assess prototypes of the upgraded opto-electronic chain from the Multi-Anode PMT photosensor to the readout and data acquisition system.Comment: 25 pages, 22 figure