Direct evidence of a sub-stellar companion around CT Cha

In our ongoing search for close and faint companions around T Tauri stars, we found a very faint (Ks=14.9mag, Ks_0=14.4mag) object, just ~2.67" northwest of the Chamaeleon star-forming region member CT Cha corresponding to a projected separation of ~440AU at 165+/-30 pc. We show that CT Cha A and this faint object form a common proper motion pair from data of the VLT Adaptive Optics (AO) instrument NACO taken in February 2006 and March 2007 and that the companion is by >=4 sigma significance not a stationary background object. Our AO integral field spectroscopy with SINFONI in J, and H+K bands yields a temperature of 2600+/-250K for the companion and an optical extinction of A_V=5.2+/-0.8mag, when compared to spectra calculated from Drift-Phoenix model atmospheres. We demonstrate the validity of the model fits by comparison to several other well-known young sub-stellar objects. Relative flux calibration of the bands was achieved using photometry from the NACO imaging data. We conclude that the CT Cha companion is a very low-mass member of Chamaeleon and very likely a physical companion to CT Cha, as the probability for a by chance alignment is <=0.01. Due to a prominent Pa-Beta emission in the J-band, accretion is probably still ongoing onto the CT Cha companion. From temperature and luminosity (log(Lbol/Lsun)= -2.68+/-0.21), we derive a radius of R=2.20+0.81-0.60 R_Jup. We find a consistent mass of M=17+/-6 MJup for the CT Cha companion from both its luminosity and temperature when placed on evolutionary tracks. Hence, the CT Cha companion is most likely a wide brown dwarf companion or possibly even a planetary mass object.Comment: 10 pages, 11 figures, accepted for publication in A&

Autonomous Bioluminescent Expression of the Bacterial Luciferase Gene Cassette (lux) in a Mammalian Cell Line

The bacterial luciferase (lux) gene cassette consists of five genes (luxCDABE) whose protein products synergistically generate bioluminescent light signals exclusive of supplementary substrate additions or exogenous manipulations. Historically expressible only in prokaryotes, the lux operon was re-synthesized through a process of multi-bicistronic, codon-optimization to demonstrate for the first time self-directed bioluminescence emission in a mammalian HEK293 cell line in vitro and in vivo.Autonomous in vitro light production was shown to be 12-fold greater than the observable background associated with untransfected control cells. The availability of reduced riboflavin phosphate (FMNH(2)) was identified as the limiting bioluminescence substrate in the mammalian cell environment even after the addition of a constitutively expressed flavin reductase gene (frp) from Vibrio harveyi. FMNH(2) supplementation led to a 151-fold increase in bioluminescence in cells expressing mammalian codon-optimized luxCDE and frp genes. When injected subcutaneously into nude mice, in vivo optical imaging permitted near instantaneous light detection that persisted independently for the 60 min length of the assay with negligible background.The speed, longevity, and self-sufficiency of lux expression in the mammalian cellular environment provides a viable and powerful alternative for real-time target visualization not currently offered by existing bioluminescent and fluorescent imaging technologies

Sensitive Dual Color In Vivo Bioluminescence Imaging Using a New Red Codon Optimized Firefly Luciferase and a Green Click Beetle Luciferase

Background: Despite a plethora of bioluminescent reporter genes being cloned and used for cell assays and molecular imaging purposes, the simultaneous monitoring of multiple events in small animals is still challenging. This is partly attributable to the lack of optimization of cell reporter gene expression as well as too much spectral overlap of the colorcoupled reporter genes. A new red emitting codon-optimized luciferase reporter gene mutant of Photinus pyralis, Ppy RE8, has been developed and used in combination with the green click beetle luciferase, CBG99. Principal Findings: Human embryonic kidney cells (HEK293) were transfected with vectors that expressed red Ppy RE8 and green CBG99 luciferases. Populations of red and green emitting cells were mixed in different ratios. After addition of the shared single substrate, D-luciferin, bioluminescent (BL) signals were imaged with an ultrasensitive cooled CCD camera using a series of band pass filters (20 nm). Spectral unmixing algorithms were applied to the images where good separation of signals was observed. Furthermore, HEK293 cells that expressed the two luciferases were injected at different depth in the animals. Spectrally-separate images and quantification of the dual BL signals in a mixed population of cells was achieved when cells were either injected subcutaneously or directly into the prostate. Significance: We report here the re-engineering of different luciferase genes for in vitro and in vivo dual color imaging applications to address the technical issues of using dual luciferases for imaging. In respect to previously used dual assays

Discovery of Diverse Small Molecule Chemotypes with Cell-Based PKD1 Inhibitory Activity

Protein kinase D (PKD) is a novel family of serine/threonine kinases regulated by diacylglycerol, which is involved in multiple cellular processes and various pathological conditions. The limited number of cell-active, selective inhibitors has historically restricted biochemical and pharmacological studies of PKD. We now markedly expand the PKD1 inhibitory chemotype inventory with eleven additional novel small molecule PKD1 inhibitors derived from our high throughput screening campaigns. The in vitro IC50s for these eleven compounds ranged in potency from 0.4 to 6.1 µM with all of the evaluated compounds being competitive with ATP. Three of the inhibitors (CID 1893668, (1Z)-1-(3-ethyl-5-methoxy-1,3-benzothiazol-2-ylidene)propan-2-one; CID 2011756, 5-(3-chlorophenyl)-N-[4-(morpholin-4-ylmethyl)phenyl]furan-2-carboxamide; CID 5389142, (6Z)-6-[4-(3-aminopropylamino)-6-methyl-1H-pyrimidin-2-ylidene]cyclohexa-2,4-dien-1-one) inhibited phorbol ester-induced endogenous PKD1 activation in LNCaP prostate cancer cells in a concentration-dependent manner. The specificity of these compounds for PKD1 inhibitory activity was supported by kinase assay counter screens as well as by bioinformatics searches. Moreover, computational analyses of these novel cell-active PKD1 inhibitors indicated that they were structurally distinct from the previously described cell-active PKD1 inhibitors while computational docking of the new cell-active compounds in a highly conserved ATP-binding cleft suggests opportunities for structural modification. In summary, we have discovered novel PKD1 inhibitors with in vitro and cell-based inhibitory activity, thus successfully expanding the structural diversity of small molecule inhibitors available for this important pharmacological target

Saturation of an Intra-Gene Pool Linkage Map: Towards a Unified Consensus Linkage Map for Fine Mapping and Synteny Analysis in Common Bean

Map-based cloning and fine mapping to find genes of interest and marker assisted selection (MAS) requires good genetic maps with reproducible markers. In this study, we saturated the linkage map of the intra-gene pool population of common bean DOR364×BAT477 (DB) by evaluating 2,706 molecular markers including SSR, SNP, and gene-based markers. On average the polymorphism rate was 7.7% due to the narrow genetic base between the parents. The DB linkage map consisted of 291 markers with a total map length of 1,788 cM. A consensus map was built using the core mapping populations derived from inter-gene pool crosses: DOR364×G19833 (DG) and BAT93×JALO EEP558 (BJ). The consensus map consisted of a total of 1,010 markers mapped, with a total map length of 2,041 cM across 11 linkage groups. On average, each linkage group on the consensus map contained 91 markers of which 83% were single copy markers. Finally, a synteny analysis was carried out using our highly saturated consensus maps compared with the soybean pseudo-chromosome assembly. A total of 772 marker sequences were compared with the soybean genome. A total of 44 syntenic blocks were identified. The linkage group Pv6 presented the most diverse pattern of synteny with seven syntenic blocks, and Pv9 showed the most consistent relations with soybean with just two syntenic blocks. Additionally, a co-linear analysis using common bean transcript map information against soybean coding sequences (CDS) revealed the relationship with 787 soybean genes. The common bean consensus map has allowed us to map a larger number of markers, to obtain a more complete coverage of the common bean genome. Our results, combined with synteny relationships provide tools to increase marker density in selected genomic regions to identify closely linked polymorphic markers for indirect selection, fine mapping or for positional cloning

Construction and application for QTL analysis of a Restriction Site Associated DNA (RAD) linkage map in barley

<p>Abstract</p> <p>Background</p> <p>Linkage maps are an integral resource for dissection of complex genetic traits in plant and animal species. Canonical map construction follows a well-established workflow: an initial discovery phase where genetic markers are mined from a small pool of individuals, followed by genotyping of selected mapping populations using sets of marker panels. A newly developed sequence-based marker technology, Restriction site Associated DNA (RAD), enables synchronous single nucleotide polymorphism (SNP) marker discovery and genotyping using massively parallel sequencing. The objective of this research was to assess the utility of RAD markers for linkage map construction, employing barley as a model system. Using the published high density EST-based SNP map in the Oregon Wolfe Barley (OWB) mapping population as a reference, we created a RAD map using a limited set of prior markers to establish linakge group identity, integrated the RAD and prior data, and used both maps for detection of quantitative trait loci (QTL).</p> <p>Results</p> <p>Using the RAD protocol in tandem with the Illumina sequence by synthesis platform, a total of 530 SNP markers were identified from initial scans of the OWB parental inbred lines - the "dominant" and "recessive" marker stocks - and scored in a 93 member doubled haploid (DH) mapping population. RAD sequence data from the structured population was converted into allele genotypes from which a genetic map was constructed. The assembled RAD-only map consists of 445 markers with an average interval length of 5 cM, while an integrated map includes 463 RAD loci and 2383 prior markers. Sequenced RAD markers are distributed across all seven chromosomes, with polymorphic loci emanating from both coding and noncoding regions in the <it>Hordeum </it>genome. Total map lengths are comparable and the order of common markers is identical in both maps. The same large-effect QTL for reproductive fitness traits were detected with both maps and the majority of these QTL were coincident with a dwarfing gene (<it>ZEO) </it>and the <it>VRS1 </it>gene, which determines the two-row and six-row germplasm groups of barley.</p> <p>Conclusions</p> <p>We demonstrate how sequenced RAD markers can be leveraged to produce high quality linkage maps for detection of single gene loci and QTLs. By combining SNP discovery and genotyping into parallel sequencing events, RAD markers should be a useful molecular breeding tool for a range of crop species. Expected improvements in cost and throughput of second and third-generation sequencing technologies will enable more powerful applications of the sequenced RAD marker system, including improvements in <it>de novo </it>genome assembly, development of ultra-high density genetic maps and association mapping.</p

Formation, evolution and multiplicity of brown dwarfs and giant exoplanets

This proceeding summarises the talk of the awardee of the Spanish Astronomical Society award to the the best Spanish thesis in Astronomy and Astrophysics in the two-year period 2006-2007. The thesis required a tremendous observational effort and covered many different topics related to brown dwarfs and exoplanets, such as the study of the mass function in the substellar domain of the young sigma Orionis cluster down to a few Jupiter masses, the relation between the cluster stellar and substellar populations, the accretion discs in cluster brown dwarfs, the frequency of very low-mass companions to nearby young stars at intermediate and wide separations, or the detectability of Earth-like planets in habitable zones around ultracool (L- and T-type) dwarfs in the solar neighbourhood.Comment: "Highlights of Spanish Astrophysics V", Proceedings of the VIII Scientific Meeting of the Spanish Astronomical Society (SEA) held in Santander, 7-11 July, 2008. Edited by J. Gorgas, L. J. Goicoechea, J. I. Gonzalez-Serrano, J. M. Diego. Invited oral contribution to plenary sessio

Mass and width of sigma(750) scalar meson from measurements of piN->pi(-)pi(+)N on polarized targets

The measurements of reactions $\pi^- p_\uparrow \to \pi^- \pi^+ n$ at 17.2 GeV/c and $\pi^+ n_\uparrow \to \pi^+ \pi^- p$ at 5.98 and 11.85 GeV/c made at CERN with polarized targets provide a model-independent and solution-independent evidence for a narrow scalar state sigma(750). The original chi^2 minimization method and the recent Monte Carlo method for amplitude analysis of data at 17.2 GeV/c are in excellent agreement. Both methods find that the mass distribution of the measured amplitude $|\overline S |^2\Sigma$ with recoil transversity ``up'' resonates near 750 MeV while the amplitude $|S|^2\Sigma$ with recoil transversity ``down'' is large and nonresonating. The amplitude $|S|^2\Sigma$ contributes as a strong background to S-wave intensity I_S = (|S|^2 + |\overline S |^2)\Sigma$and distorts the determinations of$\sigma$resonance parameters from$I_S$. To avoid this problem we perform a series of Breit-Wigner fits directly to the measured distribution$|\overline S |^2\Sigma$. The inclusion of various backgrounds causes the width of sigma(750) to become very narrow. Our best fit with$t$-averaged coherent background yields$m_\sigma = 753 \pm 19$MeV and$\Gamma_\sigma = 108 \pm 53$MeV. These values are in excellent agreement with Ellis-Lanik theorem for the width of scalar gluonium. The gluonium interpretation of$\sigma(750)$is also supported by the absence of$\sigma(750)$in reactions$\gamma\gamma \to \pi\pi$. We also show how data on polarized target invalidate essential assumptions of past determinations of$\pi\pi$ phase shifts .Comment: 77 page

Proton-Antiproton Annihilation and Meson Spectroscopy with the Crystal Barrel

This report reviews the achievements of the Crystal Barrel experiment at the Low Energy Antiproton Ring (LEAR) at CERN. During seven years of operation Crystal Barrel has collected very large statistical samples in pbarp annihilation, especially at rest and with emphasis on final states with high neutral multiplicity. The measured rates for annihilation into various two-body channels and for electromagnetic processes have been used to test simple models for the annihilation mechanism based on the quark internal structure of hadrons. From three-body annihilations three scalar mesons, a0(1450), f0(1370) and f0(1500) have been established in various decay modes. One of them, f0(1500), may be identified with the expected ground state scalar glueball.Comment: 64 pages, LATEX file, 36 figures are available as ps files at http://afuz01.cern.ch/claude/ Submitted to Reviews of Modern Physic