Targeted rapid amplification of cDNA ends (T-RACE)—an improved RACE reaction through degradation of non-target sequences

Amplification of the 5′ ends of cDNA, although simple in theory, can often be difficult to achieve. We describe a novel method for the specific amplification of cDNA ends. An oligo-dT adapter incorporating a dUTP-containing PCR primer primes first-strand cDNA synthesis incorporating dUTP. Using the Cap finder approach, another distinct dUTP containing adapter is added to the 3′ end of the newly synthesized cDNA. Second-strand synthesis incorporating dUTP is achieved by PCR, using dUTP-containing primers complimentary to the adapter sequences incorporated in the cDNA ends. The double-stranded cDNA-containing dUTP serves as a universal template for the specific amplification of the 3′ or 5′ end of any gene. To amplify the ends of cDNA, asymmetric PCR is performed using a single gene-specific primer and standard dNTPs. The asymmetric PCR product is purified and non-target transcripts containing dUTP degraded by Uracil DNA glycosylase, leaving only those transcripts produced during the asymmetric PCR. Subsequent PCR using a nested gene-specific primer and the 3′ or 5′ T-RACE primer results in specific amplification of cDNA ends. This method can be used to specifically amplify the 3′ and 5′ ends of numerous cDNAs from a single cDNA synthesis reaction

Near-Infrared Imaging of Early-Type Galaxies IV. The Physical Origins of the Fundamental Plane Scaling Relations

The physical origins of the Fundamental Plane (FP) scaling relations are investigated for early-type galaxies observed at optical and near-infrared wavelengths. The slope for the FP is shown to increase systematically with wavelength from the U-band through the K-band. A distance-independent construction of the observables is described which provides an accurate measurement of the change in the FP slope between any pair of bandpasses. The variation of the FP slope with wavelength is strong evidence of systematic variations in stellar content along the elliptical galaxy sequence. The intercept of the diagnostic relationship between log(D_K/D_V) and log(sigma_0) shows no significant dependence on environment within the uncertainties of the Galactic extinction corrections, demonstrating the universality of the stellar populations contributions at the level of Delta(V-K)=0.03 mag to the zero-point of the global scaling relations. Several other constraints on the properties of early-type galaxies --- the slope of the Mg_2-sigma_0 relation, the effects of stellar populations gradients, and deviations of early-type galaxies from a dynamically homologous family --- are included to construct an empirical, self-consistent model which provides a complete picture of the underlying physical properties which are varying along the early-type galaxy sequence. This empirical approach demonstrates that there are significant systematic variations in both age and metallicity along the elliptical galaxy sequence, and that a small, but systematic, breaking of dynamical homology (or a similar, wavelength independent effect) is required. Predictions for the evolution of the slope of the FP with redshift are described. [abriged]Comment: to appear in The Astronomical Journal; 40 pages, including 10 Postscript figures and 3 tables; uses AAS LaTeX style file

Simulating the Hot X-ray Emitting Gas in Elliptical Galaxies

We study the chemo-dynamical evolution of elliptical galaxies and their hot X-ray emitting gas using high-resolution cosmological simulations. Our Tree N-body/SPH code includes a self-consistent treatment of radiative cooling, star formation, supernovae feedback, and chemical enrichment. We present a series of LCDM cosmological simulations which trace the spatial and temporal evolution of heavy element abundance patterns in both the stellar and gas components of galaxies. X-ray spectra of the hot gas are constructed via the use of the vmekal plasma model, and analysed using XSPEC with the XMM EPN response function. Simulation end-products are quantitatively compared with the observational data in both the X-ray and optical regime. We find that radiative cooling is important to interpret the observed X-ray luminosity, temperature, and metallicity of the interstellar medium of elliptical galaxies. However, this cooled gas also leads to excessive star formation at low redshift, and therefore results in underlying galactic stellar populations which are too blue with respect to observations.Comment: 6 pages, 3 figures, to appear in the proceedings of "The IGM/Galaxy Connection - The Distribution of Baryons at z=0", ed. M. Putman & J. Rosenberg; High resolution version is available at http://astronomy.swin.edu.au/staff/dkawata/research/papers.htm

Cluster vs. Field Elliptical Galaxies and Clues on their Formation

Using new observations for a sample of 931 early-type galaxies we investigate whether the \mg2--\so relation shows any dependence on the local environment. The galaxies have been assigned to three different environments depending on the local overdensity: clusters, groups, and field, having used our completeredshift database to guide the assignment of galaxies. It is found that cluster, group and field early-type galaxies follow almost identical \mg2--\so\ relations, with the largest \mg2 zero-point difference (clusters minus field) being only $0.007\pm 0.002$ mag. No correlation of the residuals is found with the morphological type or the bulge to disk ratio. Using stellar population models in a differential fashion, this small zero-point difference implies a luminosity-weighted age difference of only $\sim 1$ Gyr between the corresponding stellar populations, with field galaxies being younger. The mass-weighted age difference could be significantly smaller, if minor events of late star formation took place preferentially in field galaxies. We combine these results with the existing evidence for the bulk of stars in cluster early-type galaxies having formed at very high redshift, and conclude that the bulk of stars in galactic spheroids had to form at high redshifts (z\gsim 3), no matter whether such spheroids now reside in low or high density regions. The cosmological implications of these findings are briefly discussed.Comment: 16 pages, 2 figures, accepted for publication in the ApJ.

Gravitational Stability of Circumnuclear Disks in Elliptical Galaxies

A significant fraction of nearby elliptical galaxies are known to have high density gas disks in their circumnuclear (CN) region (0.1 to a few kpc). Yet, ellipticals, especially luminous ones, show little signs of recent star formation (SF). To investigate the possible cause of the dearth of SF in these systems, we study the gravitational stability of CN gas disks embedded within the potentials of both the stellar bulge and the central massive black hole (BH) in ellipticals. We find that CN disks in higher mass galaxies are generally more stable than those in lower mass galaxies, because higher mass galaxies tend to have more massive BHs and more centrally concentrated stellar density profiles. We also consider the case in which the central stellar density profile has a core, which is often observed for ellipticals whose total stellar mass is higher than about 10^11 Msun. Such a cored stellar density profile leads to more unstable CN disks than the power-law density profile characteristic of less massive galaxies. However, the more massive BHs in high-mass galaxies act to stabilize the CN disk. Our results demonstrate that the gravitational potentials of both the central BH and the stellar component should be taken into account when studying the properties of CN disks, as their stability is sensitive to both the BH mass and the stellar density profile. Our results could explain the observed trend that less luminous ellipticals have a greater tendency to exhibit ongoing SF than giant ellipticals.Comment: 8 pages, 5 figures, accepted for publication in Ap

Vertical distribution of sub-micron aerosol chemical composition from North-Western Europe and the North-East Atlantic

A synthesis of UK based airborne in-situ measurements of aerosol properties representing air masses from North-West Europe and the North-East Atlantic is presented. The major focus of the study is the vertical distribution of sub-micron aerosol chemical composition. Vertical profiles are derived from a Quadrupole Aerosol Mass Spectrometer (Q-AMS). Background sub-micron aerosol vertical profiles are identified and are primarily composed of organic matter and sulphate aerosol. Such background conditions occurred predominantly during periods associated with long-range air mass transport across the Atlantic. These instances may serve as useful model input of aerosol to Western Europe. Increased mass concentration episodes are coincident with European outflow and periods of stagnant/recirculating air masses. Such periods are characterised by significantly enhanced concentrations of nitrate aerosol relative to those of organic matter and sulphate. Periods of enhanced ground level PM<sub>2.5</sub> loadings are coincident with instances of high nitrate mass fractions measured on-board the aircraft, indicating that nitrate is a significant contributor to regional pollution episodes. The vertical structure of the sulphate and organic aerosol profiles were shown to be primarily driven by large-scale dynamical processes. The vertical distribution of nitrate is likely determined by both dynamic and thermodynamic processes, with chemical partitioning of gas phase precursors to the particle phase occurring at lower temperatures at the top of the boundary layer. Such effects have profound implications for the aerosol's lifetime and subsequent impacts, highlighting the requirement for accurate representation of the aerosol vertical distribution

Virgo cluster early-type dwarf galaxies with the Sloan Digital Sky Survey. IV. The color-magnitude relation

We present an analysis of the optical colors of 413 Virgo cluster early-type dwarf galaxies (dEs), based on Sloan Digital Sky Survey imaging data. Our study comprises (1) a comparison of the color-magnitude relation (CMR) of the different dE subclasses that we identified in Paper III of this series, (2) a comparison of the shape of the CMR in low and high-density regions, (3) an analysis of the scatter of the CMR, and (4) an interpretation of the observed colors with ages and metallicities from population synthesis models. We find that the CMRs of nucleated (dE(N)) and non-nucleated dEs (dE(nN)) are significantly different from each other, with similar colors at fainter magnitudes (r > 17 mag), but increasingly redder colors of the dE(N)s at brighter magnitudes. We interpret this with older ages and/or higher metallicities of the brighter dE(N)s. The dEs with disk features have similar colors as the dE(N)s and seem to be only slightly younger and/or less metal-rich on average. Furthermore, we find a small but significant dependence of the CMR on local projected galaxy number density, consistently seen in all of u-r, g-r, and g-i, and weakly i-z. We deduce that a significant intrinsic color scatter of the CMR is present, even when allowing for a distance spread of our galaxies. No increase of the CMR scatter at fainter magnitudes is observed down to r = 17 mag (Mr = -14 mag). The color residuals, i.e., the offsets of the data points from the linear fit to the CMR, are clearly correlated with each other in all colors for the dE(N)s and for the full dE sample. We conclude that there must be at least two different formation channels for early-type dwarfs in order to explain the heterogeneity of this class of galaxy. (Abridged)Comment: 17 pages + 12 figures. Accepted for publication in A

Fast outflows in compact radio sources: evidence for AGN-induced feedback in the early stages of radio source evolution

We present intermediate resolution, wide wavelength coverage spectra for a complete sample of 14 compact radio sources taken with the aim of investigating the impact of the nuclear activity on the circumnuclear (ISM) in the early stages of radio source evolution. We observe spatially extended line emission (up to 20 kpc) in the majority of sources which is consistent with a quiescent halo. In the nuclear apertures we observe broad, highly complex emission line profiles. Multiple Gaussian modelling of the [O III]5007 line reveals 2-4 components which can have FWHM and blueshifts relative to the halo of up to 2000 km/s. We interpret these broad, blueshifted components as material in outflow and discuss the kinematical evidence for jet-driven outflows. Comparisons with samples in the literature show that compact radio sources harbour more extreme nuclear kinematics than their extended counterparts, a trend seen within our sample with larger velocities in the smaller sources. The observed velocities are also likely to be influenced by source orientation with respect to the observer's line of sight. Nine sources have associated HI absorption. In common with the optical emission line gas, the HI profiles are often highly complex with the majority of the detected components significantly blueshifted, tracing outflows in the neutral gas. The sample has been tested for stratification in the ISM (FWHM/ionisation potential/critical density) as suggested by Holt et al. (2003) for PKS1345+12 but we find no significant trends within the sample using a Spearman Rank analysis. This study supports the idea that compact radio sources are young radio loud AGN observed during the early stages of their evolution and currently shedding their natal cocoons through extreme circumnuclear outflows.Comment: Accepted for publication in MNRAS, 24 pages, 7 figure

Stellar Population Diagnostics of Elliptical Galaxy Formation

Major progress has been achieved in recent years in mapping the properties of passively-evolving, early-type galaxies (ETG) from the local universe all the way to redshift ~2. Here, age and metallicity estimates for local cluster and field ETGs are reviewed as based on color-magnitude, color-sigma, and fundamental plane relations, as well as on spectral-line indices diagnostics. The results of applying the same tools at high redshifts are then discussed, and their consistency with the low-redshift results is assessed. Most low- as well as high-redshift (z~1) observations consistently indicate 1) a formation redshift z>~3 for the bulk of stars in cluster ETGs, with their counterparts in low-density environments being on average ~1-2 Gyr younger, i.e., formed at z>~1.5-2, 2) the duration of the major star formation phase anticorrelates with galaxy mass, and the oldest stellar populations are found in the most massive galaxies. With increasing redshift there is evidence for a decrease in the number density of ETGs, especially of the less massive ones, whereas existing data appear to suggest that most of the most-massive ETGs were already fully assembled at z~1. Beyond this redshift, the space density of ETGs starts dropping significantly, and as ETGs disappear, a population of massive, strongly clustered, starburst galaxies progressively becomes more and more prominent, which makes them the likely progenitors to ETGs.Comment: To appear on Annual Review of Astronomy & Astrophysics, Vol. 44 (2006). 46 pages with 16 figures. Replaced version includes updated references, few typos less, and replaces Fig. 11 and Fig. 16 which had been skrewed u

Systematic techniques for assisting recruitment to trials (START): study protocol for embedded, randomized controlled trials

BACKGROUND: Randomized controlled trials play a central role in evidence-based practice, but recruitment of participants, and retention of them once in the trial, is challenging. Moreover, there is a dearth of evidence that research teams can use to inform the development of their recruitment and retention strategies. As with other healthcare initiatives, the fairest test of the effectiveness of a recruitment strategy is a trial comparing alternatives, which for recruitment would mean embedding a recruitment trial within an ongoing host trial. Systematic reviews indicate that such studies are rare. Embedded trials are largely delivered in an ad hoc way, with interventions almost always developed in isolation and tested in the context of a single host trial, limiting their ability to contribute to a body of evidence with regard to a single recruitment intervention and to researchers working in different contexts. METHODS/DESIGN: The Systematic Techniques for Assisting Recruitment to Trials (START) program is funded by the United Kingdom Medical Research Council (MRC) Methodology Research Programme to support the routine adoption of embedded trials to test standardized recruitment interventions across ongoing host trials. To achieve this aim, the program involves three interrelated work packages: (1) methodology - to develop guidelines for the design, analysis and reporting of embedded recruitment studies; (2) interventions - to develop effective and useful recruitment interventions; and (3) implementation - to recruit host trials and test interventions through embedded studies. DISCUSSION: Successful completion of the START program will provide a model for a platform for the wider trials community to use to evaluate recruitment interventions or, potentially, other types of intervention linked to trial conduct. It will also increase the evidence base for two types of recruitment intervention. TRIAL REGISTRATION: The START protocol covers the methodology for embedded trials. Each embedded trial is registered separately or as a substudy of the host trial