Mimotopes and Proteome Analyses Using Human Genomic and cDNA Epitope Phage Display

In the post-genomic era, validation of candidate gene targets frequently requires proteinbased strategies. Phage display is a powerful tool to define protein-protein interactions by generating peptide binders against target antigens. Epitope phage display libraries have the potential to enrich coding exon sequences from human genomic loci. We evaluated genomic and cDNA phage display strategies to identify genes in the 5q31 Interleukin gene cluster and to enrich cell surface receptor tyrosine kinase genes from a breast cancer cDNA library. A genomic display library containing 2 × 10 6 clones with exon-sized inserts was selected with antibodies specific for human Interleukin-4 (IL-4) and Interleukin-13. The library was enriched significantly after two selection rounds and DNA sequencing revealed unique clones. One clone matched a cognate IL-4 epitope; however, the majority of clone insert sequences corresponded to E. coli genomic DNA. These bacterial sequences act as ‘mimotopes’ (mimetic sequences of the true epitope), correspond to open reading frames, generate displayed peptides, and compete for binding during phage selection. The specificity of these mimotopes for IL-4 was confirmed by competition ELISA. Other E. coli mimotopes were generated using additional antibodies. Mimotopes for a receptor tyrosine kinase gene were also selected using a breast cancer SKBR-3 cDNA phage display library, screened against an anti-erbB2 monoclonal antibody. Identification of mimotopes in genomic and cDNA phage libraries is essential for phage display-based protein validation assays and two-hybrid phage approaches that examine protein-protein interactions. The predominance of E. coli mimotopes suggests that the E. coli genome may be useful to generate peptide diversity biased towards protein coding sequences

Cell-Cell Interactions and the Regulation of Testis Function

Regulatory interactions have been shown to occur between all the testicular cell types considered. The paracrine factors mediating these interactions generally influence either cellular growth or differentiation. The regulation of cellular growth is essential in the developing testis and is required for the maintenance of spermatogenesis in the adult testis. The rapid rate of germinal cell proliferation and the continuous but slowed growth of the peritubular cells and Leydig cells requires the presence of specific growth factors in the adult. Therefore, cell-cell interactions have evolved that involve growth factors such as IGF, TGF-alpha, TGF-beta and NGF. Other growth factors such as FGF or less characterized components like the seminiferous growth factor (SGF) also may be involved in the paracrine regulation of testis cell growth. An alternate cellular parameter to cell growth to consider is the regulation of cellular function and differentiation. A number of endocrine agents and locally produced paracrine factors have been shown to control and maintain testis cell function and differentiation. Cell-cell interactions mediated by factors such as androgens, POMC peptides, and PModS are all primarily directed at the regulation of cellular differentiation. Therefore, the agents which mediate cell-cell interactions in the testis can generally be categorized into factors that regulate cell growth or those which influence cellular differentiation. The specific cell-cell interactions identified will likely be the first of a large number of cellular interactions yet to be investigated. Although a number of potentially important cell-cell interactions have been identified, future research will require the elucidation of the in vivo physiological significance of these interactions. The existence of different cell types and potential cell-cell interactions in a tissue implies that the actions of an endocrine agent on a tissue will not simply involve a single hormone and single cell. The endocrine regulation of testis function will have effects on cell-cell interactions and be affected by local cell-cell interactions. The ability of LH to influence Leydig cell androgen production promotes a cascade of interactions mediated through several cell types to maintain the process of spermatogenesis. FSH actions on Sertoli cells also promote cell-cell interactions that influence germinal cell development, peritubular myoid cell differentiation and Leydig cell function. Therefore, elucidation of the endocrine regulation of testis function requires an understanding of the local cell-cell interactions in the testis

The Spitzer discovery of a galaxy with infrared emission solely due to AGN activity

We present a galaxy (SAGE1CJ053634.78-722658.5) at a redshift of 0.14 of which the IR is entirely dominated by emission associated with the AGN. We present the 5-37 um Spitzer/IRS spectrum and broad wavelength SED of SAGE1CJ053634, an IR point-source detected by Spitzer/SAGE (Meixner et al 2006). The source was observed in the SAGE-Spec program (Kemper et al., 2010) and was included to determine the nature of sources with deviant IR colours. The spectrum shows a redshifted (z=0.14+-0.005) silicate emission feature with an exceptionally high feature-to-continuum ratio and weak polycyclic aromatic hydrocarbon (PAH) bands. We compare the source with models of emission from dusty tori around AGNs from Nenkova et al. (2008). We present a diagnostic diagram that will help to identify similar sources based on Spitzer/MIPS and Herschel/PACS photometry. The SED of SAGE1CJ053634 is peculiar because it lacks far-IR emission and a clear stellar counterpart. We find that the SED and the IR spectrum can be understood as emission originating from the inner ~10 pc around an accreting black hole. There is no need to invoke emission from the host galaxy, either from the stars or from the interstellar medium, although a possible early-type host galaxy cannot be excluded based on the SED analysis. The hot dust around the accretion disk gives rise to a continuum, which peaks at 4 um, whereas the strong silicate features may arise from optically thin emission of dusty clouds within ~10 pc around the black hole. The weak PAH emission does not appear to be linked to star formation, as star formation templates strongly over-predict the measured far-IR flux levels. The SED of SAGE1CJ053634 is rare in the local universe but may be more common in the more distant universe. The conspicuous absence of host-galaxy IR emission places limits on the far-IR emission arising from the dusty torus alone.Comment: Accepted for publication in A&A, 7 pages, 6 figure

ALMA and Herschel reveal that AGN and main-sequence galaxies have different star formation rate distributions

Using deep Herschel and ALMA observations, we investigate the star formation rate (SFR) distributions of X-ray AGN host galaxies at 0.5<z<1.5 and 1.5<z<4, comparing them to that of normal, star-forming (i.e., "main-sequence", or MS) galaxies. We find 34-55 per cent of AGNs have SFRs at least a factor of two below that of the average MS galaxy, compared to ~15 per cent of all MS galaxies, suggesting significantly different SFR distributions. Indeed, when both are modelled as log-normal distributions, the mass and redshift-normalised SFR distributions of AGNs are roughly twice as broad, and peak ~0.4 dex lower, than that of MS galaxies. However, like MS galaxies, the normalised SFR distribution of AGNs appears not to evolve with redshift. Despite AGNs and MS galaxies having different SFR distributions, the linear-mean SFR of AGNs derived from our distributions is remarkably consistent with that of MS galaxies, and thus with previous results derived from stacked Herschel data. This apparent contradiction is due to the linear-mean SFR being biased by bright outliers, and thus does not necessarily represent a true characterisation of the typical SFR of AGNs

Learning radiation oncology in Europe: Results of the ESTRO multidisciplinary survey

Introduction: Radiotherapy education can be very different across Europe, despite the publication of the ESTRO core curricula in 2011. The purpose of the current study is to map the different RO European education systems, to report their perceived quality and to understand what could be improved to better teach RO. Methods: An online survey consisting of 30 questions was sent to RO professionals under 40 years of age via email and social media. Clinicians, radiobiologists, physicists and radiation therapists (RTTs) were invited to answer questions regarding (1) demographics data, (2) duration, (3) organization, (4) content, (5) quality and potential improvements of national education programs. Results: Four hundred and sixty three questionnaires were received from 34 European countries. All disciplines were represented: 45% clinicians (n = 210), 29% physicists (n = 135), 24% RTTs (n = 108) and 2% radiobiologists (n = 10). Male and female participants were well-balanced in each speciality, except for radiobiologists (80% males). Median age was 31.5 years old (range 21–40). A large range of the duration of the National RO education programs was observed: median = 9 years (range: 3–15). In half of the surveyed countries the European Credit Transfer System (ECTS), that facilitates mobility for trainees, has been implemented. Participants declared only a minority of countries have implemented the ESTRO Core Curriculum (n = 5). A quarter of participants indicated that their national education program is insufficient. Conclusion: This is the first study to examine the different RO education systems in Europe. Large differences in organization and duration of national education programs have been found, along with perceived quality across Europe within each speciality. These results show the necessity of a discussion on how to move forward in this diversity of education programs and the potential contribution that the ESTRO may fulfil

PACS Evolutionary Probe (PEP) - A Herschel Key Program

Deep far-infrared photometric surveys studying galaxy evolution and the nature of the cosmic infrared background are a key strength of the Herschel mission. We describe the scientific motivation for the PACS Evolutionary Probe (PEP) guaranteed time key program and its role in the complement of Herschel surveys, and the field selection which includes popular multiwavelength fields such as GOODS, COSMOS, Lockman Hole, ECDFS, EGS. We provide an account of the observing strategies and data reduction methods used. An overview of first science results illustrates the potential of PEP in providing calorimetric star formation rates for high redshift galaxy populations, thus testing and superseeding previous extrapolations from other wavelengths, and enabling a wide range of galaxy evolution studies.Comment: 13 pages, 12 figures, accepted for publication in A&

Concurrent Supermassive Black Hole and Galazy Growth: Linking Environment and Nuclear Activity in Zeta Equals 2.23 H Alpha Emitters

We present results from an approximately equal 100 ks Chandra observation of the 2QZ Cluster 1004+00 structure at z = 2.23 (hereafter 2QZ Clus). 2QZ Clus was originally identified as an overdensity of four optically-selected QSOs at z = 2.23 within a 15 15 arcmin square region. Narrow-band imaging in the near-IR (within the K band) revealed that the structure contains an additional overdensity of 22 z = 2.23 H alpha-emitting galaxies (HAEs), resulting in 23 unique z = 2.23 HAEs/QSOs (22 within the Chandra field of view). Our Chandra observations reveal that three HAEs in addition to the four QSOs harbor powerfully accreting supermassive black holes (SMBHs), with 2-10 keV luminosities of approximately equal (8-60) 10(exp 43) erg s(exp1) and X-ray spectral slopes consistent with unobscured active galactic nucleus (AGN). Using a large comparison sample of 210 z = 2.23 HAEs in the Chandra-COSMOS field (C-COSMOS), we find suggestive evidence that the AGN fraction increases with local HAE galaxy density. The 2QZ Clus HAEs reside in a moderately overdense environment (a factor of approximately equal 2 times over the field), and after excluding optically-selected QSOs, we find that the AGN fraction is a factor of approximately equal 3.5(+3.8/ 2.2) times higher than C-COSMOS HAEs in similar environments. Using stacking analyses of the Chandra data and Herschel SPIRE observations at 250micrometers, we respectively estimate mean SMBH accretion rates ( M(BH)) and star formation rates (SFRs) for the 2QZ Clus and C-COSMOS samples. We find that the mean 2QZ Clus HAE stacked X-ray luminosity is QSO-like (L(210 keV) approximately equal [6-10] 10(exp 43) erg s(exp 1)), and the implied M(BH)/SFR approximately equal (1.6-3.2) 10(exp 3) is broadly consistent with the local M(BH)/Stellar Mass relation and z approximately equal 2 X-ray selected AGN. In contrast, the C-COSMOS HAEs are on average an order of magnitude less X-ray luminous and have M(BH)/SFR approximately equal (0.2-0.4) 10(exp 3), somewhat lower than the local MBH/M relation, but comparable to that found for z approximately equal 1-2 star-forming galaxies with similar mean X-ray luminosities. We estimate that a periodic QSO phase with duty cycle approximately 2%-8% would be sufficient to bring star-forming galaxies onto the local M(BH)/Stellar Mass relation. This duty cycle is broadly consistent with the observed C-COSMOS HAE AGN fraction (Approximately equal 0.4%-2.3%) for powerful AGN with LX approximately greater than 10(exp 44) erg s(exp 1). Future observations of 2QZ Clus will be needed to identify key factors responsible for driving the mutual growth of the SMBHs and galaxies

The AGN content in luminous IR galaxies at z\sim2 from a global SED analysis including Herschel data

We use Herschel-PACS far-infrared data, combined with previous multi-band information and mid-IR spectra, to properly account for the presence of an active nucleus and constrain its energetic contribution in luminous infrared (IR) sources at z\sim2. The sample is composed of 24 sources in the GOODS-South field, with typical IR luminosity of 10^{12} Lo. Data from the 4 Ms Chandra X-ray imaging in this field are also used to identify and characterize AGN emission. We reproduce the observed spectral energy distribution (SED), decomposed into a host-galaxy and an AGN component. A smooth-torus model for circum-nuclear dust is used to account for the direct and re-processed contribution from the AGN. We confirm that galaxies with typical L_{8-1000um}\sim10^{12}Lo at z\sim2 are powered predominantly by star-formation. An AGN component is present in nine objects (\sim35% of the sample) at the 3sigma confidence level, but its contribution to the 8-1000 um emission accounts for only \sim5% of the energy budget. The AGN contribution rises to \sim23% over the 5-30 um range (in agreement with Spitzer IRS results) and to \sim60% over the narrow 2-6 um range. The presence of an AGN is confirmed by X-ray data for 3 (out of nine) sources, with X-ray spectral analysis indicating the presence of significant absorption, i.e. NH\sim10^{23}-10^{24} cm^{-2}. An additional source shows indications of obscured AGN emission from X-ray data. The comparison between the mid-IR--derived X-ray luminosities and those obtained from X-ray data suggests that obscuration is likely present also in the remaining six sources that harbour an AGN according to the SED-fitting analysis.Comment: 12 pages, including 5 figures. Accepted for publication in MNRA

The Quasar Feedback Survey: characterising CO excitation in quasar host galaxies

We present a comprehensive study of the molecular gas properties of 17 Type 2 quasars at $z$10^{42.1}$$\rm ergs^{-1}$), selected by their high [OIII] luminosities and displaying a large diversity of radio jet properties, but dominated by LIRG-like galaxies. With these data, we are able to investigate the impact of AGN and AGN feedback mechanisms on the global molecular interstellar medium. Using APEX and ALMA ACA observations, we measure the total molecular gas content using the CO(1-0) emission and homogeneously sample the CO spectral line energy distributions (SLEDs), observing CO transitions (J$_{up}$= 1, 2, 3, 6, 7). We observe high$r_{21}$ratios (r$_{21}$= L'$_{CO(2-1)}$/L'$_{CO(1-0)}$) with a median$r_{21}$= 1.06, similar to local (U)LIRGs (with$r_{21}$$\sim$1) and higher than normal star-forming galaxies (with r$_{21}$$\sim$0.65). Despite the high$r_{21} values, for the 7 targets with the required data we find low excitation in CO(6-5) & CO(7-6) (r_{61}$and$r_{62}$ < 0.6 in all but one target), unlike high redshift quasars in the literature, which are far more luminous and show higher line ratios. The ionised gas traced by [OIII] exhibit systematically higher velocities than the molecular gas traced by CO. We conclude that any effects of quasar feedback (e.g. via outflows and radio jets) do not have a significant instantaneous impact on the global molecular gas content and excitation and we suggest that it only occurs on more localised scales.Comment: 32 pages (20 in the main body of the paper and 12 in the appendix), 28 figures (10 in main body of paper and 18 in appendix) Accepted for publication in MNRAS. Data available at https://doi.org/10.25405/data.ncl.2431250

The XMM deep survey in the CDF-S III. Point source catalogue and number counts in the hard X-rays

Nuclear obscuration plays a key role in the initial phases of AGN growth, yet not many highly obscured active galactic nuclei (AGN) are currently known beyond the local Universe, and their search is an active topic of research. The XMM-Newton survey in the Chandra Deep Field South (XMM-CDFS) aims at detecting and studying the spectral properties of a significant number of obscured and Compton-thick (NH ≳ 1024 cm-2) AGN. The large effective area of XMM-Newton in the 2–10 and 5–10 keV bands, coupled with a 3.45 Ms nominal exposure time (2.82 and 2.45 Ms after light curve cleaning for MOS and PN, respectively), allows us to build clean samples in both bands, and makes the XMM-CDFS the deepest XMM-Newton survey currently published in the 5–10 keV band. The large multi-wavelength and spectroscopic coverage of the CDFS area allows for an immediate and abundant scientific return. In this paper, we present the data reduction of the XMM-CDFS observations, the method for source detection in the 2–10 and 5–10 keV bands, and the resulting catalogues. A number of 339 and 137 sources are listed in the above bands with flux limits of 6.6 × 10-16 and 9.5 × 10-16 erg s-1 cm-2, respectively. The flux limits at 50% of the maximum sky coverage are 1.8 × 10-15 and 4.0 × 10-15 erg s-1 cm-2, respectively. The catalogues have been cross-correlated with the Chandra ones: 315 and 130 identifications have been found with a likelihood-ratio method, respectively. A number of 15 new sources, previously undetected by Chandra, is found; 5 of them lie in the 4 Ms area. Redshifts, either spectroscopic or photometric, are available for ~ 95% of the sources. The number counts in both bands are presented and compared to other works. The survey coverage has been calculated with the help of two extensive sets of simulations, one set per band. The simulations have been produced with a newly-developed simulator, written with the aim of the most careful reproduction of the background spatial properties. For this reason, we present a detailed decomposition of the XMM-Newton background into its components: cosmic, particle, and residual soft protons.The three components have different spatial distributions. The importance of these three components depends on the band and on the camera; the particle background is the most important one (80–90% of the background counts), followed by the soft protons (4–20%)