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

Genesis of the dusty Universe: modeling submillimetre source counts

We model the evolution of IR galaxies using a phenomenological approach to match the observed source counts at different IR wavelengths. We introduce a new algorithm for reproducing source counts based on direct integration of probability distributions rather than Monte-Carlo sampling. We construct a simple model for the evolution of the luminosity function and the colour distribution of IR galaxies which utilizes a minimum number of free parameters. Moreover we analyze how each of these parameters is constrained by observational data. The model is based on pure luminosity evolution and adopts the Dale & Helou SED templates. We find that the 850um source counts and their redshift distribution depend strongly on the shape of the luminosity evolution function, but only weakly on the details of the SEDs. We derive the best-fit evolutionary model using the 850um counts and redshift distribution as constraints. Moreover our best-fit shows a flattening of the faint end of the luminosity function towards high redshifts and requires a colour evolution which implies the typical dust temperatures of objects with the same luminosities to decrease with redshift. We compare our best-fit model to observed source counts at shorter and longer wavelengths which indicates our model reproduces the 70um and 1100um source counts remarkably well, but under-produces the counts at intermediate wavelengths. Analysis reveals that the discrepancy arises at low redshifts, indicating that revision of the adopted SED library towards lower dust temperatures (at a fixed infrared luminosity) is required. This modification is equivalent to a population of cold galaxies existing at low redshifts, as also indicated by recent Herschel results, which are underrepresented in IRAS sample. We show that the modified model successfully reproduces the source counts in a wide range of IR and submm wavelengths.Comment: 21 pages, 11 figures, 2 tables. Accepted for publication in MNRAS. Supplementary information could be found at http://www.strw.leidenuniv.nl/genesis

Fluorescent T7 display phages obtained by translational frameshift

Lytic phages form a powerful platform for the display of large cDNA libraries and offer the possibility to screen for interactions with almost any substrate. To visualize these interactions directly by fluorescence microscopy, we constructed fluorescent T7 phages by exploiting the flexibility of phages to incorporate modified versions of its capsid protein. By applying translational frameshift sequences, helper plasmids were constructed that expressed a fixed ratio of both wild-type capsid protein (gp10) and capsid protein fused to enhanced yellow fluorescent protein (EYFP). The frameshift sequences were inserted between the 3′ end of the capsid gene and the sequence encoding EYFP. Fluorescent fusion proteins are only formed when the ribosome makes a −1 shift in reading frame during translation. Using standard fluorescence microscopy, we could sensitively monitor the enrichment of specific binders in a cDNA library displayed on fluorescent T7 phages. The perspectives of fluorescent display phages in the fast emerging field of single molecule detection and sorting technologies are discussed

Tracing the cosmic growth of supermassive black holes to z~3 with Herschel

We study a sample of Herschel selected galaxies within the Great Observatories Origins Deep Survey-South and the Cosmic Evolution Survey fields in the framework of the Photodetector Array Camera and Spectrometer (PACS) Evolutionary Probe project. Starting from the rich multiwavelength photometric data sets available in both fields, we perform a broad-band spectral energy distribution decomposition to disentangle the possible active galactic nucleus (AGN) contribution from that related to the host galaxy. We find that 37 per cent of the Herschel-selected sample shows signatures of nuclear activity at the 99 per cent confidence level. The probability of revealing AGN activity increases for bright (L 1−1000 > 10 11 L ? ) star-forming galaxies at z > 0.3, becoming about 80 per cent for the brightest (L 1−1000 > 10 12 L ? ) Infrared (IR) galaxies at z≥1. Finally, we reconstruct the AGN bolometric luminosity function and the supermassive black hole growth rate across cosmic time up to z ∼ 3 from a far-IR perspective. This work shows general agreement with most of the panchromatic estimates from the literature, with the global black hole growth peaking at z ∼ 2 and reproducing the observed local black hole mass density with consistent values of the radiative efficiency Erad (∼0.07)

The INTEGRAL/IBIS AGN catalogue I: X-ray absorption properties versus optical classification

In this work we present the most comprehensive INTEGRAL AGN sample which lists 272 objects. Here we mainly use this sample to study the absorption properties of active galaxies, to probe new AGN classes and to test the AGN unification scheme. We find that half (48%) of the sample is absorbed while the fraction of Compton thick AGN is small (~7%). In line with our previous analysis, we have however shown that when the bias towards heavily absorbed objects which are lost if weak and at large distance is removed, as it is possible in the local Universe, the above fractions increase to become 80% and 17%. We also find that absorption is a function of source luminosity, which implies some evolution in the obscuration properties of AGN. Few peculiar classes, so far poorly studied in the hard X-ray band, have been detected and studied for the first time such as 5 XBONG, 5 type 2 QSOs and 11 LINERs. In terms of optical classification, our sample contains 57% of type 1 and 43% of type 2 AGN; this subdivision is similar to that found in X-rays if unabsorbed versus absorbed objects are considered, suggesting that the match between optical and X-ray classification is overall good. Only a small percentage of sources (12%) does not fulfill the expectation of the unified theory as we find 22 type 1 AGN which are absorbed and 10 type 2 AGN which are unabsorbed. Studying in depth these outliers we found that most of the absorbed type 1 AGN have X-ray spectra characterized by either complex or warm/ionized absorption more likely due to ionized gas located in an accretion disk wind or in the biconical structure associated to the central nucleus, therefore unrelated to the toroidal structure. Among 10 type 2 AGN which resulted to be unabsorbed, at most 3-4% is still eligible to be classified as a "true" type 2 AGN.Comment: 21 pages, 6 figures, 5 tables. Accepted for publication on MNRAS. arXiv admin note: text overlap with arXiv:0709.2077 by other author

Accounting for intimate partner violence perpetration. A cross-cultural comparison of English and Brazilian male substance users' explanations

Introduction and Aims: This paper describes how substance use features in the accounts of intimate partner violence (IPV) perpetrators in treatment in England and Brazil. The aim of the research was to better understand cross cultural constructions of IPV perpetration amongst men in treatment for substance use. Design and Methods: Semi-structured interviews were conducted with 40 men in community substance use treatment in Sao Paolo, Brazil and London and the South East of England who had reported IPV perpetration in a questionnaire survey. A thematic, narrative analysis was carried out of men's explanations for IPV perpetration. Findings: Three types of narratives were distinguished: (i) disputes, centred on substance use, that escalate to IPV perpetration; (ii) IPV perpetration that is explained by uncharacteristic loss of control, as a result of intoxication; and (iii) IPV perpetration provoked by a perceived betrayal, in which substance use is incidental. In all types of accounts hegemonic principles of male and female roles and behaviour provided a context for and make IPV perpetration explicable. Discussion and Conclusions: Substance use and IPV are culturally constructed and contextually defined. Understanding the meaning-making of substance using IPV perpetrators has implications for the treatment of both substance abuse and IPV

Researching underwater: a submerged study

This chapter explores the unknown territory of a lost project: an ethnography of a public swimming pool. The discussion is contextualised within my broader sociological theory of ‘nothing’, as a category of unmarked, negative social phenomena, including no-things, no-bodies, no-wheres, non-events and non-identities. These meaningful symbolic objects are constituted through social interaction, which can take two forms: acts of commission and acts of omission. I tell the story of how this project did not happen, through the things I did not do or that did not materialise, and how I consequently did not become a certain type of researcher. I identify three types of negative phenomena that I did not observe and document – invisible figures, silent voices and empty vessels – and, consequently, the knowledge I did not acquire. However, nothing is also productive, generating new symbolic objects as substitutes, alternatives and replacements: the somethings, somebodies and somewheres that are done or made instead. Thus finally, I reflect on how not doing this project led me to pursue others, cultivating a different research identity that would not otherwise have existed

GOODS-Herschel: star formation, dust attenuation, and the FIR-radio correlation on the main sequence of star-forming galaxies up to z=4

We use deep panchromatic data sets in the GOODS-N field, from GALEX to the deepest Herschel far-infrared (FIR) and VLA radio continuum imaging, to explore the evolution of star-formation activity and dust attenuation properties of star-forming galaxies to z sime 4, using mass-complete samples. Our main results can be summarized as follows: (i) the slope of the star-formation rate–M* correlation is consistent with being constant sime0.8 up to z sime 1.5, while its normalization keeps increasing with redshift; (ii) for the first time we are able to explore the FIR–radio correlation for a mass-selected sample of star-forming galaxies: the correlation does not evolve up to z sime 4; (iii) we confirm that galaxy stellar mass is a robust proxy for UV dust attenuation in star-forming galaxies, with more massive galaxies being more dust attenuated. Strikingly, we find that this attenuation relation evolves very weakly with redshift, with the amount of dust attenuation increasing by less than 0.3 mag over the redshift range [0.5–4] for a fixed stellar mass; (iv) the correlation between dust attenuation and the UV spectral slope evolves with redshift, with the median UV slope becoming bluer with redshift. By z sime 3, typical UV slopes are inconsistent, given the measured dust attenuations, with the predictions of commonly used empirical laws. (v) Finally, building on existing results, we show that gas reddening is marginally larger (by a factor of around 1.3) than the stellar reddening at all redshifts probed. Our results support a scenario where the ISM conditions of typical star-forming galaxies evolve with redshift, such that at z ≥ 1.5 Main Sequence galaxies have ISM conditions moving closer to those of local starbursts

The VLA-COSMOS 3 GHz Large Project: continuum data and source catalog release

We present the VLA-COSMOS 3 GHz Large Project based on 384 hours of observations with the Karl G. Jansky Very Large Array (VLA) at 3 GHz (10 cm) toward the two square degree Cosmic Evolution Survey (COSMOS) field. The final mosaic reaches a median rms of 2.3 uJy/beam over the two square degrees at an angular resolution of 0.75". To fully account for the spectral shape and resolution variations across the broad (2 GHz) band, we image all data with a multiscale, multifrequency synthesis algorithm. We present a catalog of 10,830 radio sources down to 5 sigma, out of which 67 are combined from multiple components. Comparing the positions of our 3 GHz sources with those from the Very Long Baseline Array (VLBA)-COSMOS survey, we estimate that the astrometry is accurate to 0.01" at the bright end (signal-to-noise ratio, S/N_3GHz > 20). Survival analysis on our data combined with the VLA-COSMOS 1.4~GHz Joint Project catalog yields an expected median radio spectral index of alpha=-0.7. We compute completeness corrections via Monte Carlo simulations to derive the corrected 3 GHz source counts. Our counts are in agreement with previously derived 3 GHz counts based on single-pointing (0.087 square degrees) VLA data. In summary, the VLA-COSMOS 3 GHz Large Project simultaneously provides the largest and deepest radio continuum survey at high (0.75") angular resolution to date, bridging the gap between last-generation and next-generation surveys

Rapidly growing black holes and host galaxies in the distant universe from the Herschel Radio Galaxy Evolution Project

We present results from a comprehensive survey of 70 radio galaxies at redshifts 1 2.5 are higher than the sSFR of typical star forming galaxies over the same redshift range, but are similar or perhaps lower than the galaxy population for radio galaxies at z< 2.5. By comparing the sSFR and the specific ṀBH (sṀBH), we conclude that black holes in radio loud AGN are already, or soon will be, overly massive compared to their host galaxies in terms of expectations from the local MBH–MGal relation. In order to catch up with the black hole, the galaxies require about an order of magnitude more time to grow in mass at the observed SFRs compared to the time the black hole is actively accreting. However, during the current cycle of activity, we argue that this catching up is likely to be difficult because of the short gas depletion times. Finally, we speculate on how the host galaxies might grow sufficiently in stellar mass to ultimately fall onto the local MBH–MGal relation