The SCUBA HAlf degree extragalactic survey - III. Identification of radio and mid-infrared counterparts to submillimetre galaxies

Determining an accurate position for a submillimetre (submm) galaxy (SMG) is the crucial step that enables us to move from the basic properties of an SMG sample - source counts and 2D clustering - to an assessment of their detailed, multiwavelength properties, their contribution to the history of cosmic star formation and their links with present-day galaxy populations. In this paper, we identify robust radio and/or infrared (IR) counterparts, and hence accurate positions, for over two-thirds of the SCUBA HAlf-Degree Extragalactic Survey (SHADES) Source Catalogue, presenting optical, 24-μm and radio images of each SMG. Observed trends in identification rate have given no strong rationale for pruning the sample. Uncertainties in submm position are found to be consistent with theoretical expectations, with no evidence for significant additional sources of error. Employing the submm/radio redshift indicator, via a parametrization appropriate for radio-identified SMGs with spectroscopic redshifts, yields a median redshift of 2.8 for the radio-identified subset of SHADES, somewhat higher than the median spectroscopic redshift. We present a diagnostic colour-colour plot, exploiting Spitzer photometry, in which we identify regions commensurate with SMGs at very high redshift. Finally, we find that significantly more SMGs have multiple robust counterparts than would be expected by chance, indicative of physical associations. These multiple systems are most common amongst the brightest SMGs and are typically separated by 2-6 arcsec, similar to 15-20/sin i kpc at z~ 2, consistent with early bursts seen in merger simulations.

Discovery of stable and variable differences in the Mycobacterium avium subsp. paratuberculosis type I, II, and III genomes by pan-genome microarray analysis

Mycobacterium avium subsp. paratuberculosis is an important animal pathogen widely disseminated in the environment that has also been associated with Crohn's disease in humans. Three M. avium subsp. paratuberculosis genomotypes are recognized, but genomic differences have not been fully described. To further investigate these potential differences, a 60-mer oligonucleotide microarray (designated the MAPAC array), based on the combined genomes of M. avium subsp. paratuberculosis (strain K-10) and Mycobacterium avium subsp. hominissuis (strain 104), was designed and validated. By use of a test panel of defined M. avium subsp. paratuberculosis strains, the MAPAC array was able to identify a set of large sequence polymorphisms (LSPs) diagnostic for each of the three major M. avium subsp. paratuberculosis types. M. avium subsp. paratuberculosis type II strains contained a smaller genomic complement than M. avium subsp. paratuberculosis type I and M. avium subsp. paratuberculosis type III genomotypes, which included a set of genomic regions also found in M. avium subsp. hominissuis 104. Specific PCRs for genes within LSPs that differentiated M. avium subsp. paratuberculosis types were devised and shown to accurately screen a panel (n = 78) of M. avium subsp. paratuberculosis strains. Analysis of insertion/deletion region INDEL12 showed deletion events causing a reduction in the complement of mycobacterial cell entry genes in M. avium subsp. paratuberculosis type II strains and significantly altering the coding of a major immunologic protein (MPT64) associated with persistence and granuloma formation. Analysis of MAPAC data also identified signal variations in several genomic regions, termed variable genomic islands (vGIs), suggestive of transient duplication/deletion events. vGIs contained significantly low GC% and were immediately flanked by insertion sequences, integrases, or short inverted repeat sequences. Quantitative PCR demonstrated that variation in vGI signals could be associated with colony growth rate and morphology.