Galaxy And Mass Assembly (GAMA)

The GAMA survey aims to deliver 250,000 optical spectra (3--7Ang resolution) over 250 sq. degrees to spectroscopic limits of r_{AB} <19.8 and K_{AB}<17.0 mag. Complementary imaging will be provided by GALEX, VST, UKIRT, VISTA, HERSCHEL and ASKAP to comparable flux levels leading to a definitive multi-wavelength galaxy database. The data will be used to study all aspects of cosmic structures on 1kpc to 1Mpc scales spanning all environments and out to a redshift limit of z ~ 0.4. Key science drivers include the measurement of: the halo mass function via group velocity dispersions; the stellar, HI, and baryonic mass functions; galaxy component mass-size relations; the recent merger and star-formation rates by mass, types and environment. Detailed modeling of the spectra, broad SEDs, and spatial distributions should provide individual star formation histories, ages, bulge-disc decompositions and stellar bulge, stellar disc, dust disc, neutral HI gas and total dynamical masses for a significant subset of the sample (~100k) spanning both the giant and dwarf galaxy populations. The survey commenced March 2008 with 50k spectra obtained in 21 clear nights using the Anglo Australian Observatory's new multi-fibre-fed bench-mounted dual-beam spectroscopic system (AAOmega).Comment: Invited talk at IAU 254 (The Galaxy Disk in Cosmological Context, Copenhagen), 6 pages, 5 figures, high quality PDF version available at http://www.eso.org/~jliske/gama

Laplace Operators on Fractals and Related Functional Equations

We give an overview over the application of functional equations, namely the classical Poincar\'e and renewal equations, to the study of the spectrum of Laplace operators on self-similar fractals. We compare the techniques used to those used in the euclidean situation. Furthermore, we use the obtained information on the spectral zeta function to define the Casimir energy of fractals. We give numerical values for this energy for the Sierpi\'nski gasket

Predicting consumer biomass, size-structure, production, catch potential, responses to fishing and associated uncertainties in the world's marine ecosystems

Existing estimates of fish and consumer biomass in the world’s oceans are disparate. This creates uncertainty about the roles of fish and other consumers in biogeochemical cycles and ecosystem processes, the extent of human and environmental impacts and fishery potential. We develop and use a size-based macroecological model to assess the effects of parameter uncertainty on predicted consumer biomass, production and distribution. Resulting uncertainty is large (e.g. median global biomass 4.9 billion tonnes for consumers weighing 1 g to 1000 kg; 50% uncertainty intervals of 2 to 10.4 billion tonnes; 90% uncertainty intervals of 0.3 to 26.1 billion tonnes) and driven primarily by uncertainty in trophic transfer efficiency and its relationship with predator-prey body mass ratios. Even the upper uncertainty intervals for global predictions of consumer biomass demonstrate the remarkable scarcity of marine consumers, with less than one part in 30 million by volume of the global oceans comprising tissue of macroscopic animals. Thus the apparently high densities of marine life seen in surface and coastal waters and frequently visited abundance hotspots will likely give many in society a false impression of the abundance of marine animals. Unexploited baseline biomass predictions from the simple macroecological model were used to calibrate a more complex size- and trait-based model to estimate fisheries yield and impacts. Yields are highly dependent on baseline biomass and fisheries selectivity. Predicted global sustainable fisheries yield increases ≈4 fold when smaller individuals (< 20 cm from species of maximum mass < 1kg) are targeted in all oceans, but the predicted yields would rarely be accessible in practice and this fishing strategy leads to the collapse of larger species if fishing mortality rates on different size classes cannot be decoupled. Our analyses show that models with minimal parameter demands that are based on a few established ecological principles can support equitable analysis and comparison of diverse ecosystems. The analyses provide insights into the effects of parameter uncertainty on global biomass and production estimates, which have yet to be achieved with complex models, and will therefore help to highlight priorities for future research and data collection. However, the focus on simple model structures and global processes means that non-phytoplankton primary production and several groups, structures and processes of ecological and conservation interest are not represented. Consequently, our simple models become increasingly less useful than more complex alternatives when addressing questions about food web structure and function, biodiversity, resilience and human impacts at smaller scales and for areas closer to coasts

GAMA: towards a physical understanding of galaxy formation

The Galaxy And Mass Assembly (GAMA) project is the latest in a tradition of large galaxy redshift surveys, and is now underway on the 3.9m Anglo-Australian Telescope at Siding Spring Observatory. GAMA is designed to map extragalactic structures on scales of 1kpc - 1Mpc in complete detail to a redshift of z~0.2, and to trace the distribution of luminous galaxies out to z~0.5. The principal science aim is to test the standard hierarchical structure formation paradigm of Cold Dark Matter (CDM) on scales of galaxy groups, pairs, discs, bulges and bars. We will measure (1) the Dark Matter Halo Mass Function (as inferred from galaxy group velocity dispersions); (2) baryonic processes, such as star formation and galaxy formation efficiency (as derived from Galaxy Stellar Mass Functions); and (3) the evolution of galaxy merger rates (via galaxy close pairs and galaxy asymmetries). Additionally, GAMA will form the central part of a new galaxy database, which aims to contain 275,000 galaxies with multi-wavelength coverage from coordinated observations with the latest international ground- and space-based facilities: GALEX, VST, VISTA, WISE, HERSCHEL, GMRT and ASKAP. Together, these data will provide increased depth (over 2 magnitudes), doubled spatial resolution (0.7"), and significantly extended wavelength coverage (UV through Far-IR to radio) over the main SDSS spectroscopic survey for five regions, each of around 50 deg^2. This database will permit detailed investigations of the structural, chemical, and dynamical properties of all galaxy types, across all environments, and over a 5 billion year timeline.Comment: GAMA overview which appeared in the October 2009 issue of Astronomy & Geophysics, ref: Astron.Geophys. 50 (2009) 5.1

Exploiting differential Wnt target gene expression to generate a molecular biomarker for colorectal cancer stratification

OBJECTIVE Pathological Wnt pathway activation is a conserved hallmark of colorectal cancer. Wnt-activating mutations can be divided into: i) ligand-independent (LI) alterations in intracellular signal transduction proteins (, β-catenin), causing constitutive pathway activation and ii) ligand-dependent (LD) mutations affecting the synergistic R-Spondin axis (, -fusions) acting through amplification of endogenous Wnt signal transmembrane transduction. Our aim was to exploit differential Wnt target gene expression to generate a mutation-agnostic biomarker for LD tumours. DESIGN We undertook harmonised multi-omic analysis of discovery (n=684) and validation cohorts (n=578) of colorectal tumours collated from publicly available data and the Stratification in Colorectal Cancer Consortium. We used mutation data to establish molecular ground truth and subdivide lesions into LI/LD tumour subsets. We contrasted transcriptional, methylation, morphological and clinical characteristics between groups. RESULTS Wnt disrupting mutations were mutually exclusive. Desmoplastic stromal upregulation of may compensate for absence of epithelial mutation in a subset of stromal-rich tumours. Key Wnt negative regulator genes were differentially expressed between LD/LI tumours, with targeted hypermethylation of some genes (, ) occurring even in CIMP-negative LD cancers. mRNA expression was used as a discriminatory molecular biomarker to distinguish LD/LI tumours (area under the curve >0.93). CONCLUSIONS Epigenetic suppression of appropriate Wnt negative feedback loops is selectively advantageous in LD tumours and differential expression in LD/LI lesions can be exploited as a molecular biomarker. Distinguishing between LD/LI tumour types is important; patients with LD tumours retain sensitivity to Wnt ligand inhibition and may be stratified at diagnosis to clinical trials of Porcupine inhibitors

Discovery and Validation of Molecular Biomarkers for Colorectal Adenomas and Cancer with Application to Blood Testing

BACKGROUND & AIMS: Colorectal cancer incidence and deaths are reduced by the detection and removal of early-stage, treatable neoplasia but we lack proven biomarkers sensitive for both cancer and pre-invasive adenomas. The aims of this study were to determine if adenomas and cancers exhibit characteristic patterns of biomarker expression and to explore whether a tissue-discovered (and validated) biomarker is differentially expressed in the plasma of patients with colorectal adenomas or cancer. METHODS: Candidate RNA biomarkers were identified by oligonucleotide microarray analysis of colorectal specimens (222 normal, 29 adenoma, 161 adenocarcinoma and 50 colitis) and validated in a previously untested cohort of 68 colorectal specimens using a custom-designed oligonucleotide microarray. One validated biomarker, KIAA1199, was assayed using qRT-PCR on plasma extracted RNA from 20 colonoscopy-confirmed healthy controls, 20 patients with adenoma, and 20 with cancer. RESULTS: Genome-wide analysis uncovered reproducible gene expression signatures for both adenomas and cancers compared to controls. 386/489 (79%) of the adenoma and 439/529 (83%) of the adenocarcinoma biomarkers were validated in independent tissues. We also identified genes differentially expressed in adenomas compared to cancer. KIAA1199 was selected for further analysis based on consistent up-regulation in neoplasia, previous studies and its interest as an uncharacterized gene. Plasma KIAA1199 RNA levels were significantly higher in patients with either cancer or adenoma (31/40) compared to neoplasia-free controls (6/20). CONCLUSIONS: Colorectal neoplasia exhibits characteristic patterns of gene expression. KIAA1199 is differentially expressed in neoplastic tissues and KIAA1199 transcripts are more abundant in the plasma of patients with either cancer or adenoma compared to controls

The Herschel–ATLAS data release 2, Paper I. Submillimeter and far-infrared images of the South and North Galactic Poles: the largest Herschel survey of the extragalactic sky

We present the largest submillimeter images that have been made of the extragalactic sky. The Herschel Astrophysical Terahertz Large Area Survey (H-ATLAS) is a survey of 660 deg2 with the PACS and SPIRE cameras in five photometric bands: 100, 160, 250, 350, and 500 μm. In this paper we present the images from our two largest fields, which account for ~75% of the survey. The first field is 180.1 deg2 in size, centered on the north Galactic pole (NGP), and the second is 317.6 deg2 in size, centered on the south Galactic pole. The NGP field serendipitously contains the Coma cluster. Over most (~80%) of the images, the pixel noise, including both instrumental noise and confusion noise, is approximately 3.6, and 3.5 mJy pix−1 at 100 and 160 μm, and 11.0, 11.1 and 12.3 mJy beam−1 at 250, 350 and 500 μm, respectively, but reaches lower values in some parts of the images. If a matched filter is applied to optimize point-source detection, our total 1σ map sensitivity is 5.7, 6.0, and 7.3 mJy at 250, 350, and 500 μm, respectively. We describe the results of an investigation of the noise properties of the images. We make the most precise estimate of confusion in SPIRE maps to date, finding values of 3.12 ± 0.07, 4.13 ± 0.02, and 4.45 ± 0.04 mJy beam−1 at 250, 350, and 500 μm in our un-convolved maps. For PACS we find an estimate of the confusion noise in our fast-parallel observations of 4.23 and 4.62 mJy beam−1 at 100 and 160 μm. Finally, we give recipes for using these images to carry out photometry, both for unresolved and extended sources

The Transformation of Citizenship in Complex Societies

The main purpose of this paper is to propose a theoretical framework for understanding the transformation of citizenship in complex societies. To this end, the paper is divided into six sections. The first section elucidates the main reasons for the renaissance of the concept of citizenship in the contemporary social sciences. The second section argues that a comprehensive sociological theory of citizenship needs to account for the importance of four dimensions: the content, the type, the conditions, and the arrangements of citizenship. The third section suggests that in order to understand the sociological significance of T.H. Marshall’s account of legal, political, and social rights we need to explore the particular historical contexts in which citizenship rights became ideologically and institutionally relevant. The fourth section offers some critical reflections on the main shortcomings of the Marshallian approach to citizenship. The fifth section draws an analogy between the transformation of social movements and the transformation of citizenship. The sixth section sheds light on the fact that contemporary citizenship studies are confronted with a curious paradox: the differentiation of citizenship has led to both the relativistic impoverishment and the pluralistic enrichment of contemporary accounts of ‘the social’ and ‘the political’.The paper concludes by arguing that, under conditions of late modernity, the state’s capacity to gain political legitimacy increasingly depends on its ability to confront the normative challenges posed by the ubiquity of societal complexity

Connecting Quorum Sensing, c-di-GMP, Pel Polysaccharide, and Biofilm Formation in Pseudomonas aeruginosa through Tyrosine Phosphatase TpbA (PA3885)

With the opportunistic pathogen Pseudomonas aeruginosa, quorum sensing based on homoserine lactones was found to influence biofilm formation. Here we discern a mechanism by which quorum sensing controls biofilm formation by screening 5850 transposon mutants of P. aeruginosa PA14 for altered biofilm formation. This screen identified the PA3885 mutant, which had 147-fold more biofilm than the wild-type strain. Loss of PA3885 decreased swimming, abolished swarming, and increased attachment, although this did not affect production of rhamnolipids. The PA3885 mutant also had a wrinkly colony phenotype, formed pronounced pellicles, had substantially more aggregation, and had 28-fold more exopolysaccharide production. Expression of PA3885 in trans reduced biofilm formation and abolished aggregation. Whole transcriptome analysis showed that loss of PA3885 activated expression of the pel locus, an operon that encodes for the synthesis of extracellular matrix polysaccharide. Genetic screening identified that loss of PelABDEG and the PA1120 protein (which contains a GGDEF-motif) suppressed the phenotypes of the PA3885 mutant, suggesting that the function of the PA3885 protein is to regulate 3,5-cyclic diguanylic acid (c-di-GMP) concentrations as a phosphatase since c-di-GMP enhances biofilm formation by activating PelD, and c-di-GMP inhibits swarming. Loss of PA3885 protein increased cellular c-di-GMP concentrations; hence, PA3885 protein is a negative regulator of c-di-GMP production. Purified PA3885 protein has phosphatase activity against phosphotyrosine peptides and is translocated to the periplasm. Las-mediated quorum sensing positively regulates expression of the PA3885 gene. These results show that the PA3885 protein responds to AHL signals and likely dephosphorylates PA1120, which leads to reduced c-di-GMP production. This inhibits matrix exopolysaccharide formation, which leads to reduced biofilm formation; hence, we provide a mechanism for quorum sensing control of biofilm formation through the pel locus and suggest PA3885 should be named TpbA for tyrosine phosphatase related to biofilm formation and PA1120 should be TpbB