The frontiers of participatory public engagement

Currently missing from critical literature on public engagement with academic research is a public-centric analysis of the wider contemporary context of developments in the field of public engagement and participation. Drawing on three differently useful strands of the existing theoretical literature on the public, this article compares a diverse sample of 100 participatory public engagement initiatives in order to first, analyse a selection of the myriad ways that the public is being constituted and supported across this contemporary field and second, identify what socio-cultural researchers might learn from these developments. Emerging from this research is a preliminary map of the field of public engagement and participation. This map highlights relationships and divergences that exist among diverse forms of practice and brings into clearer view a set of tensions between different contemporary approaches to public engagement and participation. Two ‘frontiers’ of participatory public engagement that socio-cultural researchers should attend are also identified. At the first, scholars need to be critical regarding the particular versions of the public that their preferred approach to engagement and participation supports and concerning how their specific identifications with the public relate to those being addressed across the wider field. At the second frontier, researchers need to consider the possibilities for political intervention that public engagement and participation practice could open out, both in the settings they are already working and also in the much broader, rapidly developing and increasingly complicated contemporary field of public engagement and participation that this article explores

Predicting Target DNA Sequences of DNA-Binding Proteins Based on Unbound Structures

DNA-binding proteins such as transcription factors use DNA-binding domains (DBDs) to bind to specific sequences in the genome to initiate many important biological functions. Accurate prediction of such target sequences, often represented by position weight matrices (PWMs), is an important step to understand many biological processes. Recent studies have shown that knowledge-based potential functions can be applied on protein-DNA co-crystallized structures to generate PWMs that are considerably consistent with experimental data. However, this success has not been extended to DNA-binding proteins lacking co-crystallized structures. This study aims at investigating the possibility of predicting the DNA sequences bound by DNA-binding proteins from the proteins' unbound structures (structures of the unbound state). Given an unbound query protein and a template complex, the proposed method first employs structure alignment to generate synthetic protein-DNA complexes for the query protein. Once a complex is available, an atomic-level knowledge-based potential function is employed to predict PWMs characterizing the sequences to which the query protein can bind. The evaluation of the proposed method is based on seven DNA-binding proteins, which have structures of both DNA-bound and unbound forms for prediction as well as annotated PWMs for validation. Since this work is the first attempt to predict target sequences of DNA-binding proteins from their unbound structures, three types of structural variations that presumably influence the prediction accuracy were examined and discussed. Based on the analyses conducted in this study, the conformational change of proteins upon binding DNA was shown to be the key factor. This study sheds light on the challenge of predicting the target DNA sequences of a protein lacking co-crystallized structures, which encourages more efforts on the structure alignment-based approaches in addition to docking- and homology modeling-based approaches for generating synthetic complexes

Functional Diversification of Paralogous Transcription Factors via Divergence in DNA Binding Site Motif and in Expression

BACKGROUND: Gene duplication is a major driver of evolutionary innovation as it allows for an organism to elaborate its existing biological functions via specialization or diversification of initially redundant gene paralogs. Gene function can diversify in several ways. Transcription factor gene paralogs in particular, can diversify either by changes in their tissue-specific expression pattern or by changes in the DNA binding site motif recognized by their protein product, which in turn alters their gene targets. The relationship between these two modes of functional diversification of transcription factor paralogs has not been previously investigated, and is essential for understanding adaptive evolution of transcription factor gene families. FINDINGS: Based on a large set of human paralogous transcription factor pairs, we show that when the DNA binding site motifs of transcription factor paralogs are similar, the expressions of the genes that encode the paralogs have diverged, so in general, at most one of the paralogs is highly expressed in a tissue. Moreover, paralogs with diverged DNA binding site motifs tend to be diverged in their function. Conversely, two paralogs that are highly expressed in a tissue tend to have dissimilar DNA binding site motifs. We have also found that in general, within a paralogous family, tissue-specific decrease in gene expression is more frequent than what is expected by chance. CONCLUSIONS: While previous investigations of paralogous gene diversification have only considered coding sequence divergence, by explicitly quantifying divergence in DNA binding site motif, our work presents a new paradigm for investigating functional diversification. Consistent with evolutionary expectation, our quantitative analysis suggests that paralogous transcription factors have survived extinction in part, either through diversification of their DNA binding site motifs or through alterations in their tissue-specific expression levels

Deep Investigation of Neutral Gas Origins (DINGO): H I stacking experiments with early science data

We present early science results from Deep Investigation of Neutral Gas Origins (DINGO), an HI survey using the Australian Square Kilometre Array Pathfinder (ASKAP). Using ASKAP sub-arrays available during its commissioning phase, DINGO early science data were taken over ~ 60 deg2 of the Galaxy And Mass Assembly (GAMA) 23 h region with 35.5 hr integration time. We make direct detections of six known and one new sources at z < 0.01. Using HI spectral stacking, we investigate the HI gas content of galaxies at 0.04 z0.09 for different galaxy colours. The results show that galaxy morphology based on optical colour is strongly linked to HI gas properties. To examine environmental impacts on the HI gas content of galaxies, three sub-samples are made based on the GAMA group catalogue. The average HI mass of group central galaxies is larger than those of satellite and isolated galaxies, but with a lower HI gas fraction. We derive a variety of HI scaling relations for physical properties of our sample, including stellar mass, stellar mass surface density, NUV-r colour, specific star formation rate, and halo mass. We find that the derived HI scaling relations are comparable to other published results, with consistent trends also observed to ~0.5 dex lower limits in stellar mass and stellar surface density. The cosmic HI densities derived from our data are consistent with other published values at similar redshifts. DINGO early science highlights the power of HI spectral stacking techniques with ASKAP

Global analysis of estrogen receptor beta binding to breast cancer cell genome reveals an extensive interplay with estrogen receptor alpha for target gene regulation

Background: Estrogen receptors alpha (ERa) and beta (ERb) are transcription factors (TFs) that mediate estrogen signaling and define the hormone-responsive phenotype of breast cancer (BC). The two receptors can be found co-expressed and play specific, often opposite, roles, with ERb being able to modulate the effects of ERa on gene transcription and cell proliferation. ERb is frequently lost in BC, where its presence generally correlates with a better prognosis of the disease. The identification of the genomic targets of ERb in hormone-responsive BC cells is thus a critical step to elucidate the roles of this receptor in estrogen signaling and tumor cell biology. Results: Expression of full-length ERb in hormone-responsive, ERa-positive MCF-7 cells resulted in a marked reduction in cell proliferation in response to estrogen and marked effects on the cell transcriptome. By ChIP-Seq we identified 9702 ERb and 6024 ERa binding sites in estrogen-stimulated cells, comprising sites occupied by either ERb, ERa or both ER subtypes. A search for TF binding matrices revealed that the majority of the binding sites identified comprise one or more Estrogen Response Element and the remaining show binding matrixes for other TFs known to mediate ER interaction with chromatin by tethering, including AP2, E2F and SP1. Of 921 genes differentially regulated by estrogen in ERb+ vs ERb- cells, 424 showed one or more ERb site within 10 kb. These putative primary ERb target genes control cell proliferation, death, differentiation, motility and adhesion, signal transduction and transcription, key cellular processes that might explain the biological and clinical phenotype of tumors expressing this ER subtype. ERb binding in close proximity of several miRNA genes and in the mitochondrial genome, suggests the possible involvement of this receptor in small non-coding RNA biogenesis and mitochondrial genome functions. Conclusions: Results indicate that the vast majority of the genomic targets of ERb can bind also ERa, suggesting that the overall action of ERb on the genome of hormone-responsive BC cells depends mainly on the relative concentration of both ERs in the cell