A complex intronic enhancer regulates expression of the CFTR gene by direct interaction with the promoter.

Genes can maintain spatiotemporal expression patterns by long-range interactions between cis-acting elements. The cystic fibrosis transmembrane conductance regulator gene (CFTR) is expressed primarily in epithelial cells. An element located within a DNase I-hypersensitive site (DHS) 10 kb into the first intron was previously shown to augment CFTR promoter activity in a tissue-specific manner. Here, we reveal the mechanism by which this element influences CFTR transcription. We employed a high-resolution method of mapping DHS using tiled microarrays to accurately locate the intron 1 DHS. Transfection of promoter-reporter constructs demonstrated that the element displays classical tissue-specific enhancer properties and can independently recruit factors necessary for transcription initiation. In vitro DNase I footprinting analysis identified a protected region that corresponds to a conserved, predicted binding site for hepatocyte nuclear factor 1 (HNF1). We demonstrate by electromobility shift assays (EMSA) and chromatin immunoprecipitation (ChIP) that HNF1 binds to this element both in vitro and in vivo. Moreover, using chromosome conformation capture (3C) analysis, we show that this element interacts with the CFTR promoter in CFTR-expressing cells. These data provide the first insight into the three- dimensional (3D) structure of the CFTR locus and confirm the contribution of intronic cis-acting elements to the regulation of CFTR gene expression.

HDAC inhibitors cause site-specific chromatin remodeling at PU.1-bound enhancers in K562 cells

BACKGROUND: Small molecule inhibitors of histone deacetylases (HDACi) hold promise as anticancer agents for particular malignancies. However, clinical use is often confounded by toxicity, perhaps due to indiscriminate hyperacetylation of cellular proteins. Therefore, elucidating the mechanisms by which HDACi trigger differentiation, cell cycle arrest, or apoptosis of cancer cells could inform development of more targeted therapies. We used the myelogenous leukemia line K562 as a model of HDACi-induced differentiation to investigate chromatin accessibility (DNase-seq) and expression (RNA-seq) changes associated with this process. RESULTS: We identified several thousand specific regulatory elements [~10 % of total DNase I-hypersensitive (DHS) sites] that become significantly more or less accessible with sodium butyrate or suberanilohydroxamic acid treatment. Most of the differential DHS sites display hallmarks of enhancers, including being enriched for non-promoter regions, associating with nearby gene expression changes, and increasing luciferase reporter expression in K562 cells. Differential DHS sites were enriched for key hematopoietic lineage transcription factor motifs, including SPI1 (PU.1), a known pioneer factor. We found PU.1 increases binding at opened DHS sites with HDACi treatment by ChIP-seq, but PU.1 knockdown by shRNA fails to block the chromatin accessibility and expression changes. A machine-learning approach indicates H3K27me3 initially marks PU.1-bound sites that open with HDACi treatment, suggesting these sites are epigenetically poised. CONCLUSIONS: We find HDACi treatment of K562 cells results in site-specific chromatin remodeling at epigenetically poised regulatory elements. PU.1 shows evidence of a pioneer role in this process by marking poised enhancers but is not required for transcriptional activation.

A comprehensive life cycle water analysis framework for residential buildings

Most studies on the environmental performance of buildings focus on energy demand and associated greenhouse gas emissions. They often neglect to consider the range of other resource demands and environmental impacts associated with buildings, including water. Studies that assess water use in buildings typically consider only operational water, which excludes the embodied water in building materials or the water associated with the mobility of building occupants. A new framework is presented that quantifies water requirements at the building scale (i.e. the embodied and operational water of the building as well as its maintenance and refurbishment) and at the city scale (i.e. the embodied water of nearby infrastructures such as roads, gas distribution and others) and the transport-related indirect water use of building occupants. A case study house located in Melbourne, Australia, is analysed using the new framework. The results show that each of the embodied, operational and transport requirements is nearly equally important. By integrating these three water requirements, the developed framework provides architects, building designers, planners and decision-makers with a powerful means to understand and effectively reduce the overall water use and associated environmental impacts of residential buildings.

Volcanic ash fuels anomalous plankton bloom in subarctic northeast Pacific

Using multiple lines of evidence, we demonstrate that volcanic ash deposition in August 2008 initiated one of the largest phytoplankton blooms observed in the subarctic North Pacific. Unusually widespread transport from a volcanic eruption in the Aleutian Islands, Alaska deposited ash over much of the subarctic NE Pacific, followed by large increases in satellite chlorophyll. Surface ocean pCO2, pH, and fluorescence reveal that the bloom started a few days after ashfall. Ship-based measurements showed increased dominance by diatoms. This evidence points toward fertilization of this normally iron-limited region by ash, a relatively new mechanism proposed for iron supply to the ocean. The observations do not support other possible mechanisms. Extrapolation of the pCO2 data to the area of the bloom suggests a modest ∼0.01 Pg carbon export from this event, implying that even large-scale iron fertilization at an optimum time of year is not very efficient at sequestering atmospheric CO2.

An Experimental Investigation into the Pressure Drop for Turbulent 90o Elbow Bends

The prediction of the pressure drop for turbulent single-phase fluid flow around sharp 90° bends is difficult owing to the complexity of the flow arising from frictional and separation effects. Several empirical equations exist, which accurately predict the pressure loss due to frictional effects. More recently, Crawford et al. [1] proposed an equation for the prediction of pressure loss due to separation of the flow. This work proposes a new composite equation for the prediction of pressure drop due to separation of the flow, which incorporates bends with ratio R/r <2. A new composite equation is proposed to predict pressure losses over the Reynolds number range 4 x 103-3 x 105. The predictions from the new equation are within a range of -4 to +6 per cent of existing experimental data.