Rapid, solid-phase based automated analysis of chromatin structure and transcription factor occupancy in living eukaryotic cells

Transcription factors, chromatin components and chromatin modification activities are involved in many diseases including cancer. However, the means by which alterations in these factors influence the epigenotype of specific cell types is poorly understood. One problem that limits progress is that regulatory regions of eukaryotic genes sometimes extend over large regions of DNA. To improve chromatin structure–function analysis over such large regions, we have developed an automated, relatively simple procedure that uses magnetic beads and a capillary sequencer for ligation-mediated-PCR (LM-PCR). We show that the procedure can be used for the rapid examination of chromatin fine-structure, nucleosome positioning as well as changes in transcription factor binding-site occupancy during cellular differentiation

Valuing Urban Wetlands of the Gnangara Mound: A Hedonic Property Price Approach in Western Australia

Up to 60% of potable water supplied to Perth in Western Australia is extracted from the Gnangara mound. Many of the urban wetlands above the Mound are groundwater-dependent. Excessive groundwater extraction and climate change have resulted in a decline in water levels in the wetlands. This study estimates the value of urban wetlands in three local government districts in the Perth metropolitan region using the hedonic property price approach. Preliminary results found that proximity to wetlands influences the sales prices of properties. The marginal implicit price of reducing the distance to the nearest wetland by 1 metre, evaluated at the mean sales value, is AU$463. If there is more than one wetland within 1.5 kilometres of a property, the second wetland will help increase the property price by AU$6,081. For a 50 ha wetland, we estimate the total premium of on sales due to wetland proximity is AU$220 million, based on average property characteristics and medium house density. These results will help inform policy makers and land developers on the value of conserving existing urban wetlands, creating new wetland areas and urbanising rural wetlands.groundwater, housing development, aquifer, marginal implicit price, Land Economics/Use,

Seasonal Climate Forecasts and Risk Management Among Georgia Farmers

Recent increases in the scientific robustness of seasonal climate forecasts have not led to substantial changes in farmers’ risk management strategies of actors, largely because there is poor integration of scientific forecasting into farmers’ decision-making processes. The goal of the research presented here is to explore the potentials and constraints for farmers’ application of seasonal climate forecasts through an analysis of the cultural contexts of their decision-making and information use. Semi-structured interviews were conducted with 38 farmers in southern Georgia, examining their approaches, risk-management, to livelihood goals and strategies, and interactions with weather and climate information. Findings indicate that farmers’ management of risks associated with climate variability is embedded within a broad array of social factors, including subjective construction of social and personal identities, goals, and values. These cultural contexts affect the ways that farmers interpret and might apply seasonal climate forecasts to agricultural decisions. These findings indicate that, rather than simply acting as a technical information input, seasonal climate forecasts and forecasters must gradually work theirway into farmers’ trusted social networks before their potential as risk management tools will be realized. Furthermore, while seeking to produce scientific information to support farmers’ adaptive practices, scientists themselves must adapt their own practices to better fit a coproduction of knowledge approach

Uranium leaching from contaminated soil utilizing rhamnolipid, EDTA, and citric acid

Biosurfactants have recently gained attention as "green" agents that can be used to enhance the remediation of heavy metals and some organic matter in contaminated soils. The overall objective of this paper was to investigate rhamnolipid, a microbial produced biosurfactant, and its ability to leach uranium present in contaminated soil from an abandoned mine site. Soil samples were collected from two locations in northern Arizona: Cameron (site of open pit mining) and Leupp (control-no mining). The approach taken was to first determine the total uranium content in each soil using a hydrofluoric acid digestion, then comparing the amount of metal removed by rhamnolipid to other chelating agents EDTA and citric acid, and finally determining the amount of soluble metal in the soil matrix using a sequential extraction. Results suggested a complex system for metal removal from soil utilizing rhamnolipid. It was determined that rhamnolipid at a concentration of 150 mu M was as effective as EDTA but not as effective as citric acid for the removal of soluble uranium. However, the rhamnolipid was only slightly better at removing uranium from the mining soil compared to a purified water control. Overall, this study demonstrated that rhamnolipid ability to remove uranium from contaminated soil is comparable to EDTA and to a lesser extent citric acid, but, for the soils investigated, it is not significantly better than a simple water wash

A Phase Lag between Disk and Corona in GRMHD Simulations of Precessing Tilted Accretion Disks

In the course of its evolution, a black hole (BH) accretes gas from a wide range of directions. Given a random accretion event, the typical angular momentum of an accretion disc would be tilted by $\sim$60$^\circ$ relative to the BH spin. Misalignment causes the disc to precess at a rate that increases with BH spin and tilt angle. We present the first general-relativistic magnetohydrodynamic (GRMHD) simulations spanning a full precession period of highly tilted (60$^\circ$), moderately thin ($h/r=0.1$) accretion discs around a rapidly spinning ($a\simeq0.9$) BH. While the disc and jets precess in phase, we find that the corona, sandwiched between the two, lags behind by $\gtrsim 10^{\circ}$. For spectral models of BH accretion, the implication is that hard non-thermal (corona) emission lags behind the softer (disc) emission, thus potentially explaining some properties of the hard energy lags seen in Type-C low frequency quasi-periodic oscillations in X-Ray binaries. While strong jets are unaffected by this disc-corona lag, weak jets stall when encountering the lagging corona at distances $r \sim 100$ black hole radii. This interaction may quench large-scale jet formation.Comment: 5 pages, 4 figures, submitted to MNRAS, see YouTube playlist for 3D renderings: https://www.youtube.com/playlist?list=PLDO1oeU33GwmwOV_Hp9s7572JdU8JPSS

The welfare costs of urban outdoor water restrictions

Outdoor water restrictions are usually implemented as bans on a particular type of watering technology (sprinklers), which allow households to substitute for labour-intensive (hand-held) watering. This paper presents a household production model approach to analysing the impact of sprinkler restrictions on consumer welfare and their efficacy as a demand management tool. Central to our empirical analysis is an experimentally derived production function which describes the relationship between irrigation and lawn quality. We demonstrate that for a typical consumer complete sprinkler bans may be little more effective than milder restrictions policies, but are substantially more costly to the household.household model, urban water demand, urban water restrictions, Resource /Energy Economics and Policy,