Correct biological timing in Arabidopsis requires multiple light-signaling pathways.

Circadian oscillators provide rhythmic temporal cues for a range of biological processes in plants and animals, enabling anticipation of the day/night cycle and enhancing fitness-associated traits. We have used engineering models to understand the control principles of a plant's response to seasonal variation. We show that the seasonal changes in the timing of circadian outputs require light regulation via feed-forward loops, combining rapid light-signaling pathways with entrained circadian oscillators. Linear time-invariant models of circadian rhythms were computed for 3,503 circadian-regulated genes and for the concentration of cytosolic-free calcium to quantify the magnitude and timing of regulation by circadian oscillators and light-signaling pathways. Bioinformatic and experimental analysis show that rapid light-induced regulation of circadian outputs is associated with seasonal rephasing of the output rhythm. We identify that external coincidence is required for rephasing of multiple output rhythms, and is therefore important in general phase control in addition to specific photoperiod-dependent processes such as flowering and hypocotyl elongation. Our findings uncover a fundamental design principle of circadian regulation, and identify the importance of rapid light-signaling pathways in temporal control.

The potential for thermal energy recovery from wastewater treatment works in Southern England

There is potential to extract energy from wastewater in a number of ways, including: kinetic energy using micro-hydro systems, chemical energy through the incineration of sludge, biomass energy from the biogas produced after anaerobic sludge digestion, and thermal energy as heat. This paper considers the last option and asks how much heat could be recovered under UK climatic conditions and can this heat be used effectively by wastewater treatment plants to reduce their carbon footprint? Four wastewater treatment sites in southern England are investigated and the available heat that can be recovered at those sites is quantified. Issues relating to the environmental, economic and practical constraints on how energy can be realistically recovered and utilised are discussed .The results show there is a definite possibility for thermal energy recovery with potential savings at some sites of up to 35,000 tonnes of total long-cycle carbon equivalent (fossil fuel) emissions per year being achievable. The paper also shows that the financial feasibility of three options for using the heat (either for district heating, sludge drying or thermophilic heating in sludge digestion processes) is highly dependant upon the current shadow price of carbon. Without the inclusion of the cost of carbon, the financial feasibility is significantly limited. An environmental constraint for the allowable discharge temperature of effluent after heat-extraction was found to be the major limitation to the amount of energy available for recovery. The paper establishes the true potential of thermal energy recovery from wastewater in English conditions and the economic feasibility of reducing the carbon footprint of wastewater treatment operations using this approach.

Bayesian correlated clustering to integrate multiple datasets.

MOTIVATION: The integration of multiple datasets remains a key challenge in systems biology and genomic medicine. Modern high-throughput technologies generate a broad array of different data types, providing distinct-but often complementary-information. We present a Bayesian method for the unsupervised integrative modelling of multiple datasets, which we refer to as MDI (Multiple Dataset Integration). MDI can integrate information from a wide range of different datasets and data types simultaneously (including the ability to model time series data explicitly using Gaussian processes). Each dataset is modelled using a Dirichlet-multinomial allocation (DMA) mixture model, with dependencies between these models captured through parameters that describe the agreement among the datasets. RESULTS: Using a set of six artificially constructed time series datasets, we show that MDI is able to integrate a significant number of datasets simultaneously, and that it successfully captures the underlying structural similarity between the datasets. We also analyse a variety of real Saccharomyces cerevisiae datasets. In the two-dataset case, we show that MDI's performance is comparable with the present state-of-the-art. We then move beyond the capabilities of current approaches and integrate gene expression, chromatin immunoprecipitation-chip and protein-protein interaction data, to identify a set of protein complexes for which genes are co-regulated during the cell cycle. Comparisons to other unsupervised data integration techniques-as well as to non-integrative approaches-demonstrate that MDI is competitive, while also providing information that would be difficult or impossible to extract using other methods.

Full cost accounting for the life cycle of coal.

Each stage in the life cycle of coal-extraction, transport, processing, and combustion-generates a waste stream and carries multiple hazards for health and the environment. These costs are external to the coal industry and are thus often considered "externalities." We estimate that the life cycle effects of coal and the waste stream generated are costing the U.S. public a third to over one-half of a trillion dollars annually. Many of these so-called externalities are, moreover, cumulative. Accounting for the damages conservatively doubles to triples the price of electricity from coal per kWh generated, making wind, solar, and other forms of nonfossil fuel power generation, along with investments in efficiency and electricity conservation methods, economically competitive. We focus on Appalachia, though coal is mined in other regions of the United States and is burned throughout the world.

The closed thorium-transuranic fuel cycle in reduced-moderation PWRs and BWRs

Multiple recycle of long-lived actinides has the potential to greatly reduce the required storage time for spent nuclear fuel or high level nuclear waste. This is generally thought to require fast reactors as most transuranic (TRU) isotopes have low fission probabilities in thermal reactors. Reduced-moderation LWRs are a potential alternative to fast reactors with reduced time to deployment as they are based on commercially mature LWR technology. Thorium (Th) fuel is neutronically advantageous for TRU multiple recycle in LWRs due to a large improvement in the void coefficient. If Th fuel is used in reduced-moderation LWRs, it appears neutronically feasible to achieve full actinide recycle while burning an external supply of TRU, with related potential improvements in waste management and fuel utilization. In this paper, the fuel cycle of TRU-bearing Th fuel is analysed for reduced-moderation PWRs and BWRs (RMPWRs and RBWRs). RMPWRs have the advantage of relatively rapid implementation and intrinsically low conversion ratios, which is desirable to maximize the TRU burning rate. However, it is challenging to simultaneously satisfy operational and fuel cycle constraints. An RBWR may potentially take longer to implement than an RMPWR due to more extensive changes from current BWR technology. However, the harder neutron spectrum can lead to favourable fuel cycle performance. A two-stage TRU burning cycle, where the first stage is Th-Pu MOX in a conventional PWR feeding a second stage continuous burn in RMPWR or RBWR, is technically reasonable, although it is more suitable for the RBWR implementation. In this case, the fuel cycle performance is relatively insensitive to the discharge burn-up of the first stage. © 2013 Elsevier Ltd. All rights reserved.