High-throughput isolation and mapping of C. elegans mutants susceptible to pathogen infection.

We present a novel strategy that uses high-throughput methods of isolating and mapping C. elegans mutants susceptible to pathogen infection. We show that C. elegans mutants that exhibit an enhanced pathogen accumulation (epa) phenotype can be rapidly identified and isolated using a sorting system that allows automation of the analysis, sorting, and dispensing of C. elegans by measuring fluorescent bacteria inside the animals. Furthermore, we validate the use of Amplifluor as a new single nucleotide polymorphism (SNP) mapping technique in C. elegans. We show that a set of 9 SNPs allows the linkage of C. elegans mutants to a 5-8 megabase sub-chromosomal region.

ANALYSIS AND SIMULATION OF ENERGY USE AND COST AT A MUNICIPAL WASTEWATER TREATMENT PLANT

The cost of electricity, a major operating cost of municipal wastewater treatment plants, is related to influent flow rate, power price, and power load. With knowledge of inflow and price patterns, plant operators can manage processes to reduce electricity costs. Records of influent flow, power price, and load are evaluated for Blue Plains Advanced Wastewater Treatment Plant. Diurnal and seasonal trends are analyzed. Power usage is broken down among treatment processes. A simulation model of influent pumping, a large power user, is developed. It predicts pump discharge and power usage based on wet-well level. Individual pump characteristics are tested in the plant. The model accurately simulates plant inflow and power use for two pumping stations [R2 = 0.68, 0.93 (inflow), R2 =0.94, 0.91(power)]. Wet-well stage-storage relationship is estimated from data. Time-varying wet-well level is added to the model. A synthetic example demonstrates application in managing pumps to reduce electricity cost.

High-coverage sequencing and annotated assemblies of the budgerigar genome.

BACKGROUND: Parrots belong to a group of behaviorally advanced vertebrates and have an advanced ability of vocal learning relative to other vocal-learning birds. They can imitate human speech, synchronize their body movements to a rhythmic beat, and understand complex concepts of referential meaning to sounds. However, little is known about the genetics of these traits. Elucidating the genetic bases would require whole genome sequencing and a robust assembly of a parrot genome. FINDINGS: We present a genomic resource for the budgerigar, an Australian Parakeet (Melopsittacus undulatus) -- the most widely studied parrot species in neuroscience and behavior. We present genomic sequence data that includes over 300× raw read coverage from multiple sequencing technologies and chromosome optical maps from a single male animal. The reads and optical maps were used to create three hybrid assemblies representing some of the largest genomic scaffolds to date for a bird; two of which were annotated based on similarities to reference sets of non-redundant human, zebra finch and chicken proteins, and budgerigar transcriptome sequence assemblies. The sequence reads for this project were in part generated and used for both the Assemblathon 2 competition and the first de novo assembly of a giga-scale vertebrate genome utilizing PacBio single-molecule sequencing. CONCLUSIONS: Across several quality metrics, these budgerigar assemblies are comparable to or better than the chicken and zebra finch genome assemblies built from traditional Sanger sequencing reads, and are sufficient to analyze regions that are difficult to sequence and assemble, including those not yet assembled in prior bird genomes, and promoter regions of genes differentially regulated in vocal learning brain regions. This work provides valuable data and material for genome technology development and for investigating the genomics of complex behavioral traits.

Modelling high particulate matter and ozone episodes in the Trans-Manche region

There is concern in the Cross-Channel region of Nord-Pas-de-Calais (France) and Kent (Great Britain), regarding the extent of atmospheric pollution detected in the area from emitted gaseous (VOC, NOx, S02)and particulate substances. In particular, the air quality of the Cross-Channel or "Trans-Manche" region is highly affected by the heavily industrial area of Dunkerque, in addition to transportation sources linked to cross-channel traffic in Kent and Calais, posing threats to the environment and human health. In the framework of the cross-border EU Interreg IIIA activity, the joint Anglo-French project, ATTMA, has been commissioned to study Aerosol Transport in the Trans-Manche Atmosphere. Using ground monitoring data from UK and French networks and with the assistance of satellite images the project aims to determine dispersion patterns. and identify sources responsible for the pollutants. The findings of this study will increase awareness and have a bearing on future air quality policy in the region. Public interest is evident by the presence of local authorities on both sides of the English Channel as collaborators. The research is based on pollution transport simulations using (a) Lagrangian Particle Dispersion (LPD) models, (b) an Eulerian Receptor Based model. This paper is concerned with part (a), the LPD Models. Lagrangian Particle Dispersion (LPD) models are often used to numerically simulate the dispersion of a passive tracer in the planetary boundary layer by calculating the Lagrangian trajectories of thousands of notional particles. In this contribution, the project investigated the use of two widely used particle dispersion models: the Hybrid Single Particle Lagrangian Integrated Trajectory (HYSPLIT) model and the model FLEXPART. In both models forward tracking and inverse (or·. receptor-based) modes are possible. Certain distinct pollution episodes have been selected from the monitor database EXPER/PF and from UK monitoring stations, and their likely trajectory predicted using prevailing weather data. Global meteorological datasets were downloaded from the ECMWF MARS archive. Part of the difficulty in identifying pollution sources arises from the fact that much of the pollution outside the monitoring area. For example heightened particulate concentrations are to originate from sand storms in the Sahara, or volcanic activity in Iceland or the Caribbean work identifies such long range influences. The output of the simulations shows that there are notable differences between the formulations of and Hysplit, although both models used the same meteorological data and source input, suggesting that the identification of the primary emissions during air pollution episodes may be rather uncertain.

International perspectives on energy policy and the role of nuclear power

In this book, expert energy economists assess the energy policy of thirty-one countries and the role of nuclear power. For many years the shock of Chernobyl took nuclear power off the agenda in most countries. Intense public relations activities by the industry, increasing evidence of climate change and failures to effectively reduce greenhouse gas emissions, have brought nuclear power issues back to the forefront of policy discussion in the nuclear renaissance countries. But some countries are just not prepared to go in that direction and, indeed, are still divesting themselves of their nuclear legacy, the nuclear phase-out countries. And how are nuclear issues being approached in the industrializing countries? An in-depth country-by-country analysis is presented within this framework. Out of such an analysis emerge thematic discussions on, among others, strategy in energy policy; nuclear plant safety, the impacts of nuclear accidents; the adequacy of nuclear power expertise. [Source: publisher's product description].

Late winter under ice pelagic microbial communities in the high Arctic Ocean and the impact of short-term exposure to elevated CO2 levels

Polar Oceans are natural CO2 sinks because of the enhanced solubility of CO2 in cold water. The Arctic Ocean is at additional risk of accelerated ocean acidification (OA) because of freshwater inputs from sea ice and rivers, which influence the carbonate system. Winter conditions in the Arctic are of interest because of both cold temperatures and limited CO2 venting to the atmosphere when sea ice is present. Earlier OA experiments on Arctic microbial communities conducted in the absence of ice cover, hinted at shifts in taxa dominance and diversity under lowered pH. The Catlin Arctic Survey provided an opportunity to conduct in situ, under-ice, OA experiments during late Arctic winter. Seawater was collected from under the sea ice off Ellef Ringnes Island, and communities were exposed to three CO2 levels for 6 days. Phylogenetic diversity was greater in the attached fraction compared to the free-living fraction in situ, in the controls and in the treatments. The dominant taxa in all cases were Gammaproteobacteria but acidification had little effect compared to the effects of containment. Phylogenetic net relatedness indices suggested that acidification may have decreased the diversity within some bacterial orders, but overall there was no clear trend. Within the experimental communities, alkalinity best explained the variance among samples and replicates, suggesting subtle changes in the carbonate system need to be considered in such experiments. We conclude that under ice communities have the capacity to respond either by selection or phenotypic plasticity to heightened CO2 levels over the short term.

Energy production and ecosystem services

Ecosystems provide a range of goods and services that contribute toward human well-being. It is increasingly recognized that factors such as a growing and increasingly affluent world population, coupled with increased globalization of trade, are significantly influencing the delivery of ecosystem goods and services. This chapter argues that future energy policy must be designed based on a broad set of environmental and social considerations that examine the national and international implications of each energy technology. This approach ensures a more holistic overview of the costs and benefits associated with energy production, allowing society to make more informed choices about their futures, including how their energy is sourced, generated, and delivered.

Energy systems and their impacts on marine ecosystem services

Global warming and its link to the burning of fossil fuels has prompted many governments around the world to set legally binding greenhouse gas reduction targets which are to be partially realised through a stronger reliance on renewable (e.g. wind) and other lower carbon (i.e. natural gas and nuclear) energy commodities. The marine environment will play a key role in hosting or supporting these new energy strategies. However, it is unclear how the construction, operation and eventual decommissioning of these energy systems, and their related infrastructure, will impact the marine environment, the ecosystem services (i.e. cultural, regulating, provisioning and supporting) and in turn the benefits it provides for human well-being. This uncertainty stems from a lack of research that has synthesised into a common currency the various effects of each energy sector on marine ecosystems and the benefits humans derive from it. To address this gap, the present study reviews existing ecosystem impact studies for offshore components of nuclear, offshore wind, offshore gas and offshore oil sectors and translates them into the common language of ecosystem service impacts that can be used to evaluate current policies. The results suggest that differences exist in the way in which energy systems impact ecosystem services, with the nuclear sector having a predominantly negative impact on cultural ecosystem services; oil and gas a predominately negative impact on cultural, provisioning, regulating and supporting ecosystem services; while wind has a mix of impacts on cultural, provisioning and supporting services and an absence of studies for regulating services. This study suggests that information is still missing with regard to the full impact of these energy sectors on specific types of benefits that humans derive from the marine environment and proposes possible areas of targeted research.

The CO2 microalgae biorefinery: high value products and biofuels using halophilic microalgae in the “D-Factory”

Fuel-only algal systems are not economically feasible because yields are too low and costs too high for producing microalgal biomass compared to using agricultural residues e.g. straw. Biorefineries which integrate biomass conversion processes and equipment to produce fuels, power and chemicals from biomass, offer a solution. The CO2 microalgae biorefinery (D-Factory) is a 10 million Euro FP7-funded project which will cultivate the microalga Dunaliella in highly saline non-potable waters in photobioreactors and open raceways and apply biorefinery concepts and European innovations in biomass processing technologies to develop a basket of compounds from Dunaliella biomass, including the high value nutraceutical, β-carotene, and glycerol. Glycerol now finds markets both as a green chemical intermediate and as a biofuel in CHP applications as a result of novel combustion technology. Driving down costs by recovering the entire biomass of Dunaliella cells from saline cultivation water poses one of the many challenges for the D-Factory because Dunaliella cells are both motile, and do not possess an external cell wall, making them highly susceptible to cell rupture. Controlling expression of desired metabolic pathways to deliver the desired portfolio of compounds flexibly and sustainably to meet market demand is another. The first prototype D-Factory in Europe will be operational in 48 months, and will serve as a robust manifestation of the business case for global investment in algae biorefineries and in large-scale production of microalgae.