Microarrays have proven to be a useful and high-throughput method to provide targeted DNA sequence information for up to many thousands of specific genetic regions in a single test. A microarray consists of multiple DNA oligonucleotide probes that, under high stringency conditions, hybridize only to specific complementary nucleic acid sequences (targets). A fluorescent signal indicates the presence and, in many cases, the abundance of genetic regions of interest. In this chapter we will look at how microarrays are used in microbial ecology, especially with the recent increase in microbial community DNA sequence data. Of particular interest to microbial ecologists, phylogenetic microarrays are used for the analysis of phylotypes in a community and functional gene arrays are used for the analysis of functional genes, and, by inference, phylotypes in environmental samples. A phylogenetic microarray that has been developed by the Andersen laboratory, the PhyloChip, will be discussed as an example of a microarray that targets the known diversity within the 16S rRNA gene to determine microbial community composition. Using multiple, confirmatory probes to increase the confidence of detection and a mismatch probe for every perfect match probe to minimize the effect of cross-hybridization by non-target regions, the PhyloChip is able to …

The environmental condition called vacuum is created any time the pressure of a gas is reduced compared to atmospheric pressure. On earth we typically create a vacuum by connecting a pump capable of moving gas to a relatively leak free vessel. Through operation of the gas pump the number of gas molecules per unit volume is decreased within the vessel. As soon as one creates a vacuum natural forces (in this case entropy) work to restore equilibrium pressure; the practical effect of this is that gas molecules attempt to enter the evacuated space by any means possible. It is useful to think of vacuum in terms of a gas at a pressure below atmospheric pressure. In even the best vacuum vessels ever created there are approximately 3,500,000 molecules of gas per cubic meter of volume remaining inside the vessel. The lowest pressure environment known is in interstellar space where there are approximately four molecules of gas per cubic meter. Researchers are currently developing vacuum technology components (pumps, gauges, valves, etc.) using micro electro mechanical systems (MEMS) technology. Miniature vacuum components and systems will open the possibility for significant savings in energy cost and will open the doors to advances in …

This fact sheet discusses how to keep a home cool using natural ventilation, attic ventilation, mechanical ventilation, fans, whole-house fans, and evaporative or swamp coolers.

For better or worse, natural gas has become the fuel of choice for new power plants being built across the United States. According to the Energy Information Administration (EIA), natural gas-fired units account for nearly 90% of the total generating capacity added in the U.S. between 1999 and 2005 (EIA 2006b), bringing the nationwide market share of gas-fired generation to 19%. Looking ahead over the next decade, the EIA expects this trend to continue, increasing the market share of gas-fired generation to 22% by 2015 (EIA 2007a). Though these numbers are specific to the US, natural gas-fired generation is making similar advances in many other countries as well. A large percentage of the total cost of gas-fired generation is attributable to fuel costs--i.e., natural gas prices. For example, at current spot prices of around $7/MMBtu, fuel costs account for more than 75% of the levelized cost of energy from a new combined cycle gas turbine, and more than 90% of its operating costs (EIA 2007a). Furthermore, given that gas-fired plants are often the marginal supply units that set the market-clearing price for all generators in a competitive wholesale market, there is a direct link between natural gas prices and wholesale …

This is the Newsletter for DOE Biofuels Program. Articles are presented on collection and use of corn stover for bioethanol production, the state workshop program on ethanol, and a subcontract to Genencor for improvement of cellulase enzyme production.

Fact sheet for homeowners and contractors on how to supply hot water in the home while saving energy.

Sulfate reducing bacteria are physiologically important given their nearly ubiquitous presence and have important applications in the areas of bioremediation and bioenergy. This chapter provides details on the steps used for homologous-recombination mediated chromosomal manipulation of Desulfovibrio vulgaris Hildenborough, a well-studied sulfate reducer. More specifically, we focus on the implementation of a 'parts' based approach for suicide vector assembly, important aspects of anaerobic culturing, choices for antibiotic selection, electroporation-based DNA transformation, as well as tools for screening and verifying genetically modified constructs. These methods, which in principle may be extended to other sulfate-reducing bacteria, are applicable for functional genomics investigations, as well as metabolic engineering manipulations.

Crosswell seismic acquisition provides an ideal geometry for monitoring travel time changes in the subsurface. Analysis of delay time in terms of a characteristic frequency allows us to estimate optimal acquisition parameters (frequency and distance). We have deployed standard data acquisition equipment for continuous monitoring of crosswell travel time in two separate field experiments, with well spacing of 3 and 30 m. The acquisition hardware used for the field experiments is described, along with environmental effects (such as temperature) that influence the measurements. Two field experiments are described that correlate changes in travel time (and therefore velocity) with changes in barometric pressure. The results from the two field sites show a pressure sensitivity for velocity of 10{sup -6}/Pa to 10{sup -8}/Pa.

With the advent of massively parallel computer systems, scientists are now able to simulate complex phenomena (e.g., explosions of a stars). Such scientific simulations typically generate large-scale data sets over the spatio-temporal space. Unfortunately, the sheer sizes of the generated data sets make efficient exploration of them impossible. Constructing queriable statistical models is an essential step in helping scientists glean new insight from their computer simulations. We define queriable statistical models to be descriptive statistics that (1) summarize and describe the data within a user-defined modeling error, and (2) are able to answer complex range-based queries over the spatiotemporal dimensions. In this chapter, we describe systems that build queriable statistical models for large-scale scientific simulation data sets. In particular, we present our Ad-hoc Queries for Simulation (AQSim) infrastructure, which reduces the data storage requirements and query access times by (1) creating and storing queriable statistical models of the data at multiple resolutions, and (2) evaluating queries on these models of the data instead of the entire data set. Within AQSim, we focus on three simple but effective statistical modeling techniques. AQSim's first modeling technique (called univariate mean modeler) computes the ''true'' (unbiased) mean of systematic partitions of the data. AQSim's …

Arsenic is a naturally occurring trace element that poses a threat to human and ecosystem health, particularly when incorporated into food or water supplies. The greatest risk imposed by arsenic to human health results from contamination of drinking water, for which the World Health Organization recommends a maximum limit of 10 {micro}g L{sup -1}. Continued ingestion of drinking water having hazardous levels of arsenic can lead to arsenicosis and cancers of the bladder, skin, lungs and kidneys. Unfortunately, arsenic tainted drinking waters are a global threat and presently having a devastating impact on human health within Asia. Nearly 100 million people, for example, are presently consuming drinking water having arsenic concentrations exceeding the World Health Organization's recommended limit (Ahmed et al., 2006). Arsenic contamination of the environment often results from human activities such as mining or pesticide application, but recently natural sources of arsenic have demonstrated a devastating impact on water quality. Arsenic becomes problematic from a health perspective principally when it partitions into the aqueous rather than the solid phase. Dissolved concentrations, and the resulting mobility, of arsenic within soils and sediments are the combined result of biogeochemical processes linked to hydrologic factors. Processes favoring the partitioning of As …

An overview of the U.S. Department of Energy Office of Codes and Standards programs to establish minimum efficiency codes, standards, and guidelines for reduced energy use and lower operating costs in U.S. building components.

An overview of the Energy Star program sponsored by the U.S. Department of Energy and the Environmental Protection Agency

An overview of the voluntary network of community partnerships joined with the US Department of Energy to improve the energy efficiency of their communities buildings.

An overview of the U.S. Department of Energy Office of State and Community Programs activities and partnership approaches.

Cometabolic bioremediation is probably the most under appreciated bioremediation strategy currently available. Cometabolism strategies stimulate only indigenous microbes with the ability to degrade the contaminant and cosubstrate e.g. methane, propane, toluene and others. This highly targeted stimulation insures that only those microbes that can degrade the contaminant are targeted, thus reducing amendment costs, well and formation plugging, etc. Cometabolic bioremediation has been used on some of the most recalcitrant contaminants, e.g. PCE, TCE, MTBE, TNT, dioxane, atrazine, etc. Methanotrophs have been demonstrated to produce methane monooxygense, an oxidase that can degrade over 300 compounds. Cometabolic bioremediation also has the advantage of being able to degrade contaminants to trace concentrations, since the biodegrader is not dependent on the contaminant for carbon or energy. Increasingly we are finding that in order to protect human health and the environment that we must remediate to lower and lower concentrations, especially for compounds like endocrine disrupters, thus cometabolism may be the best and maybe the only possibility that we have to bioremediate some contaminants.

This is a report on the comebiotic bioremediation which is the most under-appreciated strategy currently available.

Houses built by Pulte Homes as part of DOE's Building America program in Las Vegas, Nevada, save money for the homeowners by reducing electric air conditioning costs and gas heating costs with little or no additional investment. And, the houses have better indoor air quality than typical new construction.

The interaction of metal ions and oxyanions with nanoscale mineral phases has not yet been extensively studied despite the increased recognition of their prevalence in natural systems as a significant component of geomedia. A combination of macroscopic uptake studies to investigate the adsorption behavior of As(V), Cu(II), Hg(II), and Zn(II) onto nanoparticulate goethite ({alpha}-FeOOH) as a function of aging time at elevated temperature (75 C) and synchrotron-based X-ray studies to track changes in both the sorption mode and the rate of nanoparticle growth reveal the effects that uptake has on particle growth. Metal(loid) species which sorb quickly to the iron oxyhydroxide particles (As(V), Cu(II)) appear to passivate the particle surface, impeding the growth of the nanoparticles with progressive aging; in contrast, species that sorb more slowly (Hg(II), Zn(II)) have considerably less impact on particle growth. Progressive changes in the speciation of these particular metals with time suggest shifts in the mode of metal uptake with time, possibly indicating structural incorporation of the metal(loid) into the nanoparticle; this is supported by the continued increase in uptake concomitant with particle growth, implying that metal species may transform from surface-sorbed species to more structurally incorporated forms. This type of incorporation would have implications …

As concerns regarding increasing energy prices, global warming and renewable resources continue to grow, so has scientific discovery into agricultural biomass conversion. Plant Biomass Conversion addresses both the development of plant biomass and conversion technology, in addition to issues surrounding biomass conversion, such as the affect on water resources and soil sustainability. This book also offers a brief overview of the current status of the industry and examples of production plants being used in current biomass conversion efforts.

Inertial confinement fusion (ICF) has progressed from the detonation of large-scale fusion explosions initiated by atomic bombs in the early 1950s to final preparations for initiating small-scale fusion explosions with giant lasers. The next major step after ignition will be development of high performance targets that can be initiated with much smaller, lower cost lasers. In the 21st century and beyond, ICF's grand challenge is to develop practical power plants that generate low cost, clean, inexhaustible fusion energy. In this chapter, I first describe the origin in 1960-61 of ICF target concepts, early speculations on laser driven 'Thermonuclear Engines' for power production and rocket propulsion, and encouraging large-scale nuclear explosive experiments conducted in 1962. Next, I recall the 40-year, multi-billion dollar ignition campaign - to develop a matched combination of sufficiently high-performance implosion lasers and sufficiently stable targets capable of igniting small fusion explosions. I conclude with brief comments on the NIF ignition campaign and very high-performance targets, and speculations on ICF's potential in a centuries-long Darwinian competition of future energy systems. My perspectives in this chapter are those of a nuclear explosive designer, optimistic proponent of ICF energy, and Livermore Laboratory leader. The perspectives of Livermore's post 1970 laser …

Measurements of circular dichroism (CD) in the UV and vacuum UV have used photoelastic modulators (PEMs) for high sensitivity (to about 10{sup -6}). While a simple technique for wavelength calibration of the PEMs has been used with good results, several features of these calibration curves have not been understood. The authors have calibrated a calcium fluoride PEM and a lithium fluoride PEM using the National Synchrotron Light Source (NSLS) at Brookhaven National Laboratory as a light source. These experiments showed calibration graphs that are linear bit do not pass through the graph origin. A second ''multiple pass'' experiment with laser light of a single wavelength, performed on the calcium fluoride PEM, demonstrates the linearity of the PEM electronics. This implies that the calibration behavior results from intrinsic physical properties of the PEM optical element material. An algorithm for generating calibration curves for calcium fluoride and lithium fluoride PEMs has been developed. The calibration curves for circular dichroism measurement for the two PEMs investigated in this study are given as examples.

Sulfate, one of the inorganic constituents that could be present in the nuclear waste repository, forms complexes with U(VI) and affects its migration in the environment. Results show that the complexation of U(VI) with sulfate is enhanced by the increase in temperature. The effect of temperature on the complexation and speciation of U(VI) in sulfate solutions is discussed.

Even on small boilers, the prevention of scale formation can produce substantial energy savings. Scale creates a problem because it typically possesses a thermal conductivity an order of magnitude less than the corresponding value of bare steel.

Fact sheet for homeowners and contractors that explains the energy savings potential of efficient appliances, how to purchase them, and how to maintain them.