Implementation Plans for a Systems Microbiology and Extremophile Research Facility

Introduction Biological organisms long ago solved many problems for which scientists and engineers seek solutions. Microbes in particular offer an astonishingly diverse set of capabilities that can help revolutionize our approach to solving many important DOE problems. For example, photosynthetic organisms can generate hydrogen from light while simultaneously sequestering carbon. Others can produce enzymes that break down cellulose and other biomass to produce liquid fuels. Microbes in water and soil can capture carbon and store it in the earth and ocean depths. Understanding the dynamic interaction between living organisms and the environment is critical to predicting and mitigating the impacts of energy-production-related activities on the environment and human health. Collectively, microorganisms contain most of the biochemical diversity on Earth and they comprise nearly one-half of its biomass. They primary impact the planet by acting as catalysts of biogeochemical cycles; they capture light energy and fix CO2 in the worlds oceans, they degrade plant polymers and convert them to humus in soils, they weather rocks and facilitate mineral precipitation. Although the ability of selected microorganisms to participate in these processes is known, they rarely live in monoculture but rather function within communities. In spite of this, little is known about the composition of microbial communities and how individual species function within them. We lack an understanding of the nature of the individual organisms and their genes, how they interact to perform complex functions such as energy and materials exchange, how they sense and respond to their environment and how they evolve and adapt to environmental change. Understanding these aspects of microbes and their communities would be transformational with far-reaching impacts on climate, energy and human health. This knowledge would create a foundation for predicting their behavior and, ultimately, manipulating them to solve DOE problems. Recent advances in whole-genome sequencing for a variety of organisms and improvements in high-throughput instrumentation have contributed to a rapid transition of the biological research paradigm towards understanding biology at a systems level. As a result, biology is evolving from a descriptive to a quantitative, ultimately predictive science where the ability to collect and productively use large amounts of biological data is crucial. Understanding how the ensemble of proteins in cells gives rise to biological outcomes is fundamental to systems biology. These advances will require new technologies and approaches to measure and track the temporal and spatial disposition of proteins in cells and how networks of proteins and other regulatory molecules give rise to specific activities. The DOE has a strong interest in promoting the application of systems biology to understanding microbial function and this comprises a major focus of its Genomics:GTL program. A major problem in pursuing what has been termed “systems microbiology” is the lack of the facilities and infrastructure for conducting this new style of research. To solve this problem, the Genomics:GTL program has funded a number of large-scale research centers focused on either mission-oriented outcomes, such as bioenergy, or basic technologies, such as gene sequencing, high-throughput proteomics or the identification of protein complexes. Although these centers generate data that will be useful to the research community, their scientific goals are relatively narrow and are not designed to accommodate the general community need for advanced capabilities for systems microbiology research

A 20 Ghz Depolarization Experiment Using the ATS-6 Satellite

A depolarization experiment using the 20 GHz downlink from the ATS-6 satellite was described. The following subjects were covered: (1) an operational summary of the experiment, (2) a description of the equipment used with emphasis on improvements made to the signal processing receiver used with the ATS-5 satellite, (3) data on depolarization and attenuation in one snow storm and two rain storms at 45 deg elevation, (4) data on low angle propagation, (5) conclusions about depolarization on satellite paths, and (6) recommendations for the depolarization portion of the CTS experiment

A depolarization and attenuation experiment using the CTS satellite. Volume 1: Experiment description

An experiment for measuring precipitation attenuation and depolarization on the Communications Technology Satellite (CTS) 11.7 GHz downlink is described. Attenuation and depolarization of the signal received from the spacecraft is monitored on a 24 hour basis. Data is correlated with ground weather conditions. Theoretical models for millimeter wave propagation through rain are refined for maximum agreement with observed data. Techniques are developed for predicting and mimimizing the effects of rain scatter and depolarization on future satellite communication systems

Genomic islands of divergence in the Yellow Tang and the Brushtail Tang Surgeonfishes.

The current ease of obtaining thousands of molecular markers challenges the notion that full phylogenetic concordance, as proposed by phylogenetic species concepts, is a requirement for defining species delimitations. Indeed, the presence of genomic islands of divergence, which may be the cause, or in some cases the consequence, of speciation, precludes concordance. Here, we explore this issue using thousands of RAD markers on two sister species of surgeonfishes (Teleostei: Acanthuridae), Zebrasoma flavescens and Z. scopas, and several populations within each species. Species are readily distinguished based on their colors (solid yellow and solid brown, respectively), yet populations and species are neither distinguishable using mitochondrial markers (cytochrome c oxidase 1), nor using 5193 SNPs (pairwise Φst = 0.034). In contrast, when using outlier loci, some of them presumably under selection, species delimitations, and strong population structure follow recognized taxonomic positions (pairwise Φst = 0.326). Species and population delimitation differences based on neutral and selected markers are likely due to local adaptation, thus being consistent with the idea that these genomic islands of divergence arose as a consequence of isolation. These findings, which are not unique, raise the question of a potentially important pathway of divergence based on local adaptation that is only evident when looking at thousands of loci

Fabrication and magnetic properties of Fe nanostructures in anodic alumina membrane

Several Fe nanostructures with different lengths, diameters, and separations of the constituting magnetic components have been synthesized using anodized alumina membranes (AAMs) to understand the influence of these parameters on their magnetic properties. Fe nanostructures with high crystallinity and (110) orientation were synthesized by electrodeposition at room temperature in regular AAMs and mild-hard AAM (Mi-Ha AAM). Fe nanostructures with different aspect ratios (1:1, 1:10, and 1:75) in the form of nanodots, nanorods, or nanowires were synthesized in regular AAMs with the 100 nm interpore distance. Mi-Ha AAMs with two different pore sizes (70 and 120 nm) and 250 nm interpore distances were used to investigate the effect of the interactions and of the diameter of the wires on their magnetic behavior. Nearly linear magnetization characteristics with small coercivity, observed for Fe nanowires, suggest the magnetization rotation to be the predominant magnetization process for the field applied transverse to the wires. The anisotropy of the arrays was governed by the shape anisotropy of the magnetic objects with different aspect ratios. Reduced interactions between the nanowires grown in Mi-Ha AAMs resulted in enhancement of the average anisotropy. It is believed that due to difference in spin configuration, the increased diameter of the nanowires led to reduction in the coercivity in the case of the field applied along the wires

Physical Acoustics

Contains research objectives and reports on three research projects.U.S. Navy (Office of Naval Research) under Contract Nonr-1841(42

Transient x-ray diffraction used to diagnose shock compressed Si crystals on the Nova laser

Transient x-ray diffraction is used to record time-resolved information about the shock compression of materials. This technique has been applied on Nova shock experiments driven using a hohlraum x-ray drive. Data were recorded from the shock release at the free surface of a Si crystal, as well as from Si at an embedded ablator/Si interface. Modeling has been done to simulate the diffraction data incorporating the strained crystal rocking curves and Bragg diffraction efficiencies. Examples of the data and post-processed simulations are presented

Insect-mediated cross-pollination in soybean [Glycine max (L.) Merrill] : I. Agronomic performance

In soybean, manual cross-pollination to produce large quantities of F1 hybrid seed for yield trials is difficult and time-consuming. Conversely, insect-mediated cross-pollination has been shown to produce large quantities of hybrid seed in soybean and could facilitate the identification of heterotic patterns. The objective of our study was: (1) evaluate F1hybrid soybean plants from single crosses for yield and agronomic traits over several environments and (2) compare hybrid performance of the single crosses to lines developed from three-way crosses and backcrosses. In 2003, F1 seed of single-crosses and their parent lines were evaluated in replicated experiments at three locations. Also in 2003, three-way crosses, and BC1F1 seed were produced. In 2004, three-way crosses, BC1F1 crosses, and their parent lines were evaluated at one location. High-parent heterosis (HPH) in single-crosses for grain yield ranged from −41.11% to +11.19%; for protein content from −4.34% to +3.53%, and for oil content from −13.22% to −0.84%. In three-way crosses, HPH for yield ranged from −25.21% to −4.50%, for protein from −2.72% to +1.92%, and for oil from −5.87% to −1.20%. For BC1F1 crosses, HPH for yield ranged from −15.65% to +41.97%, for protein from −2.57% to +1.69%, and for oil from −2.47% to +2.22%. Although positive heterosis levels were observed across all populations tested to determine the economic feasibility it is imperative that more tests of more cross-combinations be evaluated in replicated environments. Extensive research in different environments must be conducted to determine what parental combinations will produce the highest heterosis levels, and to develop criteria for selecting the parents with the best combining ability. This will be important to maximize agronomic performance that can economically justify the use of hybrids in soybean production