Showing papers by "Oak Ridge National Laboratory published in 2003"
University of California, Berkeley1, Goddard Space Flight Center2, Paul Scherrer Institute3, Lawrence Berkeley National Laboratory4, Oak Ridge National Laboratory5, ETH Zurich6, Montana State University7, University of Alabama in Huntsville8, University of Glasgow9, Rice University10, Open University11
TL;DR: RHESSI as discussed by the authors is a Principal Investigator (PI) mission, where the PI is responsible for all aspects of the mission except the launch vehicle, and is designed to investigate particle acceleration and energy release in solar flares, through imaging and spectroscopy of hard X-ray/gamma-ray continua emitted by energetic electrons, and of gamma-ray lines produced by energetic ions.
Abstract: RHESSI is the sixth in the NASA line of Small Explorer (SMEX) missions and the first managed in the Principal Investigator mode, where the PI is responsible for all aspects of the mission except the launch vehicle. RHESSI is designed to investigate particle acceleration and energy release in solar flares, through imaging and spectroscopy of hard X-ray/gamma-ray continua emitted by energetic electrons, and of gamma-ray lines produced by energetic ions. The single instrument consists of an imager, made up of nine bi-grid rotating modulation collimators (RMCs), in front of a spectrometer with nine cryogenically-cooled germanium detectors (GeDs), one behind each RMC. It provides the first high-resolution hard X-ray imaging spectroscopy, the first high-resolution gamma-ray line spectroscopy, and the first imaging above 100 keV including the first imaging of gamma-ray lines. The spatial resolution is as fine as ~ 2.3 arc sec with a full-Sun (≳ 1°) field of view, and the spectral resolution is ~ 1–10 keV FWHM over the energy range from soft X-rays (3 keV) to gamma-rays (17 MeV). An automated shutter system allows a wide dynamic range (> 107) of flare intensities to be handled without instrument saturation. Data for every photon is stored in a solid-state memory and telemetered to the ground, thus allowing for versatile data analysis keyed to specific science objectives. The spin-stabilized (~ 15 rpm) spacecraft is Sun-pointing to within ~ 0.2° and operates autonomously. RHESSI was launched on 5 February 2002, into a nearly circular, 38° inclination, 600-km altitude orbit and began observations a week later. The mission is operated from Berkeley using a dedicated 11-m antenna for telemetry reception and command uplinks. All data and analysis software are made freely and immediately available to the scientific community.
1,991 citations
TL;DR: The experience with selecting perennial grasses for bioenergy production in both the US and Europe is summarized, and an overview of the characteristics and requirements of the four most investigated perennial rhizomatous grasses; switchgrass, miscanthus, reed canarygrass and giant reed are given.
Abstract: Perennial grasses display many beneficial attributes as energy crops, and there has been increasing interest in their use in the US and Europe since the mid-1980s. In the US, the Herbaceous Energy Crops Research Program (HECP), funded by the US Department of Energy (DOE), was established in 1984. After evaluating 35 potential herbaceous crops of which 18 were perennial grasses it was concluded that switchgrass (Panicum virgatum) was the native perennial grass which showed the greatest potential. In 1991, the DOE's Bioenergy Feedstock Development Program (BFDP), which evolved from the HECP, decided to focus research on a “model” crop system and to concentrate research resources on switchgrass, in order to rapidly attain its maximal output as a biomass crop. In Europe, about 20 perennial grasses have been tested and four perennial rhizomatous grasses (PRG), namely miscanthus (Miscanthus spp.), reed canarygrass (Phalaris arundinacea), giant reed (Arundo donax) and switchgrass (Panicum virgatum) were chosen for more extensive research programs. Reed canarygrass and giant reed are grasses with the C3 photosynthetic pathway, and are native to Europe. Miscanthus, which originated in Southeast Asia, and switchgrass, native to North America, are both C4 grasses. These four grasses differ in their ecological/climatic demands, their yield potentials, biomass characteristics and crop management requirements. Efficient production of bioenergy from such perennial grasses requires the choice of the most appropriate grass species for the given ecological/climatic conditions. In temperate and warm regions, C4 grasses outyield C3 grasses due to their more efficient photosynthetic pathway. However, the further north perennial grasses are planted, the more likely cool season grasses are to yield more than warm season grasses. Low winter temperatures and short vegetation periods are major limits to the growth of C4 grasses in northern Europe. With increasing temperatures towards central and southern Europe, the productivity of C4 grasses and therefore their biomass yields and competitiveness increase.
Since breeding of and research on perennial rhizomatous grasses (PRG) is comparatively recent, there is still a significant need for further development. Some of the given limitations, like insufficient biomass quality or the need for adaption to certain ecological/climatic zones, may be overcome by breeding varieties especially for biomass production. Furthermore, sure and cost-effective establishment methods for some of the grasses, and effective crop production and harvest methods, have yet to be developed.
This review summarizes the experience with selecting perennial grasses for bioenergy production in both the US and Europe, and gives an overview of the characteristics and requirements of the four most investigated perennial rhizomatous grasses; switchgrass, miscanthus, reed canarygrass and giant reed.
1,318 citations
TL;DR: In this article, a review of nanostructures of functional oxides, including nanobelts, nanowires, nanosheets, and nanodiskettes, has been presented.
Abstract: Functional oxides are the fundamentals of smart devices. This article reviews novel nanostructures of functional oxides, including nanobelts, nanowires, nanosheets, and nanodiskettes, that have been synthesized in the authors’ laboratory. Among the group of ZnO, SnO2, In2O3, Ga2O3, CdO, and PbO2, which belong to different crystallographic systems and structures, a generic nanobelt structure has been synthesized. The nanobelts are single crystalline and dislocation-free, and their surfaces are atomically flat. The oxides are semiconductors, and have been used for fabrication of nanodevices such as field-effect transistors and gas sensors. Taking SnO2 and SnO as examples, other types of novel nanostructures are illustrated. Their growth, phase transformation, and stability are discussed. The nanobelts and related nanostructures are a unique group that is likely to have important applications in electronic, optical, sensor, and optoelectronic nanodevices.
1,139 citations
TL;DR: The genomes of two Prochlorococcus strains that span the largest evolutionary distance within the Pro chlorococcus lineage are compared and reveal dynamic genomes that are constantly changing in response to myriad selection pressures.
Abstract: The marine unicellular cyanobacterium Prochlorococcus is the smallest-known oxygen-evolving autotroph1. It numerically dominates the phytoplankton in the tropical and subtropical oceans2,3, and is responsible for a significant fraction of global photosynthesis. Here we compare the genomes of two Prochlorococcus strains that span the largest evolutionary distance within the Prochlorococcus lineage4 and that have different minimum, maximum and optimal light intensities for growth5. The high-light-adapted ecotype has the smallest genome (1,657,990 base pairs, 1,716 genes) of any known oxygenic phototroph, whereas the genome of its low-light-adapted counterpart is significantly larger, at 2,410,873 base pairs (2,275 genes). The comparative architectures of these two strains reveal dynamic genomes that are constantly changing in response to myriad selection pressures. Although the two strains have 1,350 genes in common, a significant number are not shared, and these have been differentially retained from the common ancestor, or acquired through duplication or lateral transfer. Some of these genes have obvious roles in determining the relative fitness of the ecotypes in response to key environmental variables, and hence in regulating their distribution and abundance in the oceans.
1,106 citations
TL;DR: In this paper, a review focusing on promising candidate materials (such as GaN, GaP and ZnO) is presented, where the introduction of Mn into these and other materials under the right conditions is found to produce ferromagnetism near or above room temperature.
Abstract: Recent advances in the theory and experimental realization of ferromagnetic semiconductors give hope that a new generation of microelectronic devices based on the spin degree of freedom of the electron can be developed. This review focuses primarily on promising candidate materials (such as GaN, GaP and ZnO) in which there is already a technology base and a fairly good understanding of the basic electrical and optical properties. The introduction of Mn into these and other materials under the right conditions is found to produce ferromagnetism near or above room temperature. There are a number of other potential dopant ions that could be employed (such as Fe, Ni, Co, Cr) as suggested by theory [see, for example, Sato and Katayama-Yoshida, Jpn. J. Appl. Phys., Part 2 39, L555 (2000)]. Growth of these ferromagnetic materials by thin film techniques, such as molecular beam epitaxy or pulsed laser deposition, provides excellent control of the dopant concentration and the ability to grow single-phase layers. T...
968 citations
TL;DR: The first global synthesis of plant canopy leaf area index (LAI) measurements from more than 1000 published estimates representing ∼ 400 unique field sites was presented in this article, where the data provide input to terrestrial ecosystem and land-surface models, for evaluation of global remote sensing products, for comparison to field studies, and other applications.
Abstract: Aim We present the first global synthesis of plant canopy leaf area index (LAI) measurements from more than 1000 published estimates representing ∼ 400 unique field sites. LAI is a key variable for regional and global models of biosphereatmosphere exchanges of energy, carbon dioxide, water vapour, and other materials. Location The location is global, geographically distributed. Results Biomes with LAI values well represented in the literature included croplands, forests and plantations. Biomes not well represented were deserts, shrublands, tundra and wetlands. Nearly 40% of the records in the database were published in the past 10 years (1991‐2000), with a further 20% collected between 1981 and 1990. Mean ( ± SD) LAI, distributed between 15 biome classes, ranged from 1.3 ± 0.9 for deserts to 8.7 ± 4.3 for tree plantations, with temperate evergreen forests (needleleaf and broadleaf) displaying the highest average LAI (5.1‐6.7) among the natural terrestrial vegetation classes. Following a statistical outlier analysis, the global mean ( ± SD) LAI decreased from 5.2 (4.1) to 4.5 (2.5), with a maximum LAI of 18. Biomes with the highest LAI values were plantations > temperate evergreen forests > wetlands. Those with the lowest LAI values were deserts < grasslands < tundra. Mean LAI values for all biomes did not differ statistically by the methodology employed. Direct and indirect measurement approaches produced similar LAI results. Mean LAI values for all biomes combined decreased significantly in the 1990s, a period of substantially more studies and improved methodologies. Main conclusions Applications of the LAI database span a wide range of ecological, biogeochemical, physical, and climate research areas. The data provide input to terrestrial ecosystem and land-surface models, for evaluation of global remote sensing products, for comparisons to field studies, and other applications. Example uses of the database for global plant productivity, fractional energy absorption, and remote sensing studies are highlighted.
772 citations
TL;DR: In this article, the stability of standing, spherical accretion shocks is examined in core-collapse supernovae, star formation, and accreting white dwarfs and neutron stars.
Abstract: We examine the stability of standing, spherical accretion shocks. Accretion shocks arise in core-collapse supernovae (the focus of this paper), star formation, and accreting white dwarfs and neutron stars. We present a simple analytic model and use time-dependent hydrodynamics simulations to show that this solution is stable to radial perturbations. In two dimensions we show that small perturbations to a spherical shock front can lead to rapid growth of turbulence behind the shock, driven by the injection of vorticity from the now nonspherical shock. We discuss the ramifications this instability may have for the supernova mechanism.
691 citations
TL;DR: In this article, the mechanisms of deformation and damage evolution in electrodeposited, fully dense, nanocrystalline Ni with an average grain size of ~30 nm and a narrow grain size distribution were investigated by recourse to (i) tensile tests performed in situ in the transmission electron microscope and (ii) microscopic observations made at high resolution following ex situ deformation induced by compression, rolling and nanoindentation.
689 citations
TL;DR: The genome of WH8102 seems to have been greatly influenced by horizontal gene transfer, partially through phages, and is more of a generalist than two related marine cyanobacteria.
Abstract: Marine unicellular cyanobacteria are responsible for an estimated 20–40% of chlorophyll biomass and carbon fixation in the oceans1. Here we have sequenced and analysed the 2.4-megabase genome of Synechococcus sp. strain WH8102, revealing some of the ways that these organisms have adapted to their largely oligotrophic environment. WH8102 uses organic nitrogen and phosphorus sources and more sodium-dependent transporters than a model freshwater cyanobacterium. Furthermore, it seems to have adopted strategies for conserving limited iron stores by using nickel and cobalt in some enzymes, has reduced its regulatory machinery (consistent with the fact that the open ocean constitutes a far more constant and buffered environment than fresh water), and has evolved a unique type of swimming motility. The genome of WH8102 seems to have been greatly influenced by horizontal gene transfer, partially through phages. The genetic material contributed by horizontal gene transfer includes genes involved in the modification of the cell surface and in swimming motility. On the basis of its genome, WH8102 is more of a generalist than two related marine cyanobacteria2.
634 citations
TL;DR: It is found that the aerosol-induced increase in diffuse radiation by the volcano enhanced the terrestrial carbon sink and contributed to the temporary decline in the growth rate of atmospheric carbon dioxide after the eruption.
Abstract: Volcanic aerosols from the 1991 Mount Pinatubo eruption greatly increased diffuse radiation worldwide for the following 2 years. We estimated that this increase in diffuse radiation alone enhanced noontime photosynthesis of a deciduous forest by 23% in 1992 and 8% in 1993 under cloudless conditions. This finding indicates that the aerosol-induced increase in diffuse radiation by the volcano enhanced the terrestrial carbon sink and contributed to the temporary decline in the growth rate of atmospheric carbon dioxide after the eruption.
584 citations
TL;DR: In this paper, the vibrational heat capacity of crystal and glass data was used for analysis of macromolecules in the semicrystalline state and the transitions of the rigid-amorphous phase and the major reversible processes involving latent heats.
TL;DR: In this article, the anisotropy parameter of the second harmonic of the azimuthal particle distribution has been measured with the PHENIX detector in Au+Au collisions at roots(NN)=200 GeV for identified and inclusive charged particle production at central rapidities.
Abstract: The anisotropy parameter (v(2)), the second harmonic of the azimuthal particle distribution, has been measured with the PHENIX detector in Au+Au collisions at roots(NN)=200 GeV for identified and inclusive charged particle production at central rapidities (eta 2 GeV/c, in marked contrast to the predictions of a hydrodynamical model. A quark-coalescence model is also investigated.
TL;DR: This genome has provided new insights into the growth and metabolism of ammonia-oxidizing bacteria as well as predicted insertion sequence elements in eight different families.
Abstract: Nitrosomonas europaea (ATCC 19718) is a gram-negative obligate chemolithoautotroph that can derive all its energy and reductant for growth from the oxidation of ammonia to nitrite. Nitrosomonas europaea participates in the biogeochemical N cycle in the process of nitrification. Its genome consists of a single circular chromosome of 2,812,094 bp. The GC skew analysis indicates that the genome is divided into two unequal replichores. Genes are distributed evenly around the genome, with ∼47% transcribed from one strand and ∼53% transcribed from the complementary strand. A total of 2,460 protein-encoding genes emerged from the modeling effort, averaging 1,011 bp in length, with intergenic regions averaging 117 bp. Genes necessary for the catabolism of ammonia, energy and reductant generation, biosynthesis, and CO 2 and NH 3 assimilation were identified. In contrast, genes for catabolism of organic compounds are limited. Genes encoding transporters for inorganic ions were plentiful, whereas genes encoding transporters for organic molecules were scant. Complex repetitive elements constitute ca. 5% of the genome. Among these are 85 predicted insertion sequence elements in eight different families. The strategy of N. europaea to accumulate Fe from the environment involves several classes of Fe receptors with more than 20 genes devoted to these receptors. However, genes for the synthesis of only one siderophore, citrate, were identified in the genome. This genome has provided new insights into the growth and metabolism of ammonia-oxidizing bacteria.
TL;DR: In this paper, the authors observed a narrow state near 2.32 GeV/c(2) in the inclusive D(+)(s)pi(0) invariant mass distribution from e(+)e(-) annihilation data at energies near 10.6 GeV.
Abstract: We have observed a narrow state near 2.32 GeV/c(2) in the inclusive D(+)(s)pi(0) invariant mass distribution from e(+)e(-) annihilation data at energies near 10.6 GeV. The observed width is consistent with the experimental resolution. The small intrinsic width and the quantum numbers of the final state indicate that the decay violates isospin conservation. The state has natural spin-parity and the low mass suggests a J(P)=0(+) assignment. The data sample corresponds to an integrated luminosity of 91 fb(-1) recorded by the BABAR detector at the SLAC PEP-II asymmetric-energy e(+)e(-) storage ring.
TL;DR: In this paper, the authors show that the mechanism of electrochemical alloying is electrochemically-driven solid state amorphization, a process closely analogous to the diffusive solid-state amomorphization of thin films.
TL;DR: In this paper, the authors measured the transverse momentum spectra of neutral pions in the range 1 < p_T < 10 GeV/c and showed that the pi^0 multiplicity in central reactions is significantly below the yields measured at the same squarert(s_NN) in peripheral Au+Au and p+p reactions scaled by the number of nucleon-nucleon collisions.
Abstract: Transverse momentum spectra of neutral pions in the range 1 < p_T < 10 GeV/c have been measured at mid-rapidity by the PHENIX experiment at RHIC in Au+Au collisions at sqrt(s_NN) = 200 GeV. The pi^0 multiplicity in central reactions is significantly below the yields measured at the same sqrt(s_NN) in peripheral Au+Au and p+p reactions scaled by the number of nucleon-nucleon collisions. For the most central bin, the suppression factor is ~2.5 at p_T = 2 GeV/c and increases to ~4-5 at p_T ~= 4 GeV/c. At larger p_T, the suppression remains constant within errors. The deficit is already apparent in semi-peripheral reactions and increases smoothly with centrality.
TL;DR: In this paper, root turnover with the use of an isotope tracer in two forest free-air carbon dioxide enrichment experiments was assessed, and root turnover varied from 1.2 to 9 years, depending on root diameter and dominant tree species.
Abstract: Estimates of forest net primary production (NPP) demand accurate estimates of root production and turnover. We assessed root turnover with the use of an isotope tracer in two forest free-air carbon dioxide enrichment experiments. Growth at elevated carbon dioxide did not accelerate root turnover in either the pine or the hardwood forest. Turnover of fine root carbon varied from 1.2 to 9 years, depending on root diameter and dominant tree species. These long turnover times suggest that root production and turnover in forests have been overestimated and that sequestration of anthropogenic atmospheric carbon in forest soils may be lower than currently estimated.
TL;DR: In this article, an expression for separation distance was derived from the force balance equations for the leading and trailing partials by considering the Peach-Koehler force from an applied stress field, repulsive force between leading and leading partial dislocations, attractive force due to the stacking fault energy, and resistance (or damping) force to the glide of the partials.
TL;DR: A conceptual approach to evaluate glass-forming ability for variousGlass-forming systems has been proposed from a physical metallurgy point of view and this approach was confirmed and validated by experimental data in various glass-formation systems including oxide glasses, cryoprotectants, and metallic glasses.
Abstract: A conceptual approach to evaluate glass-forming ability for various glass-forming systems has been proposed from a physical metallurgy point of view. It was found that the glass-forming ability for noncrystalline materials was related mainly to two factors, i.e., 1/(T(g)+T(l)) and Tx (wherein Tx is the onset crystallization temperature, T ( g) the glass transition temperature, and T(l) the liquidus temperature), and could be predicated by a unified parameter gamma defined as T(x)/(T(g)+T(l)). This approach was confirmed and validated by experimental data in various glass-forming systems including oxide glasses, cryoprotectants, and metallic glasses.
TL;DR: In this paper, single-walled and multiplewalled carbon nanotubes were functionalized with poly(vinyl alcohol) (PVA) in esterification reactions.
Abstract: Single-walled and multiple-walled carbon nanotubes were functionalized with poly(vinyl alcohol) (PVA) in esterification reactions Similar to the parent PVA, the functionalized carbon nanotube samples are soluble in highly polar solvents such as DMSO and water The common solubilities have allowed the intimate mixing of the functionalized nanotubes with the matrix polymer for the wet-casting of nanocomposite thin films The PVA−carbon nanotube composite films are of high optical quality, without any observable phase separation, and the carbon nanotubes in the films are as well-dispersed as in solution The functionalization of carbon nanotubes by the matrix polymer is apparently an effective way in the homogeneous nanotube dispersion for high-quality polymeric carbon nanocomposite materials Results from characterizations of the solubilized carbon nanotubes and the nanocomposite thin films are presented and discussed
01 Mar 2003-Nuclear Instruments & Methods in Physics Research Section A-accelerators Spectrometers Detectors and Associated Equipment
TL;DR: The PHENIX detector as mentioned in this paper is designed to perform a broad study of A-A, p-A and p-p collisions to investigate nuclear matter under extreme conditions, and is used to study systematic variations with species and energy as well as to measure the spin structure of the nucleon.
Abstract: The PHENIX detector is designed to perform a broad study of A-A, p-A, and p-p collisions to investigate nuclear matter under extreme conditions A wide variety of probes, sensitive to all timescales, are used to study systematic variations with species and energy as well as to measure the spin structure of the nucleon Designing for the needs of the heavy-ion and polarized-proton programs has produced a detector with unparalleled capabilities PHENIX measures electron and muon pairs, photons, and hadrons with excellent energy and momentum resolution The detector consists of a large number of subsystems that are discussed in other papers in this volume The overall design parameters of the detector are presented (C) 2002 Elsevier Science BV All rights reserved
TL;DR: In this article, the authors summarize recent progress in dilute magnetic semiconductors (DMS) such as (Ga, Mn)N, (Ga and Mn)P, (Zn, Mn), O, and SiGeN2 exhibiting room temperature ferromagnetic properties.
Abstract: Existing semiconductor electronic and photonic devices utilize the charge on electrons and holes in order to perform their specific functionality such as signal processing or light emission. The relatively new field of semiconductor spintronics seeks, in addition, to exploit the spin of charge carriers in new generations of transistors, lasers and integrated magnetic sensors. The ability to control of spin injection, transport and detection leads to the potential for new classes of ultra-low power, high speed memory, logic and photonic devices. The utility of such devices depends on the availability of materials with practical (>300 K) magnetic ordering temperatures. In this paper, we summarize recent progress in dilute magnetic semiconductors (DMS) such as (Ga, Mn)N, (Ga, Mn)P, (Zn, Mn)O and (Zn, Mn)SiGeN2 exhibiting room temperature ferromagnetism, the origins of the magnetism and its potential applications in novel devices such as spin-polarized light emitters and spin field effect transistors.
TL;DR: S synchronous spectral peak intensity and its red shift in the region of about 450-480 nm may be used to indicate the presence or absence of high molecular weight and polycondensed humic organic components, or the multicomponent nature of NOM or NOM subcomponents.
TL;DR: A unique process for the fabrication of high-thermal-conductivity carbon foam was developed at Oak Ridge National Laboratory (ORNL) as discussed by the authors, which does not require the traditional blowing and stabilization steps and therefore is less costly.
TL;DR: The yield ratio does not show the suppression observed in central Au+Au collisions at RHIC, but there is a small enhancement in the yield of high momentum particles.
Abstract: Transverse momentum spectra of charged hadrons with p(T)<8 GeV/c and neutral pions with p(T)<10 GeV/c have been measured at midrapidity by the PHENIX experiment at BNL RHIC in d+Au collisions at sqrt[s(NN)]=200 GeV. The measured yields are compared to those in p+p collisions at the same sqrt[s(NN)] scaled up by the number of underlying nucleon-nucleon collisions in d+Au. The yield ratio does not show the suppression observed in central Au+Au collisions at RHIC. Instead, there is a small enhancement in the yield of high momentum particles.
TL;DR: In this article, the links between many-body pairing as it evolves from the underlying nucleon-nucleon interaction and the eventual experimental and theoretical manifestations of superfluidity in infinite nuclear matter and of pairing in finite nuclei are discussed.
Abstract: We discuss several pairing-related phenomena in nuclear systems, ranging from superfluidity in neutron stars to the gradual breaking of pairs in finite nuclei. We focus on the links between many-body pairing as it evolves from the underlying nucleon-nucleon interaction and the eventual experimental and theoretical manifestations of superfluidity in infinite nuclear matter and of pairing in finite nuclei. We analyse the nature of pair correlations in nuclei and their potential impact on nuclear structure experiments. We also describe recent experimental evidence that points to a relation between pairing and phase transitions (or transformations) in finite nuclear systems. Finally, we discuss recent investigations of ground-state properties of random two-body interactions where pairing plays little role although the interactions yield interesting nuclear properties such as 0+ ground states in even-even nuclei.
TL;DR: A microfluidic device is reported that integrated cell handling, rapid cell lysis, and electrophoretic separation and detection of fluorescent cytosolic dyes and are >100 times faster than those reported using standard bench-scale capillary electrophoresis.
Abstract: A microfluidic device is reported that integrated cell handling, rapid cell lysis, and electrophoretic separation and detection of fluorescent cytosolic dyes The device function was demonstrated using Jurkat cells that were loaded with the fluorogenic dyes - carboxyfluorescein diacetate, Oregon green carboxylic acid diacetate, or Calcein AM The loaded cells were hydrodynamically transported from the cell-containing reservoir to a region on the microfluidic device where they were focused and then rapidly lysed using an electric field Complete lysis was accomplished in 100 times faster than those reported using standard bench-scale capillary electrophoresis
TL;DR: These studies demonstrated that specific, sensitive and quantitative detection could be obtained with both functional gene arrays and community genome arrays, which are useful for defining genome diversity and bacterial relatedness.
TL;DR: Microarray data suggest that DEIRA cells efficiently coordinate their recovery by a complex network, within which both DNA repair and metabolic functions play critical roles, including a predicted distinct ATP-dependent DNA ligase and metabolic pathway switching that could prevent additional genomic damage elicited by metabolism-induced free radicals.
Abstract: Deinococcus radiodurans R1 (DEIRA) is a bacterium best known for its extreme resistance to the lethal effects of ionizing radiation, but the molecular mechanisms underlying this phenotype remain poorly understood. To define the repertoire of DEIRA genes responding to acute irradiation (15 kGy), transcriptome dynamics were examined in cells representing early, middle, and late phases of recovery by using DNA microarrays covering ≈94% of its predicted genes. At least at one time point during DEIRA recovery, 832 genes (28% of the genome) were induced and 451 genes (15%) were repressed 2-fold or more. The expression patterns of the majority of the induced genes resemble the previously characterized expression profile of recA after irradiation. DEIRA recA, which is central to genomic restoration after irradiation, is substantially up-regulated on DNA damage (early phase) and down-regulated before the onset of exponential growth (late phase). Many other genes were expressed later in recovery, displaying a growth-related pattern of induction. Genes induced in the early phase of recovery included those involved in DNA replication, repair, and recombination, cell wall metabolism, cellular transport, and many encoding uncharacterized proteins. Collectively, the microarray data suggest that DEIRA cells efficiently coordinate their recovery by a complex network, within which both DNA repair and metabolic functions play critical roles. Components of this network include a predicted distinct ATP-dependent DNA ligase and metabolic pathway switching that could prevent additional genomic damage elicited by metabolism-induced free radicals.
TL;DR: This article used unique mesocosms to examine the role that plants play in accumulating and transforming atmospheric Hg and found that approximately 80% of the total Hg accumulated in the aboveground biomass was found in the leaves, and roughly 1% of that Hg was methylated.