Showing papers by "Oak Ridge National Laboratory published in 2006"
Oak Ridge National Laboratory1, University of Tennessee2, West Virginia University3, Umeå University4, University of British Columbia5, United States Department of Energy6, Ghent University7, Swedish University of Agricultural Sciences8, Institut national de la recherche agronomique9, Virginia Tech10, Michigan Technological University11, University of Toronto12, Pennsylvania State University13, University of Provence14, University of Georgia15, University of Florida16, University of California, Berkeley17, Lawrence Berkeley National Laboratory18, University of Arizona19, Purdue University20, Stanford University21, United States Department of Agriculture22, University of Helsinki23, University of Turku24, Massachusetts Institute of Technology25, University of Tennessee Health Science Center26, University of Tübingen27
TL;DR: The draft genome of the black cottonwood tree, Populus trichocarpa, has been reported in this paper, with more than 45,000 putative protein-coding genes identified.
Abstract: We report the draft genome of the black cottonwood tree, Populus trichocarpa. Integration of shotgun sequence assembly with genetic mapping enabled chromosome-scale reconstruction of the genome. More than 45,000 putative protein-coding genes were identified. Analysis of the assembled genome revealed a whole-genome duplication event; about 8000 pairs of duplicated genes from that event survived in the Populus genome. A second, older duplication event is indistinguishably coincident with the divergence of the Populus and Arabidopsis lineages. Nucleotide substitution, tandem gene duplication, and gross chromosomal rearrangement appear to proceed substantially more slowly in Populus than in Arabidopsis. Populus has more protein-coding genes than Arabidopsis, ranging on average from 1.4 to 1.6 putative Populus homologs for each Arabidopsis gene. However, the relative frequency of protein domains in the two genomes is similar. Overrepresented exceptions in Populus include genes associated with lignocellulosic wall biosynthesis, meristem development, disease resistance, and metabolite transport.
4,025 citations
TL;DR: A program for calculating the semi-classic transport coefficients is described, based on a smoothed Fourier interpolation of the bands, which in principle should be exact within Boltzmann theory.
3,909 citations
Los Alamos National Laboratory1, National Nuclear Data Center2, Oak Ridge National Laboratory3, Argonne National Laboratory4, Lawrence Livermore National Laboratory5, National Institute of Standards and Technology6, Rensselaer Polytechnic Institute7, Idaho National Laboratory8, Westinghouse Electric9, Atomic Energy of Canada Limited10, Nuclear Research and Consultancy Group11
TL;DR: The ENDF/B-VII.0 as discussed by the authors file contains data primarily for reactions with incident neutrons, protons, and photons on almost 400 isotopes, based on experimental data and theory predictions.
1,913 citations
TL;DR: This work uses a combination of state-of-the-art experimental and computational techniques to resolve the atomic-level structure of amorphous alloys and elucidate the different types of short-range order as well as the nature of the medium- range order.
Abstract: Unlike the well-defined long-range order that characterizes crystalline metals, the atomic arrangements in amorphous alloys remain mysterious at present. Despite intense research activity on metallic glasses and relentless pursuit of their structural description, the details of how the atoms are packed in amorphous metals are generally far less understood than for the case of network-forming glasses. Here we use a combination of state-of-the-art experimental and computational techniques to resolve the atomic-level structure of amorphous alloys. By analysing a range of model binary systems that involve different chemistry and atomic size ratios, we elucidate the different types of short-range order as well as the nature of the medium-range order. Our findings provide a reality check for the atomic structural models proposed over the years, and have implications for understanding the nature, forming ability and properties of metallic glasses.
1,657 citations
TL;DR: In this paper, the authors review quantitative cellulase activity assays using soluble and insoluble substrates, and focus on their advantages and limitations, and hypothesize that continuous culture using insoluble cellulosic substrates could be a powerful selection tool for enriching beneficial cellulase mutants from the large library displayed on the cell surface.
1,495 citations
TL;DR: In this paper, a zinc-based metal-organic framework (MOF) can be transformed reversibly from an open (a) to a dense (b) configuration, and the microporous solid is the first example of a MOF that is highly selective in the gas-chromatographic separation of alkanes.
Abstract: A zinc-based metal-organic framework (MOF) can be transformed reversibly from an open (a) to a dense (b) configuration. The microporous solid is the first example of a MOF that is highly selective in the gas-chromatographic separation of alkanes.
1,127 citations
TL;DR: In this article, the Dzyaloshinskii-Moriya interaction (DMI) provides the microscopic mechanism for the coexistence and strong coupling between ferroelectricity and incommensurate magnetism.
Abstract: With the perovskite multiferroic $R\mathrm{Mn}{\mathrm{O}}_{3}$ $(R=\mathrm{Gd},\mathrm{Tb},\mathrm{Dy})$ as guidance, we argue that the Dzyaloshinskii-Moriya interaction (DMI) provides the microscopic mechanism for the coexistence and strong coupling between ferroelectricity and incommensurate magnetism. We use Monte Carlo simulations and zero-temperature exact calculations to study a model incorporating the double-exchange, superexchange, Jahn-Teller, and DMI terms. The phase diagram contains a multiferroic phase between $A$ and $E$ antiferromagnetic phases, in excellent agreement with experiments.
1,042 citations
Virginia Tech1, Lawrence Berkeley National Laboratory2, Joint Genome Institute3, Wageningen University and Research Centre4, University of Warwick5, Imperial College London6, University of California, Berkeley7, Cornell University8, Ohio Agricultural Research and Development Center9, Agriculture and Agri-Food Canada10, Agricultural Research Service11, Lawrence Livermore National Laboratory12, North Carolina State University13, University of Tennessee14, Oak Ridge National Laboratory15, University of California, Merced16, University of Queensland17, Wilkes University18, Bowling Green State University19, Hokkaido University20
TL;DR: Comparison of the two species' genomes reveals a rapid expansion and diversification of many protein families associated with plant infection such as hydrolases, ABC transporters, protein toxins, proteinase inhibitors, and, in particular, a superfamily of 700 proteins with similarity to known oömycete avirulence genes.
Abstract: Draft genome sequences have been determined for the soybean pathogen Phytophthora sojae and the sudden oak death pathogen Phytophthora ramorum. Oomycetes such as these Phytophthora species share the kingdom Stramenopila with photosynthetic algae such as diatoms, and the presence of many Phytophthora genes of probable phototroph origin supports a photosynthetic ancestry for the stramenopiles. Comparison of the two species' genomes reveals a rapid expansion and diversification of many protein families associated with plant infection such as hydrolases, ABC transporters, protein toxins, proteinase inhibitors, and, in particular, a superfamily of 700 proteins with similarity to known oomycete avirulence genes.
1,016 citations
TL;DR: The genetic make-up of a cancer cell may realize its invasive potential through a clonal evolution process driven by definable microenvironmental selective forces, and this mathematical model provides a theoretical/experimental framework to quantitatively characterize this selective pressure for invasion and test ways to eliminate it.
751 citations
TL;DR: A general method based on two-phase polymerization has been described to synthesize mesoporous carbons via self-assembly through two phase polymerization, with obvious advantages over the techniques previously reported.
Abstract: A general method based on two-phase polymerization has been described to synthesize mesoporous carbons via self-assembly. Mild reacting conditions and wide composition ranges are the obvious advantages of this method over the techniques previously reported.
728 citations
TL;DR: In this paper, the asymptotic modulus of wheat straw, barley straw, corn stover, switchgrass, and switchgrass were determined at different compressive forces, particle sizes and moisture contents.
Abstract: Mechanical properties of wheat straw, barley straw, corn stover and switchgrass were determined at different compressive forces, particle sizes and moisture contents. Ground biomass samples were compressed with five levels of compressive forces (1000, 2000, 3000, 4000 and 4400 N) and three levels of particle sizes (3.2, 1.6 and 0.8 mm) at two levels of moisture contents (12% and 15% (wet basis)) to establish compression and relaxation data. Compressed sample dimensions and mass were measured to calculate pellet density. Corn stover produced the highest pellet density at low pressure during compression. Compressive force, particle size and moisture content significantly affected the pellet density of barley straw, corn stover and switchgrass. However, different particle sizes of wheat straw did not produce any significant difference on pellet density. The relaxation data were analyzed to determine the asymptotic modulus of biomass pellets. Barley straw had the highest asymptotic modulus among all biomass indicating that pellets made from barley straw were more rigid than those of other pellets. Asymptotic modulus increased linearly with an increase in compressive pressure. A simple linear model was developed to relate asymptotic modulus and maximum compressive pressure.
TL;DR: The ALICE Collaboration as mentioned in this paper is a general-purpose heavy-ion experiment designed to study the physics of strongly interacting matter and the quark-gluon plasma in nucleus-nucleus collisions at the LHC.
Abstract: ALICE is a general-purpose heavy-ion experiment designed to study the physics of strongly interacting matter and the quark–gluon plasma in nucleus–nucleus collisions at the LHC. It currently involves more than 900 physicists and senior engineers, from both the nuclear and high-energy physics sectors, from over 90 institutions in about 30 countries.The ALICE detector is designed to cope with the highest particle multiplicities above those anticipated for Pb–Pb collisions (dNch/dy up to 8000) and it will be operational at the start-up of the LHC. In addition to heavy systems, the ALICE Collaboration will study collisions of lower-mass ions, which are a means of varying the energy density, and protons (both pp and pA), which primarily provide reference data for the nucleus–nucleus collisions. In addition, the pp data will allow for a number of genuine pp physics studies.The detailed design of the different detector systems has been laid down in a number of Technical Design Reports issued between mid-1998 and the end of 2004. The experiment is currently under construction and will be ready for data taking with both proton and heavy-ion beams at the start-up of the LHC.Since the comprehensive information on detector and physics performance was last published in the ALICE Technical Proposal in 1996, the detector, as well as simulation, reconstruction and analysis software have undergone significant development. The Physics Performance Report (PPR) provides an updated and comprehensive summary of the performance of the various ALICE subsystems, including updates to the Technical Design Reports, as appropriate.The PPR is divided into two volumes. Volume I, published in 2004 (CERN/LHCC 2003-049, ALICE Collaboration 2004 J. Phys. G: Nucl. Part. Phys. 30 1517–1763), contains in four chapters a short theoretical overview and an extensive reference list concerning the physics topics of interest to ALICE, the experimental conditions at the LHC, a short summary and update of the subsystem designs, and a description of the offline framework and Monte Carlo event generators.The present volume, Volume II, contains the majority of the information relevant to the physics performance in proton–proton, proton–nucleus, and nucleus–nucleus collisions. Following an introductory overview, Chapter 5 describes the combined detector performance and the event reconstruction procedures, based on detailed simulations of the individual subsystems. Chapter 6 describes the analysis and physics reach for a representative sample of physics observables, from global event characteristics to hard processes.
TL;DR: A review of living and controlled/living methodologies for the synthesis of polymers with different macromolecular architectures is presented in this paper, along with a few representative examples.
TL;DR: In this article, 1600 t of CO2 were injected at 1500 m depth into a 24m-thick sandstone section of the Frio Formation, a regional brine and oil reservoir in the U.S Gulf Coast.
Abstract: To investigate the potential for the geologic storage of CO2 in saline sedimentary aquifers, 1600 t of CO2 were injected at 1500 m depth into a 24-m-thick sandstone section of the Frio Formation, a regional brine and oil reservoir in the U.S. Gulf Coast. Fluid samples obtained from the injection and observation wells before CO2 injection showed a Na-CaCl‐type brine with 93,000 mg/L total dissolved solids (TDS) at near saturation with CH4 at reservoir conditions. Following CO2 breakthrough, samples showed sharp drops in pH (6.5‐5.7), pronounced increases in alkalinity (100‐3000 mg/L as HCO3) and Fe (30‐1100 mg/L), and significant shifts in the isotopic compositions of H2O, dissolved inorganic carbon (DIC), and CH4. Geochemical modeling indicates that brine pH would have dropped lower but for the buffering by dissolution of carbonate and iron oxyhydroxides. This rapid dissolution of carbonate and other minerals could ultimately create pathways in the rock seals or well cements for CO2 and brine leakage. Dissolution of minerals, especially iron oxyhydroxides, could mobilize toxic trace metals and, where residual oil or suitable organics are present, the injected CO2 could also mobilize toxic organic compounds. Environmental impacts could be major if large brine volumes with mobilized toxic metals and organics migrated into potable groundwater. The d 18 O values for brine and CO2 samples indicate that supercritical CO2 comprises ;50% of pore-fluid volume ;6 mo after the end of injection. Postinjection sampling, coupled with geochemical modeling, indicates that the brine gradually will return to its preinjection composition.
TL;DR: The emerging approaches reviewed in this article, with reference to their diagnostic potential, include nanotextured surfaces for proteomics, a two-particle sandwich assay for the biological amplification of low-concentration biomolecular signals, and silicon-based nanostructures for the transduction of molecular binding into electrical and mechanical signals.
TL;DR: An overview of the results obtained with lattice models of the fracture, highlighting the relations with statistical physics theories and more conventional fracture mechanics approaches is presented.
Abstract: Disorder and long-range interactions are two of the key components that make material failure an interesting playfield for the application of statistical mechanics. The cornerstone in this respect has been lattice models of the fracture in which a network of elastic beams, bonds, or electrical fuses with random failure thresholds are subject to an increasing external load. These models describe on a qualitative level the failure processes of real, brittle, or quasi-brittle materials. This has been particularly important in solving the classical engineering problems of material strength: the size dependence of maximum stress and its sample-to-sample statistical fluctuations. At the same time, lattice models pose many new fundamental questions in statistical physics, such as the relation between fracture and phase transitions. Experimental results point out to the existence of an intriguing crackling noise in the acoustic emission and of self-affine fractals in the crack surface morphology. Recent advances ...
TL;DR: Based on the formation constants obtained in this study, speciation calculations indicate that at low Ca2+ concentration (e.g., <2.2 mmol/L), CaUO2(CO3)3(2-) is more important than Ca2UO 2(CO 3)3 and that the Ca2 UO2-CO3-3 distribution increased with increasing Ca2- concentration.
Abstract: The formation constants of ternary complexes (MUO2(CO3)32- and M2UO2(CO3)30) of uranyl and carbonate with alkaline earth metals (M2+ denotes Mg2+, Ca2+, Sr2+, and Ba2+) were determined with an anion exchange method by varying the metal concentrations (01−5 mmol/L) at pH 81 and a constant ionic strength (01 mol/L NaNO3) under equilibrium with atmospheric CO2 The results indicate that the complexes of MUO2(CO3)32- and M2UO2(CO3)3 are simultaneously formed for Ca2+ and Ba2+, while Mg2+ and Sr2+ form only the MUO2(CO3)32- complex under our experimental conditions The cumulative stability constants for the MUO2(CO3)32- complex obtained at I = 0 are as follows: logβ113 = 2611 ± 004, 2718 ± 006, 2686 ± 004, and 2668 ± 004 for Mg2+, Ca2+, Sr2+, and Ba2+, respectively For M2UO2(CO3)30, the value of logβ213 at I = 0 was measured to be 3070 ± 005 and 2975 ± 007 for Ca2+ and Ba2+, respectively Based on the formation constants obtained in this study, speciation calculations indicate that at low Ca2
TL;DR: The nu p process as mentioned in this paper is a nucleosynthesis process that occurs in supernovae (and possibly gamma-ray bursts) when strong neutrino fluxes create proton-rich ejecta.
Abstract: We present a new nucleosynthesis process that we denote as the nu p process, which occurs in supernovae (and possibly gamma-ray bursts) when strong neutrino fluxes create proton-rich ejecta. In this process, antineutrino absorptions in the proton-rich environment produce neutrons that are immediately captured by neutron-deficient nuclei. This allows for the nucleosynthesis of nuclei with mass numbers A>64, , making this process a possible candidate to explain the origin of the solar abundances of (92,94)Mo and (96,98)Ru. This process also offers a natural explanation for the large abundance of Sr seen in a hyper-metal-poor star.
TL;DR: A review of the relevant literature pertaining to both focused electron-beam-induced etching and deposition can be found in this paper, which summarizes the associated physics of electron-solid-vapor interactions, discusses related physical processes, and provides an introduction.
Abstract: Focused electron-beam-induced (FEB-induced) deposition and etching are versatile, direct-write nanofabrication schemes that allow for selective deposition or removal of a variety of materials. Fundamentally, these processes are governed by an electron-induced reaction with a precursor vapor, which may either result in decomposition to a solid deposit or formation of a volatile etch by-product. The ability to induce such localized reactions by placement of a nanometer-sized focused electron probe has recently drawn considerable attention. In response, we have reviewed much of the relevant literature pertaining to both focused electron-beam-induced etching and deposition. Because these nanoscale processing techniques are still in their relative infancy, a significant amount of scientific research is being conducted to understand, and hence improve, the processes. This article summarizes the associated physics of electron-solid-vapor interactions, discusses related physical processes, and provides an introdu...
TL;DR: Benefits of the critical current in self-field as well as excellent retention of this current in high applied magnetic fields were achieved in the thick films via incorporation of a periodic array of extended columnar defects, composed of self-aligned nanodots of nonsuperconducting material extending through the entire thickness of the film.
Abstract: We demonstrated short segments of a superconducting wire that meets or exceeds performance requirements for many large-scale applications of high-temperature superconducting materials, especially those requiring a high supercurrent and/or a high engineering critical current density in applied magnetic fields. The performance requirements for these varied applications were met in 3-micrometer-thick YBa 2 Cu 3 O 7-δ films epitaxially grown via pulsed laser ablation on rolling assisted biaxially textured substrates. Enhancements of the critical current in self-field as well as excellent retention of this current in high applied magnetic fields were achieved in the thick films via incorporation of a periodic array of extended columnar defects, composed of self-aligned nanodots of nonsuperconducting material extending through the entire thickness of the film. These columnar defects are highly effective in pinning the superconducting vortices or flux lines, thereby resulting in the substantially enhanced performance of this wire.
TL;DR: By controlling the specimen aspect ratio and strain rate, compressive strains as high as 80% were obtained in an otherwise brittle metallic glass, and a systematic strain-induced softening was observed which contrasts sharply with the hardening typically observed in crystalline metals.
Abstract: By controlling the specimen aspect ratio and strain rate, compressive strains as high as 80% were obtained in an otherwise brittle metallic glass. Physical and mechanical properties were measured after deformation, and a systematic strain-induced softening was observed which contrasts sharply with the hardening typically observed in crystalline metals. If the deformed glass is treated as a composite of hard amorphous grains surrounded by soft shear-band boundaries, analogous to nanocrystalline materials that exhibit inverse Hall-Petch behavior, the correct functional form for the dependence of hardness on shear-band spacing is obtained. Deformation-induced softening leads naturally to shear localization and brittle fracture.
Goddard Space Flight Center1, Institut national de la recherche agronomique2, Boston University3, University of Maryland, College Park4, Canada Centre for Remote Sensing5, University of Alberta6, University of Helsinki7, Finnish Forest Research Institute8, Finnish Meteorological Institute9, United States Environmental Protection Agency10, University of Milano-Bicocca11, United States Department of Agriculture12, Oregon State University13, Pennsylvania State University14, Oak Ridge National Laboratory15
TL;DR: In this paper, the authors describe the main components of this international validation effort, including the current participants, their ground LAI measurements and scaling techniques, and the metadata and infrastructure established to share data.
Abstract: Initiated in 1984, the Committee Earth Observing Satellites' Working Group on Calibration and Validation (CEOS WGCV) pursues activities to coordinate, standardize and advance calibration and validation of civilian satellites and their data. One subgroup of CEOS WGCV, Land Product Validation (LPV), was established in 2000 to define standard validation guidelines and protocols and to foster data and information exchange relevant to the validation of land products. Since then, a number of leaf area index (LAI) products have become available to the science community at both global and regional extents. Having multiple global LAI products and multiple, disparate validation activities related to these products presents the opportunity to realize efficiency through international collaboration. So the LPV subgroup established an international LAI intercomparison validation activity. This paper describes the main components of this international validation effort. The paper documents the current participants, their ground LAI measurements and scaling techniques, and the metadata and infrastructure established to share data. The paper concludes by describing plans for sharing both field data and high-resolution LAI products from each site. Many considerations of this global LAI intercomparison can apply to other products, and this paper presents a framework for such collaboration
TL;DR: In this article, the authors describe the framework development of a dynamic integrated biomass supply analysis and logistics model (IBSAL) to simulate the collection, storage, and transport operations for supplying agricultural biomass to a biorefinery.
Abstract: This paper describes the framework development of a dynamic integrated biomass supply analysis and logistics model (IBSAL) to simulate the collection, storage, and transport operations for supplying agricultural biomass to a biorefinery. The model consists of time dependent events representing the working rate of equipment and queues representing the capacity of storage structures. The discrete event and queues are inter-connected to represent the entire network of material flow from field to a biorefinery. Weather conditions including rain and snow influence the moisture content and the dry matter loss of biomass through the supply chain and are included in the model. The model is developed using an object oriented high level simulation language EXTEND™. A case of corn stover collection and transport scenario using baling system is described.
TL;DR: In this paper, the authors established an analytic model for nano-indentation hardness based on the maximum allowable density of geometrically necessary dislocations and gave a simple relation between indentation hardness and depth, which degenerates to Nix and Gao [1998.
Abstract: The indentation hardness–depth relation established by Nix and Gao [1998. Indentation size effects in crystalline materials: a law for strain gradient plasticity. J. Mech. Phys. Solids 46, 411–425] agrees well with the micro-indentation but not nano-indentation hardness data. We establish an analytic model for nano-indentation hardness based on the maximum allowable density of geometrically necessary dislocations. The model gives a simple relation between indentation hardness and depth, which degenerates to Nix and Gao [1998. Indentation size effects in crystalline materials: a law for strain gradient plasticity. J. Mech. Phys. Solids 46, 411–425] for micro-indentation. The model agrees well with both micro- and nano-indentation hardness data of MgO and iridium.
TL;DR: The ability to control synthetically the electronic properties of nanowires using band structure design in III-nitride radial nanowire heterostructures opens up new opportunities for nanoelectronics and provides a new platform to study the physics of low-dimensional electron gases.
Abstract: We report the rational synthesis of dopant-free GaN/AlN/AlGaN radial nanowire heterostructures and their implementation as high electron mobility transistors (HEMTs). The radial nanowire heterostructures were prepared by sequential shell growth immediately following nanowire elongation using metal−organic chemical vapor deposition (MOCVD). Transmission electron microscopy (TEM) studies reveal that the GaN/AlN/AlGaN radial nanowire heterostructures are dislocation-free single crystals. In addition, the thicknesses and compositions of the individual AlN and AlGaN shells were unambiguously identified using cross-sectional high-angle annular darkfield scanning transmission electron microscopy (HAADF-STEM). Transport measurements carried out on GaN/AlN/AlGaN and GaN nanowires prepared using similar conditions demonstrate the existence of electron gas in the undoped GaN/AlN/AlGaN nanowire heterostructures and also yield an intrinsic electron mobility of 3100 cm2/Vs and 21 000 cm2/Vs at room temperature and 5 K,...
TL;DR: In this article, the authors report an analysis of the land component of the community climate system model (CCSM) for multidecadal simulations and find that high latitudes of northern winter are biased sufficiently warm to have a significant impact on the simulated value of global land temperature.
Abstract: Several multidecadal simulations have been carried out with the new version of the Community Climate System Model (CCSM). This paper reports an analysis of the land component of these simulations. Global annual averages over land appear to be within the uncertainty of observational datasets, but the seasonal cycle over land of temperature and precipitation appears to be too weak. These departures from observations appear to be primarily a consequence of deficiencies in the simulation of the atmospheric model rather than of the land processes. High latitudes of northern winter are biased sufficiently warm to have a significant impact on the simulated value of global land temperature. The precipitation is approximately doubled from what it should be at some locations, and the snowpack and spring runoff are also excessive. The winter precipitation over Tibet is larger than observed. About two-thirds of this precipitation is sublimated during the winter, but what remains still produces a snowpack tha...
TL;DR: It is predicted that the polarization induced by the E-type magnetic order can potentially be enhanced by up to 2 orders of magnitude with respect to that in the spiral magnetic phases of TbMnO3 and similar multiferroic compounds.
Abstract: We show that the symmetry of the spin zigzag chain E phase of the orthorhombic perovskite manganites and nickelates allows for the existence of a finite ferroelectric polarization. The proposed microscopic mechanism is independent of spin-orbit coupling. We predict that the polarization induced by the E-type magnetic order can potentially be enhanced by up to 2 orders of magnitude with respect to that in the spiral magnetic phases of TbMnO3 and similar multiferroic compounds.
TL;DR: The genome sequence of T. denitrificans will enable elucidation of the mechanisms of aerobic and anaerobic sulfur-compound oxidation by beta-proteobacteria and will help reveal the molecular basis of this organism's role in major biogeochemical cycles and groundwater restoration.
Abstract: The complete genome sequence of Thiobacillus denitrificans ATCC 25259 is the first to become available for an obligately chemolithoautotrophic, sulfur-compound-oxidizing, β-proteobacterium. Analysis of the 2,909,809-bp genome will facilitate our molecular and biochemical understanding of the unusual metabolic repertoire of this bacterium, including its ability to couple denitrification to sulfur-compound oxidation, to catalyze anaerobic, nitrate-dependent oxidation of Fe(II) and U(IV), and to oxidize mineral electron donors. Notable genomic features include (i) genes encoding c-type cytochromes totaling 1 to 2 percent of the genome, which is a proportion greater than for almost all bacterial and archaeal species sequenced to date, (ii) genes encoding two [NiFe]hydrogenases, which is particularly significant because no information on hydrogenases has previously been reported for T. denitrificans and hydrogen oxidation appears to be critical for anaerobic U(IV) oxidation by this species, (iii) a diverse complement of more than 50 genes associated with sulfur-compound oxidation (including sox genes, dsr genes, and genes associated with the AMP-dependent oxidation of sulfite to sulfate), some of which occur in multiple (up to eight) copies, (iv) a relatively large number of genes associated with inorganic ion transport and heavy metal resistance, and (v) a paucity of genes encoding organic-compound transporters, commensurate with obligate chemolithoautotrophy. Ultimately, the genome sequence of T. denitrificans will enable elucidation of the mechanisms of aerobic and anaerobic sulfur-compound oxidation by β-proteobacteria and will help reveal the molecular basis of this organism's role in major biogeochemical cycles (i.e., those involving sulfur, nitrogen, and carbon) and groundwater restoration.
TL;DR: The synthesis of the composite mimics the natural biomineralization of bone indicating that bacterial cellulose can be used as a template for biomimetic apatite formation and may have potential use as an orthopedic biomaterial.