Showing papers by "Oak Ridge National Laboratory published in 1993"

Biochemical Limitations to Carbon Assimilation in C3 Plants—A Retrospective Analysis of the A/Ci Curves from 109 Species

Abstract: differences in the assimilation of atmospheric CO2 depends upon differences in the capacities for the biochemical reactions that regulate the gas-exchange process. Quantifying these differences for more than a few species, however, has proven difficult. Therefore, to understand better how species differ in their capacity for CO2 assimilation, a widely used model, capable of partitioning limitations to the activity of ribulose-l,5-W.sphosphate carboxylase-oxygenase, to the rate of ribulose 1,5-tophosphate regeneration via electron transport, and to the rate of triose phosphate utilization was used to analyse 164 previously published A/C, curves for 109 C3 plant species. Based on this analysis, the maximum rate of carboxylation, Vcmax, ranged from 6/umol m~2 s"1 for the coniferous species Picea abies to 194jj,mol m" 2 s"1 for the agricultural species Beta vulgaris, and averaged 64^mol m" 2 s"1 across all species. The maximum rate of electron transport, Jmx, ranged from 17/^mol m~2 s"1 again for Picea abies to 372/j.mol m~2 s"1 for the desert annual Mahastrum rotundifolium, and averaged 134fxmol m~2 s"1 across all species. A strong positive correlation between Vc^x and Jmax indicated that the assimilation of CO2 was regulated in a co-ordinated manner by these two component processes. Of the AjC{ curves analysed, 23 showed either an insensitivity or reversed-sensitivity to increasing CO2 concentration, indicating that CO2 assimilation was limited by the utilization of triose phosphates. The rate of triose phosphate utilization ranged from 4-9/xtnol m" 2 s"1 for the tropical perennial Tabebuia rosea to 20-1 /xmol m~2 s"1 for the weedy annual Xanthium strumarium, and averaged 101 ftmol m" 2 s"1 across all species. Despite what at first glance would appear to be a wide range of estimates for the biochemical capacities that regulate CO2 assimilation, separating these species-specific results into those of broad plant categories revealed that Vcmax and Jmax were in general higher for herbaceous annuals than they were for woody perennials. For annuals, Vc^^ and Jmax averaged 75 and 154ftmol m~2 s"1, while for perennials these same two parameters averaged only 44 and 97/xmol m~2 s"1, respectively. Although these differences between groups may be coincidental, such an observation points to differences between annuals and perennials in either the availability or allocation of resources to the gas-exchange process.

An Introduction to Chordal Graphs and Clique Trees

Abstract: Clique trees and chordal graphs have carved out a niche for themselves in recent work on sparse matrix algorithms, due primarily to research questions associated with advanced computer architectures. This paper is a unified and elementary introduction to the standard characterizations of chordal graphs and clique trees. The pace is leisurely, as detailed proofs of all results are included. We also briefly discuss applications of chordal graphs and clique trees in sparse matrix computations.

A revised concept of landscape equilibrium: Disturbance and stability on scaled landscapes

Abstract: Temporal and spatial scales of disturbance and recovery are often confounded in discussions of landscape equilibrium. We developed a broad framework for the description of landscapes that separates the spatial and temporal scales of disturbance and recovery and predicts the resultant dynamics of a landscape. Two key parameters representing time and space are used to describe potential disturbance dynamics. The temporal parameter, T, is the ratio of the disturbance interval (i.e., time between successive disturbance events) to the time required for a disturbed site to recover to a mature stage. The spatial parameter, S, is the ratio of the size of the disturbance to the size of the landscape. The use of ratios in both parameters permits the comparison of landscapes across a range of spatial and temporal scales. A simple simulation model was developed to explore the implications of various combinations of S and T. For any single simulation, disturbances of a fixed size are imposed at random locations on a gridded landscape at specified intervals. Disturbed sites recover deterministically through succession. Where disturbance interval is long relative to recovery time and a small proportion of the landscape is affected, the system is stable and exhibits low variance over time (e.g., northeastern hardwood forests). These are traditional “equilibrium” systems. Where disturbance interval is comparable to recovery interval and a large proportion of the landscape is affected, the system is stable but exhibits large variance (e.g., subalpine forests in Yellowstone Park). Where disturbance interval becomes much shorter than recovery time and a large proportion of the landscape is affected, the system may become unstable and shift into a different trajectory (e.g., arid ecosystems with altered fire regimes). This framework permits the prediction of disturbance conditions that lead to qualitatively different landscape dynamics and demonstrates the scale-dependent nature of concepts of landscape equilibrium.

Atomic-resolution chemical analysis using a scanning transmission electron microscope

Abstract: THE high angle elastic scattering of electrons in scanning transmission electron microscopy depends strongly on the atomic number Z, of the sample atoms, through the Z2 dependence of the Rutherford scattering cross-section1. The detection of scattered electrons at high angles and over a large angular range (75& ndash;150 milliradians) removes the coherent effects of diffraction, and the resulting incoherent image provides a compositional map of the sample with high atomic-number contrast1. If a fine electron probe is used, and the sample is a crystalline material oriented along one of its principal axes, individual columns of atoms can be imaged in this way2. Electrons scattered at low angles are not used in this detection scheme, and are thus available for simultaneous electron energy-loss spectroscopy3; in principle, this combination of techniques should allow the direct chemical analysis of single atomic columns in crystalline materials. Here we present electron energy-loss spectra from expitaxial interfaces between cobalt silicide and silicon, which confirm that atomic resolution can be achieved by this approach. The ability to correlate structure and chemistry with atomic resolution holds great promise for the detailed study of defects and interfaces.

Reduction of Fe(III) in sediments by sulphate-reducing bacteria

Abstract: REDUCTION of ferric iron (Fe(III)) to ferrous iron (Fe(II)) is one of the most important geochemical reactions in anaerobic aquatic sediments because of its many consequences for the organic and inorganic chemistry of these environments1. In marine environments, sulphate-reducing bacteria produce H2S, which can reduce iron oxyhydroxides2 to form iron sulphides. The presence of siderite (FeCO3) in marine sediments is anomalous, however, as it is unstable in the presence of H2S. Previous work3,4 has suggested a bacterial origin of siderite. Here we describe geochemical and microbiological studies which suggest that contemporary formation of siderite concretions in a salt-marsh sediment results from the activity of sulphate-reducing bacteria. We find that, instead of reducing Fe(III) indirectly through the production of sulphide, some of these bacteria can reduce Fe(III) directly through an enzymatic mechanism, producing siderite rather than iron sulphides. Sulphate-reducing bacteria may thus be an important and previously unrecognized agent for Fe(III) reduction in aquatic sediments and ground waters.

Lacunarity indices as measures of landscape texture

Abstract: Lacunarity analysis is a multi-scaled method of determining the texture associated with patterns of spatial dispersion (i.e., habitat types or species locations) for one-, two-, and three-dimensional data. Lacunarity provides a parsimonious analysis of the overall fraction of a map or transect covered by the attribute of interest, the degree of contagion, the presence of self-similarity, the presence and scale of randomness, and the existence of hierarchical structure. For self-similar patterns, it can be used to determine the fractal dimension. The method is easily implemented on the computer and provides readily interpretable graphic results. Differences in pattern can be detected even among very sparsely occupied maps.

Yeast cells lacking 5'-->3' exoribonuclease 1 contain mRNA species that are poly(A) deficient and partially lack the 5' cap structure.

Abstract: Analysis of the slowed turnover rates of several specific mRNA species and the higher cellular levels of some of these mRNAs in Saccharomyces cerevisiae lacking 5'-->3' exoribonuclease 1 (xrn1 cells) has led to the finding that these yeast contain higher amounts of essentially full-length mRNAs that do not bind to oligo(dT)-cellulose. On the other hand, the length of mRNA poly(A) chains found after pulse-labeling of cells lacking the exoribonuclease, the cellular rate of synthesis of oligo(dT)-bound mRNA, and the initial rate of its deadenylation appeared quite similar to the same measurements in wild-type yeast cells. Examination of the 5' cap structure status of the poly(A)-deficient mRNAs by comparative analysis of the m7G content of poly(A)- and poly(A)+ RNA fractions of wild-type and xrn1 cells suggested that the xrn1 poly(A)- mRNA fraction is low in cap structure content. Further analysis of the 5' termini by measurements of the rate of 5'-->3' exoribonuclease 1 hydrolysis of specific full-length mRNA species showed that approximately 50% of the xrn1 poly(A)-deficient mRNA species lack the cap structure. Primer extension analysis of the 5' terminus of ribosomal protein 51A (RP51A) mRNA showed that about 30% of the poly(A)-deficient molecules of the xrn1 cells are slightly shorter at the 5' end. The finding of some accumulation of poly(A)-deficient mRNA species partially lacking the cap structure together with the reduction of the rate of mRNA turnover in cells lacking the enzyme suggest a possible role for 5'-->3' exoribonuclease 1 in the mRNA turnover process.

A gene for the mouse pink-eyed dilution locus and for human type II oculocutaneous albinism

Abstract: THE mouse pink-eyed dilution (p) locus on chromosome 7 is associated with defects of skin, eye and coat pigmentation1. Mutations at p cause a reduction of eumelanin (black-brown) pigment and altered morphology of black pigment granules (eumelano-somes), but have little effect on pheomelanin (yellow-red) pigment2. We show here that the human complementary DNA DN10, linked to thep locus in mice3–5, identifies the human homologue (P) of the mouse pgene, and appears to encode an integral membrane transporter protein. The expression pattern of this gene in various p mutant mice correlates with the pigmentation phenotype; moreover, an abnormally sized messenger RNA is detected in one mutant,pun, which reverts to the normal size in pun revertants. The human P gene corresponds to the D15S12locus within the chromosome segment 15qll–ql3, which is typically deleted in patients with Prader–Willi and Angelman syndrome (see ref. 5 for review). These disorders are phenotypically distinct, depending on the parent of origin of the deleted chromosome5–7, but both syndromes are often associated with hypopigmentation of the skin, hair and eyes (see ref. 8 for review), and deletion of theP gene may be responsible for this hypopigmentation. In addition, we report a mutation in both copies of the human P gene in one case of tyrosinase-positive (type II) oculocutaneous albinism, recently linked to 15qll–ql3 (ref. 9).

Seasonal and topographic patterns of forest floor CO2 efflux from an upland oak forest

Abstract: Forest floor CO(2) efflux (FF(cer)) is an important component of global carbon budgets, but the spatial variability of forest floor respiration within a forest type is not well documented. Measurements of FF(cer) were initiated in mid-March of 1991 and continued at biweekly to monthly intervals until mid-November. Observations were made at 45 sites along topographic gradients of the Walker Branch Watershed, Tennessee including northeast and southwest facing slopes, valley-bottoms, and exposed ridge-top locations. The FF(cer) measurements were made with a portable gas-exchange system, and all observations were accompanied by soil temperature and soil water content measurements. As expected, FF(cer) exhibited a distinct seasonal trend following patterns of soil temperature, but soil water content and the volume percent of the soil's coarse fraction were also correlated with observed rates. Over the entire measurement period, FF(cer) ranged from a typical minimum of 0.8 micro mol m(-2) s(-1) to an average maximum near 5.7 micro mol m(-2) s(-1). No significant differences in FF(cer) were observed among the ridge-top and slope positions, but FF(cer) in the valley-bottom locations was lower on several occasions. An empirical model of FF(cer) based on these observations is suggested for application to whole-stand estimates of forest carbon sequestration.

A critique of ecosystem health concepts and indexes

Abstract: Because people wish to preserve their health and do something equivalent for ecosystems, the metaphor of ecosystem health springs to mind. This paper presents the argument that it is a mistake for environmental scientists to treat this metaphor as reality. First, the metaphor fails because it misrepresents both ecology and health science. Ecosystems are not organisms, so they do not behave like organisms and do not have properties of organisms such as health. Also, health is not an operational concept for physicians or health risk assessors because they must predict, diagnose, and treat specific states called diseases or injuries; they do not calculate indexes of health. Second, attempts to operationally define ecosystem health result in the creation of indexes of heterogeneous variables. Such indexes have no meaning; they cannot be predicted, so they are not applicable to most regulatory problems; they have no diagnostic power; effects on one component are eclipsed by responses of other components; and the reason for a high or low index value is unknown. Their only virtue is that they reduce the complex array of ecosystem responses to various disturbances to one number with a reassuring name. A better alternative is to assess the real arraymore » of ecosystem responses so that causes can be diagnosed, future states can be predicted, and benefits of treatments can be compared.« less

Decompositions of multiply charged oligonucleotide anions

Abstract: Multiply charged single-strand deoxyoligonucleotide anions fragment first by loss of a nucleobase followed by cleavage at the 3' C-O bond of the sugar from which the base is lost. Both steps are proposed to proceed via 1,2-elimination involving hydrogens from the sugar and to yield a stable substituted furan as one of the products. There is a strong preference for loss of charged adenine followed by loss of charged thymine. This tendency is strongly dependent, however, upon the internal Coulombic repulsion experienced by the ion. The position of the base in the chain is not a major factor in determining which base is lost first, except in the case of the base at the 3' terminus. The loss of the base at the 3' terminus tends to be disfavored, and this tendency may result in the more abundant loss of a charged thymine, for example, than the loss of charged adenine when the only deoxyadenylate present in the sequence is at the 3' terminus. Relatively small oligomers can be fully or nearly fully sequenced via several stages of mass spectrometry. Sequencing adjacent deoxyguanylate and deoxycytidylate residues tends to be difficult due to the much lower abundances of product ions formedmore » via reaction channels beginning with losses of cytidine and guanine. Multiple stages of mass spectrometry are facilitated by highly charged parent ions. 24 refs., 7 figs.« less

Polarized neutron determination of the magnetic excitations in YBa2Cu3O7.

Abstract: Polarization analysis has been used to identify the magnetic excitations in ${\mathrm{YBa}}_{2}$${\mathrm{Cu}}_{3}$${\mathrm{O}}_{7}$. The dominant feature in the spectra is a peak at the (\ensuremath{\pi},\ensuremath{\pi}) reciprocal lattice position and centered at 41 meV. The behavior of the peak is shown to change dramatically at ${\mathit{T}}_{\mathit{c}}$, so that the magnetic excitations responsible for the peak must be strongly coupled to the superconductivity. Below an energy of about 35 meV, superconductivity suppresses the continuum scattering found in addition to the 41-meV peak.

An age-specific kinetic model of lead metabolism in humans.

Abstract: Although considerable progress has been made in recent years in reducing human exposures to lead, the potential for high intake of this contaminant still exists in millions of homes and in many occupational settings. Moreover, there is growing evidence that levels of lead intake considered inconsequential just a few years ago can result in subtle, adverse health effects, particularly in children. Consequently, there have been increased efforts by health protection agencies to develop credible, versatile methods for relating levels of lead in environmental media to levels in blood and tissues of exposed humans of all ages. In a parallel effort motivated largely by the Chernobyl nuclear accident, the International Commission on Radiological Protection (ICRP) is assembling a set of age-specific biokinetic models for calculating radiation doses from environmentally important radionuclides, including radioisotopes of lead. This paper describes a new age-specific biokinetic model for lead originally developed for the ICRP but expanded to include additional features that are useful for consideration of lead as a chemical toxin. The model is developed within a generic, physiologically motivated framework designed to address a class of calciumlike elements. This framework provides a useful setting in which to synthesize experimental, occupational, and environmental data on lead and exploit common physiological properties of lead and the alkaline earth elements. The modular design is intended to allow researchers to modify specific parameter values or model components to address special problems in lead toxicology or to incorporate new information. Transport of lead between compartments is assumed to follow linear, first-order kinetics provided the concentration in red blood cells remains below a nonlinear threshold level, but a nonlinear relation between plasma lead and red blood cell lead is modeled for concentrations above that level. The model is shown to be consistent with data on human subjects exposed to lead under a variety of experimental and natural conditions.

A Quantitative Health Assessment Index for Rapid Evaluation of Fish Condition in the Field

Abstract: The health assessment index (HAI) is an extension and refinement of a previously published field necropsy system. The HAI is a quantitative index that allows statistical comparisons offish health among data sets. Index variables are assigned numerical values based on the degree of severity or damage incurred by an organ or tissue from environmental stressors. This approach has been used to evaluate the general health status offish populations in a wide range of reservoir types in the Tennessee River basin (North Carolina, Tennessee, Alabama, Kentucky), in Hartwell Reservoir (Georgia, South Carolina) that is contaminated by polychlorinated biphenyls, and in the Pigeon River (Tennessee, North Carolina) that receives effluents from a bleached kraft mill. The ability of the HAI to accurately characterize the health offish in these systems was evaluated by comparing this index to other types of fish health measures (contaminant, bioindicator, and reproductive analysis) made at the same time as the HAI...

Direct observation of magnetic flux lattice melting and decomposition in the high-Tc superconductor Bi2.15Sr1.95CaCu2O8+x

Abstract: The flux line lattice inside a single crystal of Bi2.15Sr1.95CaCu2O8+x has been observed using small-angle neutron diffraction. The diffracted intensity goes rapidly to zero at a magnetic-field-dependent flux lattice melting temperature; this melting coincides with the appearance of finite resistance within the superconducting state. The flux lattice signal can also be made to disappear at low temperatures, by applying a sufficiently high field, probably because of the decomposition of flux lines into two-dimensional 'pancake' vortices.

Excitation spectrum of Heisenberg spin ladders.

Abstract: Heisenberg antiferromagnetic spin ``ladders'' (two coupled spin chains) are low-dimensional magnetic systems which for S=1/2 interpolate between half-integer-spin chains, when the chains are decoupled, and effective integer-spin one-dimensional chains in the strong-coupling limit. The spin-1/2 ladder may be realized in nature by vanadyl pyrophosphate, (VO${)}_{2}$${\mathrm{P}}_{2}$${\mathrm{O}}_{7}$. In this paper we apply strong-coupling perturbation theory, spin-wave theory, Lanczos techniques, and a Monte Carlo method to determine the ground-state energy and the low-lying excitation spectrum of the ladder. We find evidence of a nonzero spin gap for all interchain couplings ${\mathit{J}}_{\mathrm{\ensuremath{\perp}}}$g0. A band of spin-triplet excitations above the gap is also analyzed. These excitations are unusual for an antiferromagnet, since their long-wavelength dispersion relation behaves as (k-${\mathit{k}}_{0}$${)}^{2}$ (in the strong-coupling limit ${\mathit{J}}_{\mathrm{\ensuremath{\perp}}}$\ensuremath{\gg}J, where J is the in-chain antiferromagnetic coupling). Their band is folded, with a minimum energy at ${\mathit{k}}_{0}$=\ensuremath{\pi}, and a maximum between ${\mathit{k}}_{1}$=\ensuremath{\pi}/2 (for ${\mathit{J}}_{\mathrm{\ensuremath{\perp}}}$=0) and 0 (for ${\mathit{J}}_{\mathrm{\ensuremath{\perp}}}$=\ensuremath{\infty}). We also give numerical results for the dynamical structure factor S(q,\ensuremath{\omega}), which can be determined in neutron scattering experiments. Finally, possible experimental techniques for studying the excitation spectrum are discussed.

Direct imaging of surface cusp evolution during strained-layer epitaxy and implications for strain relaxation.

Abstract: We have directly imaged the evolution of surface cusps during strained-layer epitaxy The cusps arise naturally as a result of gradients in the surface chemical potential High stress concentrations at the cusp tip have important implications for strain relaxation in the film via dislocation nucleation

Evaluation of a three-exposure mouse bone marrow micronucleus protocol: Results with 49 chemicals

Abstract: Forty-nine chemicals were tested in a mouse bone marrow micronucleus test that employed three daily exposures by intraperitoneal injection. Bone marrow samples were obtained 24 hr following the final exposure. Twenty-five rodent carcinogens and 24 noncarcinogens were selected randomly from the 44 carcinogens and 29 noncarcinogens used by Tennant et al. (Science 236:933-941, 1987) to evaluate the performance of four in vitro genetic toxicity tests. As in that study of in vitro tests, the micronucleus tests were conducted with coded chemicals and test results (positive or negative) were determined prior to decoding. This study was conducted as part of an effort to assess the ability of the micronucleus test to discriminate between rodent carcinogens and noncarcinogens and to determine its potential role, in combination with other short-term tests, in identifying genotoxic chemicals that present a carcinogenic hazard. Nine chemicals were judged to be positive in the micronucleus test. This relatively low number of positive results, along with published and unpublished results from rodent micronucleus and chromosome aberration assays on several of these 49 chemicals, contributed to the conclusion that a single micronucleus test protocol is not adequate to detect all chemicals capable of inducing chromosomal damage in the bone marrow. However, a combination of two relatively simple assays such as the Salmonella and micronucleus tests can provide important information on the genetic toxicity of test chemicals and may provide guidance on the need for and the nature and extent of future toxicity studies.

Biological Diversity, Soils, and Economics

Abstract: Terrestrial biological diversity is supported by solar energy captured by plants growing in soil. This soil-based plant productivity also provides the foundation for human societies through production of food and renewable forms of energy. Variations in plant productivity, resulting from differences in inherent soil fertility, variations in climate and weather, and differences in chemical inputs and agricultural practices, produce patterns of biological diversity that are associated with the agricultural component of economic productivity. Ecological processes lead to a generally negative relation between the diversity of plant species and potential agricultural productivity at both local and global scales. One implication of this negative relation is that preservation of areas of high plant biodiversity does not require the sacrifice of productive agricultural lands.

Picosecond nonlinear optical response of a Cu:silica nanocluster composite

Abstract: We describe the picosecond nonlinear optical response of a metal-dielectric composite made by implanting Cu ions in fused silica. The implanted Cu ions aggregate during implantation to form nanometer-diameter clusters in a dense, thin (~150 nm) layer just beneath the surface of the substrate. The third-order susceptibility X((3)) has an electronic component with a magnitude of the order of 10(-8) esu and is enhanced for laser wavelengths near the surface plasmon resonance of the copper colloids.

A review of information on ferrocyanide solids for removal of cesium from solutions

Abstract: Ferrocyanide solids have important applications to the removal of radioactive cesium from nuclear waste solutions. These materials are prepared by mixing soluble ferrocyanides and salts of divalent transition metals or other divalent cations. The simple precipitations most commonly give very fine particles or slimes of variable compositions. Special preparation procedures have been developed to control the compositions or to prepare granular solids suitable for column operation. The removal of cesium from solutions has been measured for many different ferrocyanide solids. Some of these solids show an exchange of K+, Na+, or NH4 + for cesium, but many show sorptions of cesium without a true ion exchange. The performance for cesium removal is described by measurements of the distribution coefficients for cesium with large excesses of ferrocyanides, the capacity for cesium with excess cesium in solution, and the rates of cesium removal. The chemical and physical stability, the solubility, and the el...

Equilibrium point defects in intermetallics with the B2 structure: NiAl and FeAl.

Abstract: Equilibrium point defects and their relation to the contrasting mechanical behavior of NiAl and FeAl are investigated. For NiAl, the defect structure is dominated by two types of defects---monovacancies on the Ni sites and substitutional antisite defects on the Al sites. The defect structure of FeAl differs from that of NiAl in the occurrence of antisite defects at the transition-metal sites for Al-rich alloys and the tendency for vacancy clustering. The strong ordering (and brittleness) of NiAl is attributed mainly to the difference in atomic size between constituent atoms.