bluuebunny/crossref_metadata_2025_split huggingface dataset:
ATPase/helicase motif mutants of Escherichia coli PriA protein essential for recombination‐dependent DNA replication
Authors: Tanaka Taku , Taniyama Chika , Arai Ken‐Ichi , Masai Hisao 
Published: March 2003

AbstractBackgrounds: PriA protein, a DEXH‐type helicase with C2C2 zinc‐finger motifs, plays essential roles in RecA‐dependent modes of Escherichia coli chromosomal DNA replication, namely inducible and constitutive stable DNA replication (iSDR and cSDR respectively, which may be initiated from a D‐loop or R‐loop structure), and in repair of double‐stranded DNA breaks generated by various genotoxic agents or spontaneously during the course of DNA replication. However, the roles of ATPase/DNA helicase activities in functions of PriA are not well understood.Results: We have generated and characterized mutants of PriA protein carrying amino acid substitutions in its conserved ATPase/DNA helicase motifs, namely the Walker A, B and QXXGRXGR motifs. All these mutants were deficient in ATP hydrolysis and DNA helicase activities, but showed wild‐type levels of D‐loop DNA binding, except for the Walker B mutant which showed reduced DNA binding activity, suggesting that the helicase motifs are not directly involved in the DNA binding activity of PriA protein. They also rescued the low viability and UV‐sensitivity of priA null cells. However, they did not rescue iSDR or cSDR—alternative modes of chromosomal DNA replication of the E. coli genome dependent on recombination functions—to the full extent.Conclusions: ATPase/DNA helicase activities of PriA protein are required for full‐level DNA synthesis in recombination‐dependent modes of DNA replication in E. coli.
ATP‐induced hexameric ring structure of the cyanobacterial circadian clock protein KaiC
Authors: Hayashi Fumio , Suzuki Hirofumi , Iwase Ryo , Uzumaki Tatsuya , Miyake Asako , Shen Jian‐Ren , Imada Katsumi , Furukawa Yukio , Yonekura Koji , Namba Keiichi , Ishiura Masahiro 
Published: March 2003

AbstractBackground: KaiA, KaiB and KaiC are cyanobacterial circadian clock proteins. KaiC contains two ATP/GTP‐binding Walker's motif As, and mutations in these regions affect the clock oscillations.Results: ATP induced the hexamerization of KaiC. The Km value for the ATP for the hexamerization was 1.9 µm. Triphosphate nucleotides bound to the two Walker's motif As, and their binding functioned cooperatively for the hexamerization. An unhydrolysable substrate, 5′‐adenylylimidodiphosphate (AMPPNP), also induced the hexamerization, indicating that nucleotide binding, but not its hydrolysis, is essential for the hexamerization. Mutations in each of the two Walker's motif As that affect the clock phenotype increased the Km value for ATP and inhibited the hexamerization. Thus, the KaiC hexamerization seems to be necessary for its clock function. The KaiC hexamer has the shape of a hexagonal pot with a diameter and height of approximately 100 Å and with a relatively large cavity (73 Å deep and 18–34 Å wide) inside. This pot‐shaped structure suggests that KaiC functions in a similar manner to F1‐ATPase, helicase or ATP‐dependent protease/chaperon, all of which have dynamic activities inside the central cavity of their hexameric rings.Conclusion: ATP‐induced KaiC hexamerization is necessary for the clock function of KaiC.
Background velocity estimation using non‐linear optimization for reflection tomography and migration misfit
Authors: Varela Carlos L. , Stoffa Paul L. , Sen Mrinal K. 
Published: March 2003

We show that it is possible to estimate the background velocity for prestack depth migration in 2D laterally varying media using a non‐linear optimization technique called very fast simulated annealing (VFSA). We use cubic splines in the velocity model parametrization and make use of either successive pairs of shot gathers or several constant‐offset sections as input data for the inversion. A Kirchhoff summation scheme based on first‐arrival traveltimes is used to migrate/model the input data during the velocity analysis. We evaluate and compare two different measures of error. The first is defined in the recorded data or (x,t) domain and is based on a reflection‐tomography criterion. The second is defined in the migrated data or (x,z) domain and is based on a migration‐misfit criterion. Depth relaxation is used to improve the convergence and quality of the velocity analysis while simultaneously reducing the computational cost. Further, we show that by coarse sampling in the offset domain the method is still robust.Our non‐linear optimization approach to migration velocity analysis is evaluated for both synthetic and real seismic data. For the velocity‐analysis method based on the reflection‐tomography criterion, traveltimes do not have to be picked. Similarly, the migration‐misfit criterion does not require that depth images be manually compared. Interpreter intervention is required only to restrict the search space used in the velocity‐analysis problem. Extension of the proposed schemes to 3D models is straightforward but practical only for the fastest available computers.
Non‐equilibrium compaction and abnormal pore‐fluid pressures: effects on rock properties1
Authors: Carcione José M. , Gangi Anthony F. 
Published: March 2003

Knowledge of pore pressure using seismic data will help in planning the drilling process to control potentially dangerous abnormal pressures. Various physical processes cause anomalous pressures on an underground fluid. Non‐equilibrium compaction is a significant process of overpressure generation. This occurs when the sedimentation rate is so rapid that the pore fluids do not have a chance to ‘escape’ from the pore space.The model assumes a closed system and that the pore space is filled with water and hydrocarbon in a liquid state. Balancing mass and volume fractions yields the fluid pressure versus time of deposition and depth of burial. Thermal effects are taken into account. The pore pressure, together with the confining pressure, determines the effective pressure which, in turn, determines the bulk moduli of the rock matrix.We assume a sandstone saturated with hydrocarbons and water, for which calibration of the model with experimental data is possible. The seismic velocities and attenuation factors are computed by using Biot’s theory of dynamic poroelasticity and the generalized linear solid. The example shows that the formation can be overpressured or underpressured depending on the properties of the saturating fluid. Wave velocities and quality factors decrease with decreasing differential pressure. The effect is important below approximately 20 MPa. The model is in good agreement with experimental data for Berea sandstone and provides a tool for predicting pore pressure from seismic attributes.
Ray tracing in elliptical anisotropic media using the linear traveltime interpolation (LTI) method applied to traveltime seismic tomography
Authors: Cardarelli Ettore , Antonio Cerreto  
Published: March 2003

The linear traveltime interpolation (LTI) method is a suitable ray‐tracing technique for modelling first‐arrival times in isotropic media. LTI is extended to elliptical anisotropic media and applied to a tomographic inversion procedure. A theoretical formulation is first derived and then LTI implementation is discussed in terms of source–receiver arrays and cell size. The method is then combined with the tomographic inversion procedure adopted. The matching of the ray tracing with inversion in elliptical anisotropic media posed a double non‐linear problem. Thus two assumptions were made: the velocity in each cell is uniform and the main directions of anisotropy are known. To take into account the geometrical characteristics of the area under investigation (depth and velocity of the weathering, and thickness of the inner media), cells of varying size were considered. No hypothesis was made on anisotropy weakness.The algorithm was first tested on synthetic models and then applied to a field survey. On comparing the results of the synthetic models and the field survey with those obtained with a linear raypath approximation, it was found that there were fewer data misfits.
An approach to combined rock physics and seismic modelling of fluid substitution effects
Authors: Johansen Tor Arne , Drottning Åsmund , Lecomte Isabelle , Gjøystdal Håvar 
Published: March 2003

ABSTRACTThe aim of seismic reservoir monitoring is to map the spatial and temporal distributions and contact interfaces of various hydrocarbon fluids and water within a reservoir rock. During the production of hydrocarbons, the fluids produced are generally displaced by an injection fluid. We discuss possible seismic effects which may occur when the pore volume contains two or more fluids. In particular, we investigate the effect of immiscible pore fluids, i.e. when the pore fluids occupy different parts of the pore volume.The modelling of seismic velocities is performed using a differential effective‐medium theory in which the various pore fluids are allowed to occupy the pore space in different ways. The P‐wave velocity is seen to depend strongly on the bulk modulus of the pore fluids in the most compliant (low aspect ratio) pores. Various scenarios of the microscopic fluid distribution across a gas–oil contact (GOC) zone have been designed, and the corresponding seismic properties modelled. Such GOC transition zones generally give diffuse reflection regions instead of the typical distinct GOC interface. Hence, such transition zones generally should be modelled by finite‐difference or finite‐element techniques.We have combined rock physics modelling and seismic modelling to simulate the seismic responses of some gas–oil zones, applying various fluid‐distribution models. The seismic responses may vary both in the reflection time, amplitude and phase characteristics. Our results indicate that when performing a reservoir monitoring experiment, erroneous conclusions about a GOC movement may be drawn if the microscopic fluid‐distribution effects are neglected.
Resistivity of partially saturated Triassic Sandstone
Authors: Taylor Steve , Barker Ron 
Published: March 2003

ABSTRACTThe variation in resistivity with saturation of poorly cemented Triassic Sandstone samples from a site in the English Midlands has been measured. The measurements were obtained using an adapted four‐electrode technique, which utilizes conductive gelling agents between electrodes, avoiding the need to sputter electrodes directly on to samples – a difficult process with such friable samples. The measurements provide important information regarding the way in which resistivity varies with saturation in the Triassic Sandstone. The resulting variation in the observed resistivity versus saturation curves indicates the presence of significant pore‐scale variation between samples. Measurements have also been conducted on fully saturated samples. These indicate significant variation in the matrix conductivity between samples. The results have important implications for field‐scale monitoring of the unsaturated zone.
Iterative resolution estimation in least‐squares Kirchhoff migration
Authors: Fomel Sergey , Berryman James G. , Clapp Robert G. , Prucha Marie 
Published: March 2003

ABSTRACTWe apply iterative resolution estimation to least‐squares Kirchhoff migration. Reviewing the theory of iterative optimization uncovers the common origin of different optimization methods. This allows us to reformulate the pseudo‐inverse, model resolution and data resolution operators in terms of effective iterative estimates. When applied to Kirchhoff migration, plots of the diagonal of the model resolution matrix reveal low illumination areas on seismic images and provide information about image uncertainties. Synthetic and real data examples illustrate the proposed technique and confirm the theoretical expectations.
A new method to discriminate between a valid IP response and EM coupling effects
Authors: Xiang Jianping , Jones N.B. , Cheng Daizhan , Schlindwein F.S. 
Published: March 2003

ABSTRACTThe problem of discrimination between a valid induced polarization (IP) response and electromagnetic (EM) coupling effects is considered and an effective solution is provided. First, a finite dimensional approximation to the Cole‐Cole model is investigated. Using the least‐squares approach, the parameters of the approximate model are obtained. Next, based on the analysis of overvoltage, a finite dimensional structure of the IP model is produced. Using this overvoltage‐based structure, a specific finite dimensional approximation of the Cole‐Cole model is proposed. Summarizing the analysis of the finite dimensional IP model, it is concluded that the proposed IP model, which fits the field data much better than the traditional Cole‐Cole model, is essentially an RC‐circuit. From a circuit‐analysis point of view, it is well known that an electromagnetic effect can be described by an RL‐circuit. The simulation results on experimental data support this conception. According to this observation, a new method to discriminate between a valid IP response and EM coupling effects is proposed as follows: (i) use a special finite dimensional model for IP–EM systems; (ii) obtain the parameters for the model using a least‐squares approach; (iii) separate RC‐type terms and RL‐type terms – the first models the IP behaviour, the latter represents the EM part. Simulation on experimental data shows that the method is very simple and effective.
The global carbon sink: a grassland perspective
Authors: Scurlock J. M. O. , Hall D. O. 
Published: March 2003

AbstractThe challenge to identify the biospheric sinks for about half the total carbon emissions from fossil fuels must include a consideration of below‐ground ecosystem processes as well as those more easily measured above‐ground. Recent studies suggest that tropical grasslands and savannas may contribute more to the ‘missing sink’ than was previously appreciated, perhaps as much as 0.5 Pg (= 0.5 Gt) carbon per annum. The rapid increase in availability of productivity data facilitated by the Internet will be important for future scaling‐up of global change responses, to establish independent lines of evidence about the location and size of carbon sinks.
Growth dynamics and genotypic variation in tropical, field‐grown paddy rice (Oryza sativa L.) in response to increasing carbon dioxide and temperature
Authors: MOYA TOLENTINO B. , ZISKA LEWIS H. , NAMUCO OFELIA S. , OLSZYK DAVE. 
Published: March 2003

AbstractWhile previous studies have examined the growth and yield response of rice to continued increases in CO2 concentration and potential increases in air temperature, little work has focused on the long‐term response of tropical paddy rice (i.e. the bulk of world rice production) in situ, or genotypic differences among cultivars in response to increasing CO2 and/or temperature. At the International Rice Research Institute, rice (cv IR72) was grown from germination until maturity for 4 field seasons, the 1994 and 1995 wet and the 1995 and 1996 dry seasons at three different CO2 concentrations (ambient, ambient + 200 and ambient + 300 μL L–1 CO2) and two air temperatures (ambient and ambient + 4 °C) using open‐top field chambers placed within a paddy site. Overall, enhanced levels of CO2 alone resulted in significant increases in total biomass at maturity and increased seed yield with the relative degree of enhancement consistent over growing seasons across both temperatures. Enhanced levels of temperature alone resulted in decreases or no change in total biomass and decreased seed yield at maturity across both CO2 levels. In general, simultaneous increases in air temperature as well as CO2 concentration offset the stimulation of biomass and grain yield compared to the effect of CO2 concentration alone. For either the 1995 wet and 1996 dry seasons, additional cultivars (N‐22, NPT1 and NPT2) were grown in conjunction with IR72 at the same CO2 and temperature treatments. Among the cultivars tested, N‐22 showed the greatest relative response of both yield and biomass to increasing CO2, while NPT2 showed no response and IR72 was intermediate. For all cultivars, however, the combination of increasing CO2 concentration and air temperature resulted in reduced grain yield and declining harvest index compared to increased CO2 alone. Data from these experiments indicate that (a) rice growth and yield can respond positively under tropical paddy conditions to elevated CO2, but that simultaneous exposure to elevated temperature may negate the CO2 response to grain yield; and, (b) sufficient intraspecific variation exists among cultivars for future selection of rice cultivars which may, potentially, convert greater amounts of CO2 into harvestable yield.
Transferring soils from high‐ to low‐elevation forests increases nitrogen cycling rates: climate change implications
Authors: Hart Stephen C. , Perry David A. 
Published: March 2003

AbstractWe assessed the potential impact of global warming resulting from a doubling of preindustrial atmospheric CO2 on soil net N transformations by transferring intact soil cores (0–15 cm) from a high‐elevation old‐growth forest to a forest about 800 m lower in elevation in the central Oregon Cascade Mountains, USA. The lower elevation site had mean annual air and soil (10‐cm mineral soil depth) temperatures about 2.4 and 3.9 °C higher than the high‐elevation site, respectively. Annual rates of soil net N mineralization and nitrification more than doubled in soil transferred to the low‐elevation site (17.2–36.0 kg N ha–1 and 5.0–10.7 kg NO3––N ha–1, respectively). Leaching of inorganic N from the surface soil (in the absence of plant uptake) also increased. The reciprocal treatment (transferring soil cores from the low‐ to the high‐elevation site) resulted in decreases of about 70, 80, and 65% in annual rates of net N mineralization, nitrification, and inorganic N leaching, respectively. Laboratory incubations of soils under conditions of similar temperature and soil water potential suggest that the quality of soil organic matter is higher at the high‐elevation site. Similar in situ rates of soil net N transformations between the two sites occurred because the lower temperature counteracts the effects of greater substrate quantity and quality at the high elevation site. Our results support the hypothesis that high‐elevation, old‐growth forest soils in the central Cascades have higher C and N storage than their low‐elevation analogues primarily because low temperatures limit net C and N mineralization rates at higher elevations.
Seasonal and annual respiration of a ponderosa pine ecosystem
Authors: Law Beverly E. , Ryan Michael G. , Anthoni Peter M. 
Published: March 2003

AbstractThe net ecosystem exchange of CO2 between forests and the atmosphere, measured by eddy covariance, is the small difference between two large fluxes of photosynthesis and respiration. Chamber measurements of soil surface CO2 efflux (Fs), wood respiration (Fw) and foliage respiration (Ff) help identify the contributions of these individual components to net ecosystem exchange. Models developed from the chamber data also provide independent estimates of respiration costs. We measured CO2 efflux with chambers periodically in 1996–97 in a ponderosa pine forest in Oregon, scaled these measurements to the ecosystem, and computed annual totals for respiration by component. We also compared estimated half‐hourly ecosystem respiration at night (Fnc) with eddy covariance measurements. Mean foliage respiration normalized to 10 °C was 0.20 μmol m–2 (hemi‐leaf surface area) s–1, and reached a maximum of 0.24 μmol m–2 HSA s–1 between days 162 and 208. Mean wood respiration normalized to 10 °C was 5.9 μmol m–3 sapwood s–1, with slightly higher rates in mid‐summer, when growth occurs. There was no significant difference (P > 0.10) between wood respiration of young (45 years) and old trees (250 years). Soil surface respiration normalized to 10 °C ranged from 0.7 to 3.0 μmol m–2 (ground) s–1 from days 23 to 329, with the lowest rates in winter and highest rates in late spring. Annual CO2 flux from soil surface, foliage and wood was 683, 157, and 54 g C m–2 y–1, with soil fluxes responsible for 76% of ecosystem respiration. The ratio of net primary production to gross primary production was 0.45, consistent with values for conifer sites in Oregon and Australia, but higher than values reported for boreal coniferous forests. Below‐ground carbon allocation (root turnover and respiration, estimated as Fs– litterfall carbon) consumed 61% of GPP; high ratios such as this are typical of sites with more water and nutrient constraints. The chamber estimates were moderately correlated with change in CO2 storage in the canopy (Fstor) on calm nights (friction velocity u* < 0.25 m s–1; R2 = 0.60); Fstor was not significantly different from summed chamber estimates. On windy nights (u* > 0.25 m s–1), the sum of turbulent flux measured above the canopy by eddy covariance and Fstor was only weakly correlated with summed chamber estimates (R2 = 0.14); the eddy covariance estimates were lower than chamber estimates by 50%.
The effects of free‐air CO2 enrichment and soil water availability on spatial and seasonal patterns of wheat root growth
Authors: Wechsung G. , Wechsung F. , Wall G. W. , Adamsen F. J. , Kimball B. A. , Pinter JR. P. J. , Lamorte R. L. , Garcia R. L. , Kartschall TH. 
Published: March 2003

Abstract Spring wheat [
Triticum aestivum (L). cv. Yecora Rojo] was grown from December 1992 to May 1993 under two atmospheric CO2 concentrations, 550 μmol mol–1 for high‐CO2 plots, and 370 μmol mol–1 for control plots, using a Free‐Air CO2 Enrichment (FACE) apparatus. In addition to the two levels of atmospheric CO2, there were ample and limiting levels of water supply through a subsurface trip irrigation system in a strip, split‐plot design. In order to examine the temporal and spatial root distribution, root cores were extracted at six growth stages during the season at in‐row and inter‐row positions using a soil core device (86 mm ID, 1.0 m length). Such information would help determine whether and to what extent root morphology is changed by alteration of two important factors, atmospheric CO2 and soil water, in this agricultural ecosystem.Wheat root growth increased under elevated CO2 conditions during all observed developmental stages. A maximum of 37% increase in total root dry mass in the FACE vs. Control plots was observed during the period of stem elongation. Greater root growth rates were calculated due to CO2 enhancement until anthesis. During the early vegetative growth, root dry mass of the inter‐row space was significantly higher for FACE than for Control treatments suggesting that elevated CO2 promoted the production of first‐order lateral roots per main axis. Then, during the reproductive period of growth, more branching of lateral roots in the FACE treatment occurred due to water stress. Significant higher root dry mass was measured in the inter‐row space of the FACE plots where soil water supply was limiting. These sequential responses in root growth and morphology to elevated CO2 and reduced soil water supports the hypothesis that plants grown in a high‐CO2 environment may better compensate soil‐water‐stress conditions.