bluuebunny/crossref_metadata_2025_split huggingface dataset:
Quantitative Trait Loci for Component Physiological Traits Determining Salt Tolerance in Rice
Authors: Koyama Mikiko L. , Levesley Aurora , Koebner Robert M.D. , Flowers Timothy J. , Yeo Anthony R. 
Published: July 2002

Abstract
Rice (Oryza sativa) is sensitive to salinity, which affects one-fifth of irrigated land worldwide. Reducing sodium and chloride uptake into rice while maintaining potassium uptake are characteristics that would aid growth under saline conditions. We describe genetic determinants of the net quantity of ions transported to the shoot, clearly distinguishing between quantitative trait loci (QTL) for the quantity of ions in a shoot and for those that affect the concentration of an ion in the shoot. The latter coincide with QTL for vegetative growth (vigor) and their interpretation is therefore ambiguous. We distinguished those QTL that are independent of vigor and thus directly indicate quantitative variation in the underlying mechanisms of ion uptake. These QTL independently govern sodium uptake, potassium uptake, and sodium:potassium selectivity. The QTL for sodium and potassium uptake are on different linkage groups (chromosomes). This is consistent with the independent inheritance of sodium and potassium uptake in the mapping population and with the mechanistically different uptake pathways for sodium and potassium in rice under saline conditions (apoplastic leakage and membrane transport, respectively). We report the chromosomal location of ion transport and selectivity traits that are compatible with agronomic needs and we indicate markers to assist selection in a breeding program. Based upon knowledge of the underlying mechanisms of ion uptake in rice, we argue that QTL for sodium transport are likely to act through the control of root development, whereas QTL for potassium uptake are likely to act through the structure or regulation of membrane-sited transport components.
Increased Sensitivity of Photosynthesis to Antimycin A Induced by Inactivation of the Chloroplast ndhB Gene. Evidence for a Participation of the NADH-Dehydrogenase Complex to Cyclic Electron Flow around Photosystem I
Authors: Joët Thierry , Cournac Laurent , Horvath Eva M. , Medgyesy Peter , Peltier Gilles 
Published: July 2002

Abstract
Tobacco (Nicotiana tabacum var Petit Havana)ndhB-inactivated mutants (ndhB −) obtained by plastid transformation (E.M. Horvath, S.O. Peter, T. Joët, D. Rumeau, L. Cournac, G.V. Horvath, T.A. Kavanagh, C. Schäfer, G. Peltier, P. MedgyesyHorvath [2000] Plant Physiol 123: 1337–1350) were used to study the role of the NADH-dehydrogenase complex (NDH) during photosynthesis and particularly the involvement of this complex in cyclic electron flow around photosystem I (PSI). Photosynthetic activity was determined on leaf discs by measuring CO2exchange and chlorophyll fluorescence quenchings during a dark-to-light transition. In the absence of treatment, both non-photochemical and photochemical fluorescence quenchings were similar inndhB − and wild type (WT). When leaf discs were treated with 5 μm antimycin A, an inhibitor of cyclic electron flow around PSI, both quenchings were strongly affected. At steady state, maximum photosynthetic electron transport activity was inhibited by 20% in WT and by 50% inndhB −. Under non-photorespiratory conditions (2% O2, 2,500 μL L−1CO2), antimycin A had no effect on photosynthetic activity of WT, whereas a 30% inhibition was observed both on quantum yield of photosynthesis assayed by chlorophyll fluorescence and on CO2 assimilation in ndhB −. The effect of antimycin A on ndhB − could not be mimicked by myxothiazol, an inhibitor of the mitochondrial cytochromebc 1 complex, therefore showing that it is not related to an inhibition of the mitochondrial electron transport chain but rather to an inhibition of cyclic electron flow around PSI. We conclude to the existence of two different pathways of cyclic electron flow operating around PSI in higher plant chloroplasts. One of these pathways, sensitive to antimycin A, probably involves ferredoxin plastoquinone reductase, whereas the other involves the NDH complex. The absence of visible phenotype in ndhB −plants under normal conditions is explained by the complement of these two pathways in the supply of extra-ATP for photosynthesis.
Long-Distance Signaling and the Control of Branching in therms1 Mutant of Pea
Authors: Foo Eloise , Turnbull Colin G.N. , Beveridge Christine A. 
Published: July 2002

Abstract
The ramosus (rms) mutation (rms1) of pea (Pisum sativum) causes increased branching through modification of graft-transmissible signal(s) produced in rootstock and shoot. Additional grafting techniques have led us to propose that the novel signal regulated byRms1 moves acropetally in shoots and acts as a branching inhibitor. Epicotyl interstock grafts showed that wild-type (WT) epicotyls grafted between rms1 scions and rootstocks can revert mutant scions to a WT non-branching phenotype. Mutant scions grafted together with mutant and WT rootstocks did not branch despite a contiguous mutant root-shoot system. The primary action ofRms1 is, therefore, unlikely to be to block transport of a branching stimulus from root to shoot. Rather, Rms1may influence a long-distance signal that functions, directly or indirectly, as a branching inhibitor. It can be deduced that this signal moves acropetally in shoots because WT rootstocks inhibit branching in rms1 shoots, and although WT scions do not branch when grafted to mutant rootstocks, they do not inhibit branching in rms1 cotyledonary shoots growing from the same rootstocks. The acropetal direction of transport of theRms1 signal supports previous evidence that therms1 lesion is not in an auxin biosynthesis or transport pathway. The different branching phenotypes of WT andrms1 shoots growing from the same rms1rootstock provides further evidence that the shoot has a major role in the regulation of branching and, moreover, that root-exported cytokinin is not the only graft-transmissible signal regulating branching in intact pea plants.
Targeting a Nuclear Anthranilate Synthase α-Subunit Gene to the Tobacco Plastid Genome Results in Enhanced Tryptophan Biosynthesis. Return of a Gene to Its Pre-Endosymbiotic Origin
Authors: Zhang Xing-Hai , Brotherton Jeffrey E. , Widholm Jack M. , Portis Archie R. 
Published: July 2002

AbstractAnthranilate synthase (AS), the control enzyme of the tryptophan (Trp) biosynthetic pathway, is encoded by nuclear genes, but is transported into the plastids. A tobacco (Nicotiana tabacum) cDNA (ASA2) encoding a feedback-insensitive tobacco AS α-subunit was transformed into two different sites of the tobacco plastid genome through site-specific insertion to obtain transplastomic plants with normal phenotype and fertility. A high and uniform level of ASA2 mRNA was observed in the transplastomic plants but not in the wild type. Although the plants with the transgene insertion atndhF-trnL only expressed one size of theASA2 mRNA, the plants with the transgene incorporated into the region between accD and open reading frame (ORF) 184 exhibited two species of mRNA, apparently due to readthrough. The transplastomic plants exhibited a higher level of AS α-subunit protein and AS enzyme activity that was less sensitive to Trp-feedback inhibition, leading to greatly increased free Trp levels in leaves and total Trp levels in seeds. Resistance to an AS inhibitor, 5-methyl-Trp, was found during seed germination and in suspension cultures of the transplastomic plants. The resistance to the selection agent spectinomycin and to 5-methyl-Trp was transmitted maternally. These results demonstrate the feasibility of modifying the biosynthetic pathways of important metabolites through transformation of the plastid genome by relocating a native gene from the nucleus to the plastid genome. Very high and uniform levels of gene expression can be observed in different lines, probably due to the identical insertion sites, in contrast to nuclear transformation where random insertions occur.
Conformational analysis of putative regulatory subunit D of the toluene/o‐xylene‐monooxygenase complex from Pseudomonas stutzeri OX1
Authors: Scognamiglio Roberta , Notomista Eugenio , Barbieri Paola , Pucci Piero , Piaz Fabrizio Dal , Tramontano Anna , Di Donato Alberto 
Published: July 2002

AbstractA gene cluster isolated from Pseudomonas stutzeri OX1 genomic DNA and containing six ORFs codes for toluene/o‐xylene‐monooxygenase. The putative regulatory D subunit was expressed in Escherichia coli and purified. Its protein sequence was verified by mass spectrometry mapping and found to be identical to the sequence predicted on the basis of the DNA sequence. The surface topology of subunit D in solution was probed by limited proteolysis carried out under strictly controlled conditions using several proteases as proteolytic probes. The same experiments were carried out on the homologous P2 component of the multicomponent phenol hydroxylase from Pseudomonas putida CF600. The proteolytic fragments released from both proteins in their native state were analyzed by electrospray mass spectrometry, and the preferential cleavage sites were assessed.The results indicated that despite the relatively high similarity between the sequences of the two proteins, some differences in the distribution of preferential proteolytic cleavages were detected, and a much higher conformational flexibility of subunit D was inferred. Moreover, automatic modeling of subunit D was attempted, based on the known three‐dimensional structure of P2. Our results indicate that, at least in this case, standard modeling procedures based on automatic alignment on the structure of P2 fail to produce a model consistent with limited proteolysis experimental data. Thus, it is our opinion that reliable techniques such as limited proteolysis can be employed to test three‐dimensional models and highlight problems in automatic model building.
Extending the capabilities of targeted molecular dynamics: Simulation of a large conformational transition in plasminogen activator inhibitor 1
Authors: Krüger Peter , Verheyden Stefan , Declerck Paul J. , Engelborghs Yves 
Published: July 2002

AbstractPlasminogen activator inhibitor type 1 (PAI‐1) is an inhibitor of plasminogen activators such as tissue‐type plasminogen activator or urokinase‐type plasminogen activator. For this molecule, different conformations are known. The inhibiting form that interacts with the proteinases is called the active form. The noninhibitory, noncleavable form is called the latent form. X‐ray and modeling studies have revealed a large change in position of the reactive center loop (RCL), responsible for the interaction with the proteinases, that is inserted into a β‐sheet (s4A) in the latent form. The mechanism underlying this spontaneous conformational change (half‐life = 2 h at 37°C) is not known in detail. This investigation attempts to predict a transition path from the active to the latent structure at the atomic level, by using simulation techniques. Together with targeted molecular dynamics (TMD), a plausible assumption on a rigid body movement of the RCL was applied to define an initial guess for an intermediate. Different pathways were simulated, from the active to the intermediate, from the intermediate to the latent structure and vice versa under different conditions. Equilibrium simulations at different steps of the path also were performed. The results show that a continuous pathway from the active to the latent structure can be modeled. This study also shows that this approach may be applied in general to model large conformational changes in any kind of protein for which the initial and final three‐dimensional structure is known.
Environmental features are important in determining protein secondary structure
Authors: Macdonald J. Randy , Johnson W. Curtis 
Published: July 2002

AbstractWe have investigated amino acid features that determine secondary structure: (1) the solvent accessibility of each side chain, and (2) the interaction of each side chain with others one to four residues apart. Solvent accessibility is a simple model that distinguishes residue environment. The pairwise interactions represent a simple model of local side chain to side chain interactions. To test the importance of these features we developed an algorithm to separate α‐helices, β‐strands, and “other” structure. Single residue and pairwise probabilities were determined for 25,141 samples from proteins with <30% homology. Combining the features of solvent accessibility with pairwise probabilities allows us to distinguish the three structures after cross validation at the 82.0% level. We gain 1.4% to 2.0% accuracy by optimizing the propensities, demonstrating that probabilities do not necessarily reflect propensities. Optimization of residue exposures, weights of all probabilities, and propensities increased accuracy to 84.0%.
Crystal structure of a deletion mutant of human thymidylate synthase Δ (7–29) and its ternary complex with Tomudex and dUMP
Authors: Almog Rami , Waddling Christopher A. , Maley Frank , Maley Gladys F. , Van Roey Patrick 
Published: July 2002

AbstractThe crystal structures of a deletion mutant of human thymidylate synthase (TS) and its ternary complex with dUMP and Tomudex have been determined at 2.0 Å and 2.5 Å resolution, respectively. The mutant TS, which lacks 23 residues near the amino terminus, is as active as the wild‐type enzyme. The ternary complex is observed in the open conformation, similar to that of the free enzyme and to that of the ternary complex of rat TS with the same ligands. This is in contrast to Escherichia coli TS, where the ternary complex with Tomudex and dUMP is observed in the closed conformation. While the ligands interact with each other in identical fashion regardless of the enzyme conformation, they are displaced by about 1.0 Å away from the catalytic cysteine in the open conformation. As a result, the covalent bond between the catalytic cysteine sulfhydryl and the base of dUMP, which is the first step in the reaction mechanism of TS and is observed in all ternary complexes of the E. coli enzyme, is not formed. This displacement results from differences in the interactions between Tomudex and the protein that are caused by differences in the environment of the glutamyl tail of the Tomudex molecule. Despite the absence of the closed conformation, Tomudex inhibits human TS ten‐fold more strongly than E. coli TS. These results suggest that formation of a covalent bond between the catalytic cysteine and the substrate dUMP is not required for effective inhibition of human TS by cofactor analogs and could have implications for drug design by eliminating this as a condition for lead compounds.
Prediction of Flow and Heat Transfer in Rotating Two-Pass Rectangular
Channels With 45-deg Rib Turbulators
Authors: Al-Qahtani Mohammad , Jang Yong-Jun , Chen Hamn-Ching , Han Je-Chin 
Published: July 2002

Abstract
Numerical predictions of three-dimensional flow and heat transfer are presented for a rotating two-pass rectangular channel with 45-deg rib turbulators and channel aspect ratio of 2:1. The rib height-to-hydraulic diameter ratio e/Dh is 0.094 and the rib-pitch-to-height ratio P/e is 10. Two channel orientations are studied: β=90deg and 135 deg, corresponding to the mid-portion and the trailing edge regions of a turbine blade, respectively. The focus of this study is twofold; namely, to investigate the effect of the channel aspect ratio and the channel orientation on the nature of the flow and heat transfer enhancement. A multi-block Reynolds-averaged Navier-Stokes (RANS) method was employed in conjunction with a near-wall second-moment turbulence closure. In the present method, the convective transport equations for momentum, energy, and turbulence quantities are solved in curvilinear, body-fitted coordinates using the finite-analytic method. The numerical results compare reasonably well with experimental data for both stationary and rotating rectangular channels with rib turbulators at Reynolds number (Re) of 10,000, rotation number (Ro) of 0.11 and inlet coolant-to-wall density ratio (Δρ/ρ) of 0.115.
Detailed Numerical and Experimental Investigation of Non-Isothermal
Sintering of Amorphous Polymer Material
Authors: Tarafdar R. M. , Bergman T. L. 
Published: July 2002

Abstract
Simulations and experiments are performed to investigate the coupled thermal and morphological response of polymer material during non-isothermal sintering. The experimental results are utilized to validate a numerical model that describes the response of the system. Predictions of the material expansion, its subsequent contraction due to sintering, and the temperature evolution are obtained and favorably compared with experimental results. Parametric simulations are performed to acquire additional insight into the dynamics of non-isothermal sintering while a relationship is established to describe the ratio of the sintering penetration depth to the thermal penetration depth and its dependence upon the boundary and initial temperatures.
Self-Organization and Self-Similarity in Boiling Systems
Authors: Chai L. H. , Shoji M. 
Published: July 2002

AbstractBoiling system is a typical open dissipative structure. Focusing on the investigation of boundary adjacent to heating plate surface in boiling system, nonlinear non-equilibrium statistical thermodynamics theory of open systems was originally constructed. The competitive bubble formation was realized by non-equilibrium phase transition caused by the interactions among active sites or bubbles. The “natural selection” among all possible sites was mathematically outlined. It was by the means of “natural selection” that a kind of self-organized and self-similar structure was formed. The present studies theoretically explained the experimental observations from other researchers, and gave more reasonable guidance of enhancing boiling heat transfer, such as by way of installing artificial cavities. Beyond the scope of boiling systems, the present studies not only have far-reaching theoretical implications on explaining time, life, thermodynamic, self-similar, fluctuation, order and chaos etc., but also can find many promising applications from new perspectives, such as wider industrial optimization, the recognitions of pattern and reproduction pattern of by computer etc.
Stabilization of Buoyancy-Driven Unstable Vortex Flow in Mixed
Convection of Air in a Rectangular Duct by Tapering Its Top Plate
Authors: Tseng W. S. , Lin W. L. , Yin C. P. , Lin C. L. , Lin T. F. 
Published: July 2002

Abstract
Stabilization of the buoyancy-driven unstable mixed convective vortex air flow in a bottom heated rectangular duct by tapering its top plate is investigated experimentally. Specifically, the duct is tapered so that its aspect ratio at the duct inlet is 4 and gradually raised to 12 at the exit of the duct. In the study the secondary flow in the duct is visualized and the steady and transient thermal characteristics of the flow are examined by measuring the spanwise distributions of the time-average temperature. The effects of the Reynolds and Grashof numbers on the vortex flow structure are studied in detail. Moreover, the spanwise-averaged Nusselt numbers for the horizontal rectangular and tapering ducts are also measured and compared. Furthermore, the time records of the air temperature are obtained to further detect the temporal stability of the flow. Over the ranges of the Re and Gr investigated for 5⩽Re⩽102 and 1.0×104⩽Gr⩽1.7×105, the vortex flow induced in the rectangular duct exhibits temporal transition from a steady laminar to time periodic and then to chaotic state at increasing buoyancy-to-inertia ratio. Substantial change in the spatial structure of the vortex flow is also noted to accompany this temporal transition. The results for the tapering duct indicate that more vortex rolls can be induced due to the increase in the aspect ratio of the duct with the axial distance. But the vortex rolls are weaker and are completely stabilized by the tapering of the top plate. [S0022-1481(00)70301-X]
A Contribution on Quasi-Static Mooring Line Damping
Authors: Bauduin Christian , Naciri Mamoun 
Published: July 2002

Abstract
Since the pioneering work of Huse (1986, “Influence of Mooring Line Damping Upon Rig Motions,” Proc., 18th OTC Conference), it is well known that mooring lines may account for a large fraction of the overall damping present in a moored floating structure. This paper is concerned with the mooring line damping induced by the low-frequency, quasi-static, horizontal motion of the mooring line fairlead. The main advantage of the quasi-static approach is that it is much faster than the more accurate finite element methods, and, secondly, that it does not require any finite element modeling skills. A new formulation is proposed and is compared to the results of Liu et al. (1998, “Improvement on Huse’s Model for Estimating Mooring Cable-Induced Damping,” Proc., 17th OMAE Conference), as well as to time domain results obtained with FLEXRISER. The improvement with respect to the previous quasi-static methods is quite notable and our results are closer to FLEXRISER predictions. Finally, quasi-static results are compared to mooring line damping values measured during model tests for full mooring systems. The agreement between the two is very encouraging and suggests that the simpler quasi-static approach may, in some circumstances, be a valuable substitute for the more complex and time-consuming numerical tools. [S0892-7219(00)00102-3]
Abstract: Transparent conducting films
Authors: Vossen J. L. 
Published: July 2002

Transparent conductors are becoming of increasing importance because of increased interest in the interactions of light with electrically or electronically active materials, and for their high ir reflectivity which is useful for solar energy applications. The information in this presentation is largely organized by film deposition process rather than the film material because, ostensibly, the same material deposited by two different deposition techniques ordinarily yields two widely varying sets of physical properties. This is not surprising because of the complex physics and chemistry of the materials used for this purpose. Broadly speaking, there are two classes of materials: semiconducting oxides and very thin metals. The properties of the oxides depend critically upon their oxidation state and the nature and quantity of impurities trapped in the film. The properties of the thin metals depend upon nucleation and early coalescence phenomena and impurities. Both the electrical and optical properties of both classes depend strongly on the nature of the substrate used (impurities that can diffuse from the substrate into the film and the refractive index of the substrate).
Following a brief review of the physics of conductivity and transparency in these materials, detailed analysis of the following film deposition processes are given: hydrolysis of chlorides, pyrolysis, evaporation and sputtering of thin metals (with and without nucleation modifying layers), reactive evaporation and sputtering, and sputtering of oxide targets. The important process-control parameters that affect the electrical and optical properties of transparent conducting films are discussed.