bluuebunny/crossref_metadata_2025_split huggingface dataset:
Reduced Carbon Availability to Bacteroids and Elevated Ureides in Nodules, But Not in Shoots, Are Involved in the Nitrogen Fixation Response to Early Drought in Soybean
Authors: Ladrera Rubén , Marino Daniel , Larrainzar Estíbaliz , González Esther M. , Arrese-Igor Cesar 
Published: August 2007

Abstract
Nitrogen fixation (NF) in soybean (Glycine max L. Merr.) is highly sensitive to soil drying. This sensitivity has been related to an accumulation of nitrogen compounds, either in shoots or in nodules, and a nodular carbon flux shortage under drought. To assess the relative importance of carbon and nitrogen status on NF regulation, the responses to the early stages of drought were monitored with two soybean cultivars with known contrasting tolerance to drought. In the sensitive cultivar (‘Biloxi’), NF inhibition occurred earlier and was more dramatic than in the tolerant cultivar (‘Jackson’). The carbon flux to bacteroids was also more affected in ‘Biloxi’ than in ‘Jackson’, due to an earlier inhibition of sucrose synthase activity and a larger decrease of malate concentration in the former. Drought provoked ureide accumulation in nodules of both cultivars, but this accumulation was higher and occurred earlier in ‘Biloxi’. However, at this early stage of drought, there was no accumulation of ureides in the leaves of either cultivar. These results indicate that a combination of both reduced carbon flux and nitrogen accumulation in nodules, but not in shoots, is involved in the inhibition of NF in soybean under early drought.
A Novel Image-Analysis Technique for Kinematic Study of Growth and Curvature
Authors: Basu Paramita , Pal Anupam , Lynch Jonathan P. , Brown Kathleen M. 
Published: August 2007

Abstract
Kinematic analysis has provided important insights into the biology of growth by revealing the distribution of expansion within growing organs. Modern methods of kinematic analysis have made use of new image-tracking algorithms and computer-assisted evaluation, but these methods have yet to be adapted for examination of growth in a variety of plant species or for analysis of graviresponse. Therefore, a new image-analysis program, KineRoot, was developed to study spatio-temporal patterns of growth and curvature of roots. Graphite particles sprinkled on the roots create random patterns that can be followed by image analysis. KineRoot tracks the displacement of patterns created by the graphite particles over space and time using three search algorithms. Following pattern tracking, the edges of the roots are identified automatically by an edge detection algorithm that provides root diameter and root midline. Local growth rate of the root is measured by projecting the tracked points on the midline. From the shape of the root midline, root curvature is calculated. By combining curvature measurement with root diameter, the differential growth ratio between the greater and lesser curvature edges of a bending root is calculated. KineRoot is capable of analyzing a large number of images to generate local root growth and root curvature data over several hours, permitting kinematic analysis of growth and gravitropic responses for a variety of root types.
Optimizing the Distribution of Resources between Enzymes of Carbon Metabolism Can Dramatically Increase Photosynthetic Rate: A Numerical Simulation Using an Evolutionary Algorithm
Authors: Zhu Xin-Guang , de Sturler Eric , Long Stephen P. 
Published: August 2007

Abstract
The distribution of resources between enzymes of photosynthetic carbon metabolism might be assumed to have been optimized by natural selection. However, natural selection for survival and fecundity does not necessarily select for maximal photosynthetic productivity. Further, the concentration of a key substrate, atmospheric CO2, has changed more over the past 100 years than the past 25 million years, with the likelihood that natural selection has had inadequate time to reoptimize resource partitioning for this change. Could photosynthetic rate be increased by altered partitioning of resources among the enzymes of carbon metabolism? This question is addressed using an “evolutionary” algorithm to progressively search for multiple alterations in partitioning that increase photosynthetic rate. To do this, we extended existing metabolic models of C3 photosynthesis by including the photorespiratory pathway (PCOP) and metabolism to starch and sucrose to develop a complete dynamic model of photosynthetic carbon metabolism. The model consists of linked differential equations, each representing the change of concentration of one metabolite. Initial concentrations of metabolites and maximal activities of enzymes were extracted from the literature. The dynamics of CO2 fixation and metabolite concentrations were realistically simulated by numerical integration, such that the model could mimic well-established physiological phenomena. For example, a realistic steady-state rate of CO2 uptake was attained and then reattained after perturbing O2 concentration. Using an evolutionary algorithm, partitioning of a fixed total amount of protein-nitrogen between enzymes was allowed to vary. The individual with the higher light-saturated photosynthetic rate was selected and used to seed the next generation. After 1,500 generations, photosynthesis was increased substantially. This suggests that the “typical” partitioning in C3 leaves might be suboptimal for maximizing the light-saturated rate of photosynthesis. An overinvestment in PCOP enzymes and underinvestment in Rubisco, sedoheptulose-1,7-bisphosphatase, and fructose-1,6-bisphosphate aldolase were indicated. Increase in sink capacity, such as increase in ADP-glucose pyrophosphorylase, was also indicated to lead to increased CO2 uptake rate. These results suggest that manipulation of partitioning could greatly increase carbon gain without any increase in the total protein-nitrogen investment in the apparatus for photosynthetic carbon metabolism.
Regulation of One-Carbon Metabolism in Arabidopsis: The N-Terminal Regulatory Domain of Cystathionine γ-Synthase Is Cleaved in Response to Folate Starvation
Authors: Loizeau Karen , Gambonnet Bernadette , Zhang Guo-Fang , Curien Gilles , Jabrin Samuel , Van Der Straeten Dominique , Lambert Willy E. , Rébeillé Fabrice , Ravanel Stéphane 
Published: August 2007

Abstract
In all organisms, control of folate homeostasis is of vital importance to sustain the demand for one-carbon (C1) units that are essential in major metabolic pathways. In this study we induced folate deficiency in Arabidopsis (Arabidopsis thaliana) cells by using two antifolate inhibitors. This treatment triggered a rapid and important decrease in the pool of folates with significant modification in the distribution of C1-substituted folate coenzymes, suggesting an adaptive response to favor a preferential shuttling of the flux of C1 units to the synthesis of nucleotides over the synthesis of methionine (Met). Metabolic profiling of folate-deficient cells indicated important perturbation of the activated methyl cycle because of the impairment of Met synthases that are deprived of their substrate 5-methyl-tetrahydrofolate. Intriguingly, S-adenosyl-Met and Met pools declined during the initial period of folate starvation but were further restored to typical levels. Reestablishment of Met and S-adenosyl-Met homeostasis was concomitant with a previously unknown posttranslational modification that consists in the removal of 92 amino acids at the N terminus of cystathionine γ-synthase (CGS), the first specific enzyme for Met synthesis. Rescue experiments and analysis of different stresses indicated that CGS processing is specifically associated with perturbation of the folates pool. Also, CGS processing involves chloroplastic serine-type proteases that are expressed in various plant species subjected to folate starvation. We suggest that a metabolic effector, to date unidentified, can modulate CGS activity in vivo through an interaction with the N-terminal domain of the enzyme and that removal of this domain can suppress this regulation.
Reverse Genetics of Floral Scent: Application of Tobacco Rattle Virus-Based Gene Silencing in Petunia
Authors: Spitzer Ben , Zvi Michal Moyal Ben , Ovadis Marianna , Marhevka Elena , Barkai Oren , Edelbaum Orit , Marton Ira , Masci Tania , Alon Michal , Morin Shai , Rogachev Ilana , Aharoni Asaph , Vainstein Alexander 
Published: August 2007

AbstractFloral fragrance is responsible for attracting pollinators as well as repelling pathogens and pests. As such, it is of immense biological importance. Molecular dissection of the mechanisms underlying scent production would benefit from the use of model plant systems with big floral organs that generate an array of volatiles and that are amenable to methods of forward and reverse genetics. One candidate is petunia (Petunia hybrida), which has emerged as a convenient model system, and both RNAi and overexpression approaches using transgenes have been harnessed for the study of floral volatiles. Virus-induced gene silencing (VIGS) is characterized by a simple inoculation procedure and rapid results relative to transgenesis. Here, we demonstrate the applicability of the tobacco rattle virus-based VIGS system to studies of floral scent. Suppression of the anthocyanin pathway via chalcone synthase silencing was used as a reporter, allowing easy visual identification of anthocyaninless silenced flowers/tissues with no effect on the level of volatile emissions. Use of tobacco rattle virus constructs containing target genes involved in phenylpropanoid volatile production, fused to the chalcone synthase reporter, allowed simple identification of flowers with suppressed activity of the target genes. The applicability of VIGS was exemplified with genes encoding S-adenosyl-l-methionine:benzoic acid/salicylic acid carboxyl methyltransferase, phenylacetaldehyde synthase, and the myb transcription factor ODORANT1. Because this high-throughput reverse-genetics approach was applicable to both structural and regulatory genes responsible for volatile production, it is expected to be highly instrumental for large-scale scanning and functional characterization of novel scent genes.
Ethylene Is One of the Key Elements for Cell Death and Defense Response Control in the Arabidopsis Lesion Mimic Mutant vad1
Authors: Bouchez Olivier , Huard Carine , Lorrain Séverine , Roby Dominique , Balagué Claudine 
Published: August 2007

Abstract
Although ethylene is involved in the complex cross talk of signaling pathways regulating plant defense responses to microbial attack, its functions remain to be elucidated. The lesion mimic mutant vad1-1 (for vascular associated death), which exhibits the light-conditional appearance of propagative hypersensitive response-like lesions along the vascular system, is a good model for studying the role of ethylene in programmed cell death and defense. Here, we demonstrate that expression of genes associated with ethylene synthesis and signaling is enhanced in vad1-1 under lesion-promoting conditions and after plant-pathogen interaction. Analyses of the progeny from crosses between vad1-1 plants and either 35S∷ERF1 transgenic plants or ein2-1, ein3-1, ein4-1, ctr1-1, or eto2-1 mutants revealed that the vad1-1 cell death and defense phenotypes are dependent on ethylene biosynthesis and signaling. In contrast, whereas vad1-1-dependent increased resistance was abolished by ein2, ein3, and ein4 mutations, positive regulation of ethylene biosynthesis (eto2-1) or ethylene responses (35S∷ERF1) did not exacerbate this phenotype. In addition, VAD1 expression in response to a hypersensitive response-inducing bacterial pathogen is dependent on ethylene perception and signaling. These results, together with previous data, suggest that VAD1 could act as an integrative node in hormonal signaling, with ethylene acting in concert with salicylic acid as a positive regulator of cell death propagation.
TRBO: A High-Efficiency Tobacco Mosaic Virus RNA-Based Overexpression Vector
Authors: Lindbo John A. 
Published: August 2007

Abstract
Transient expression is a rapid, useful approach for producing proteins of interest in plants. Tobacco mosaic virus (TMV)-based transient expression vectors can express very high levels of foreign proteins in plants. However, TMV vectors are, in general, not efficiently delivered to plant cells by agroinfection. It was determined that agroinfection was very efficient with a 35S promoter-driven TMV replicon that lacked the TMV coat protein gene sequence. This coat protein deletion vector had several useful features as a transient expression system, including improved ease of use, higher protein expression rates, and improved biocontainment. Using this TMV expression vector, some foreign proteins were expressed at levels of 3 to 5 mg/g fresh weight of plant tissue. It is proposed that this new transient expression vector will be a useful tool for expressing recombinant proteins in plants for either research or production purposes.
Large-Scale, Lineage-Specific Expansion of a Bric-a-Brac/Tramtrack/Broad Complex Ubiquitin-Ligase Gene Family in Rice
Authors: Gingerich Derek J. , Hanada Kousuke , Shiu Shin-Han , Vierstra Richard D. 
Published: August 2007

AbstractSelective ubiquitination of proteins is directed by diverse families of ubiquitin-protein ligases (or E3s) in plants. One important type uses Cullin-3 as a scaffold to assemble multisubunit E3 complexes containing one of a multitude of bric-a-brac/tramtrack/broad complex (BTB) proteins that function as substrate recognition factors. We previously described the 80-member BTB gene superfamily in Arabidopsis thaliana. Here, we describe the complete BTB superfamily in rice (Oryza sativa spp japonica cv Nipponbare) that contains 149 BTB domain–encoding genes and 43 putative pseudogenes. Amino acid sequence comparisons of the rice and Arabidopsis superfamilies revealed a near equal repertoire of putative substrate recognition module types. However, phylogenetic comparisons detected numerous gene duplication and/or loss events since the rice and Arabidopsis BTB lineages split, suggesting possible functional specialization within individual BTB families. In particular, a major expansion and diversification of a subset of BTB proteins containing Meprin and TRAF homology (MATH) substrate recognition sites was evident in rice and other monocots that likely occurred following the monocot/dicot split. The MATH domain of a subset appears to have evolved significantly faster than those in a smaller core subset that predates flowering plants, suggesting that the substrate recognition module in many monocot MATH-BTB E3s are diversifying to ubiquitinate a set of substrates that are themselves rapidly changing. Intriguing possibilities include pathogen proteins attempting to avoid inactivation by the monocot host.
A knowledge‐based engineering tool to estimate cost and weight of composite aerospace structures at the conceptual stage of the design process
Authors: Choi Jin‐Woo , Kelly Don , Raju John 
Published: August 2007

PurposeThis paper seeks to address issues related to the development of a knowledge‐based engineering system for estimating manufacturing cost and weight of a composite structure at the conceptual stage of a design.Design/methodology/approachThe system has been developed in the CATIA V5 knowledge environment and is applied to structures made of composite materials. At the conceptual stage of the design process, a structure is often represented by simple surfaces. The system adds the details necessary to accurately estimate weight and manufacturing cost using geometry and process‐based techniques. Knowledge captured from an expert was used to construct the knowledge base in the system.FindingsIt has been found that the system can provide continuous tracking of the weight and cost as the design evolves. Structural FEA and optimisation using MSC.NASTRAN have been integrated into the design process to enables the designer to conduct “what‐if” analyses to explore different design options involving geometry parameters such as the internal configuration of the structure.Originality/valueThe paper demonstrates that tools embedded in CAD systems can be expected to be able to facilitate the task of estimation of weight and manufacturing cost at the conceptual stage of the design process.
Geometry factor determination of round specimens using fracture mechanic approaches in Al 2024‐T3
Authors: Khoshnaw Fuad M. , Hussain Nazhad A. 
Published: August 2007

PurposeThe purpose of the paper is to characterize the fatigue behavior, such as fatigue strength, and stress intensity factor values of aluminum alloy type 2024‐T3, using only a round specimen. The aim in this study is to interrelate the fatigue behavior directly with the microstructure, as an attempt to reduce other parameters that might be associated in using different specimen geometries.Design/methodology/approachFor this purpose, round specimens were machined from 2024‐T3, and the fatigue behavior was studied with various heat treatments. Two different temperatures were selected; 160 and 200°C, at different times. From stress‐number of cycles diagram, the fatigue strength is determined for the selected specimens. Moreover, the linear elastic fracture mechanic approach was used to determine threshold stress intensity factor, crack growth rate, and fracture toughness. A replica method is used for following and calculating the crack depth in round specimens. Moreover, theoretical equations and approaches have been carried out to evaluate the effect of specimen geometry (correction factor) on the results.FindingsThe results showed that the specimen aged at 160°C for five h develops greatest values of fatigue limit, ultimate strength, yield strength, and hardness. Moreover, the specimen aged at 200°C for 15 h develops greatest threshold stress intensity factor and fracture toughness.Practical implicationsThe heat treatment does not have a strong influence on crack growth rate. Generally, the specimens, which develop greatest values of strength values, and HB, had lowestKth, andKICvalues and vice versa.Originality/valueThe LEFM approaches can be used even on round specimens to follow the crack growth rate instead of plates. A specific equation as a correction factor of geometry effect has been determined for round specimen.
Vibration of anti‐symmetric angle‐ply composite plates under random excitation
Authors: Dogan Vedat 
Published: August 2007

PurposeThe transverse shear deformation and rotary inertia effects need to be included for an accurate analysis in the response of the relatively thick plates. This paper seeks to use, one of the refined theories which takes into account those effects, The First Order Shear Deformation Theory, to obtain linear and non‐linear responses for anti‐symmetric angle‐ply composite plates under random excitation.Design/methodology/approachThe random excitation is assumed to be stationary, ergodic and Gaussian with zero‐mean. A Monte Carlo Simulation of stationary random process is used. A multi‐mode Galerkin approach and numerical integration procedure are employed to find linear and non‐linear response solutions. Laminated composite plate is taken to be simply‐supported along four edges.FindingsThe vibration of composite plates at elevated temperatures is also investigated. The linear and non‐linear deflections root‐mean‐square (RMS) are obtained for various input levels, the different lamination angles and the number of layers.Practical implicationsFurther, case studies might lead to a lighter design of thick panels used in high‐performance systems such as aerospace structures.Originality/valueThe paper provides information on the linear and more realistic non‐linear vibrations of thick composite plates in time domain so that it would be possible to obtain key statistical information directly from time‐response history.
An adaptive unscented Kalman filter for quaternion‐based orientation estimation in low‐cost AHRS
Authors: Pourtakdoust S.H. , Ghanbarpour Asl H. 
Published: August 2007

PurposeThis paper aims to develop an adaptive unscented Kalman filter (AUKF) formulation for orientation estimation of aircraft and UAV utilizing low‐cost attitude and heading reference systems (AHRS).Design/methodology/approachA recursive least‐square algorithm with exponential age weighting in time is utilized for estimation of the unknown inputs. The proposed AUKF tunes its measurement covariance to yield optimal performance. Owing to nonlinear nature of the dynamic model as well as the measurement equations, an unscented Kalman filter (UKF) is chosen against the extended Kalman filter, due to its better performance characteristics. The unscented transformation of the UKF is shown to equivalently capture the effect of nonlinearities up to second order without the need for explicit calculations of the Jacobians.FindingsIn most conventional AHRS filters, severe problems can occur once the system suddenly experiences additional acceleration, resulting in erroneous orientation angles. On the contrary in the high dynamic accelerative mode of the new proposed filter the errors would not suddenly increase, since the additional to cruise accelerations are being continuously estimated resulting in substantially more accurate orientation estimation. This feature causes the associated filter errors to gradually increase, in the event of continuous vehicle acceleration, up to a point of zero additional acceleration that subsequently causes a subsidence of the error back to zero.Practical implicationsThe proposed filtering methodology can be implemented for orientation estimation of aircraft and UAV that are equipped with low‐cost AHRSs.Originality/valueTraditional AHRS algorithms utilize the accelerometers output for the computation of roll and pitch angles and magnetometer output for the heading angle. Moreover, these angles are also calculated from the gyroscopes output as well, but with errors that increase with time. Of course for some applications of AHRS system, orientation errors can be damped out with a proportional‐integral controller. In such a case, the filter cut‐off frequency is usually selected experimentally. But, for high accelerating vehicles utilizing AHRS, the system errors can become very large. A possible remedy to this problem could be to use more advanced nonlinear filter algorithms such as the one proposed.
Controlling critical Reynolds number of parallel plate flow by boundary input
Authors: Kucur Murad , Uzal Erol 
Published: August 2007

PurposeThe aim of this study is to modify the critical Reynolds number (Recr) which is the critical parameter of the transition from laminar to turbulence regime. The transition to turbulence is delayed by increasing the critical Reynolds number.Design/methodology/approachA method to control the critical Reynolds number of viscous flow between parallel plates with an imposed pressure gradient to infinitesimal harmonic disturbances is introduced. The method consists of introducing harmonic perturbations to the lower plate based on skin friction measurements at the upper plate. The size of the introduced harmonic perturbation is chosen to be proportional to the measured skin friction. The proportionality constant is the control parameter for the manipulation of the critical Reynolds number. The resulting eigenvalue problem, similar to the Orr‐Sommerfeld problem, is solved for various values of the control parameter.FindingsSolution of the eigenvalue problem shows that the critical Reynolds number for the instability with respect to infinitesimal disturbances can be increased from 5,772.22 to 37,900.Originality/valueThe paper demonstrates that it is theoretically possible to increase the critical Reynolds number of parallel plate flow from 5,772.22 to 37,900 by applying a small motion to the bottom plate, the amplitude of the motion being proportional to the skin friction measured at the upper plate.