bluuebunny/crossref_metadata_2025_split huggingface dataset:
The Organization Pattern of Root Border-Like Cells of Arabidopsis Is Dependent on Cell Wall Homogalacturonan
Authors: Durand Caroline , Vicré-Gibouin Maïté , Follet-Gueye Marie Laure , Duponchel Ludovic , Moreau Myriam , Lerouge Patrice , Driouich Azeddine 
Published: May 2009

AbstractBorder-like cells are released by Arabidopsis (Arabidopsis thaliana) root tips as organized layers of several cells that remain attached to each other rather than completely detached from each other, as is usually observed in border cells of many species. Unlike border cells, cell attachment between border-like cells is maintained after their release into the external environment. To investigate the role of cell wall polysaccharides in the attachment and organization of border-like cells, we have examined their release in several well-characterized mutants defective in the biosynthesis of xyloglucan, cellulose, or pectin. Our data show that among all mutants examined, only quasimodo mutants (qua1-1 and qua2-1), which have been characterized as producing less homogalacturonan, had an altered border-like cell phenotype as compared with the wild type. Border-like cells in both lines were released as isolated cells separated from each other, with the phenotype being much more pronounced in qua1-1 than in qua2-1. Further analysis of border-like cells in the qua1-1 mutant using immunocytochemistry and a set of anti-cell wall polysaccharide antibodies showed that the loss of the wild-type phenotype was accompanied by (1) a reduction in homogalacturonan-JIM5 epitope in the cell wall of border-like cells, confirmed by Fourier transform infrared microspectrometry, and (2) the secretion of an abundant mucilage that is enriched in xylogalacturonan and arabinogalactan-protein epitopes, in which the cells are trapped in the vicinity of the root tip.
LPA66 Is Required for EditingpsbFChloroplast Transcripts in Arabidopsis
Authors: Cai Wenhe , Ji Daili , Peng Lianwei , Guo Jinkui , Ma Jinfang , Zou Meijuan , Lu Congming , Zhang Lixin 
Published: May 2009

AbstractTo gain insight into the molecular mechanism of RNA editing, we have characterized the low psii accumulation66 (lpa66) Arabidopsis (Arabidopsis thaliana) mutant, which displays a high chlorophyll fluorescence phenotype. Its perturbed chlorophyll fluorescence is reflected in reduced levels of photosystem II (PSII) proteins. In vivo protein labeling showed that synthesis rates of the PSII reaction center protein D1/D2 were lower, and turnover rates of PSII core proteins higher, than in wild-type counterparts. The assembly of newly synthesized proteins into PSII occurs in the lpa66 mutant but with reduced efficiency compared with the wild type. LPA66 encodes a chloroplast protein of the pentatricopeptide repeat family. In lpa66 mutants, editing of psbF that converts serine to phenylalanine is specifically impaired. Thus, LPA66 is specifically required for editing the psbF transcripts in Arabidopsis, and the amino acid alternation due to lack of editing strongly affects the efficiency of the assembly of PSII complexes.
TriFLDB: A Database of Clustered Full-Length Coding Sequences from Triticeae with Applications to Comparative Grass Genomics
Authors: Mochida Keiichi , Yoshida Takuhiro , Sakurai Tetsuya , Ogihara Yasunari , Shinozaki Kazuo 
Published: May 2009

Abstract
The Triticeae Full-Length CDS Database (TriFLDB) contains available information regarding full-length coding sequences (CDSs) of the Triticeae crops wheat (Triticum aestivum) and barley (Hordeum vulgare) and includes functional annotations and comparative genomics features. TriFLDB provides a search interface using keywords for gene function and related Gene Ontology terms and a similarity search for DNA and deduced translated amino acid sequences to access annotations of Triticeae full-length CDS (TriFLCDS) entries. Annotations consist of similarity search results against several sequence databases and domain structure predictions by InterProScan. The deduced amino acid sequences in TriFLDB are grouped with the proteome datasets for Arabidopsis (Arabidopsis thaliana), rice (Oryza sativa), and sorghum (Sorghum bicolor) by hierarchical clustering in stepwise thresholds of sequence identity, providing hierarchical clustering results based on full-length protein sequences. The database also provides sequence similarity results based on comparative mapping of TriFLCDSs onto the rice and sorghum genome sequences, which together with current annotations can be used to predict gene structures for TriFLCDS entries. To provide the possible genetic locations of full-length CDSs, TriFLCDS entries are also assigned to the genetically mapped cDNA sequences of barley and diploid wheat, which are currently accommodated in the Triticeae Mapped EST Database. These relational data are searchable from the search interfaces of both databases. The current TriFLDB contains 15,871 full-length CDSs from barley and wheat and includes putative full-length cDNAs for barley and wheat, which are publicly accessible. This informative content provides an informatics gateway for Triticeae genomics and grass comparative genomics. TriFLDB is publicly available at http://TriFLDB.psc.riken.jp/.
Microbial Siderophores Exert a Subtle Role in Arabidopsis during Infection by Manipulating the Immune Response and the Iron Status
Authors: Dellagi Alia , Segond Diego , Rigault Martine , Fagard Mathilde , Simon Clara , Saindrenan Patrick , Expert Dominique 
Published: May 2009

AbstractSiderophores (ferric ion chelators) are secreted by organisms in response to iron deficiency. The pathogenic enterobacterium Erwinia chrysanthemi produces two siderophores, achromobactin and chrysobactin (CB), which are required for systemic dissemination in host plants. Previous studies have shown that CB is produced in planta and can trigger the up-regulation of the plant ferritin gene AtFER1. To further investigate the function of CB during pathogenesis, we analyzed its effect in Arabidopsis (Arabidopsis thaliana) plants following leaf infiltration. CB activates the salicylic acid (SA)-mediated signaling pathway, while the CB ferric complex is ineffective, suggesting that the elicitor activity of this siderophore is due to its iron-binding property. We confirmed this hypothesis by testing the effect of siderophores structurally unrelated to CB, including deferrioxamine. There was no activation of SA-dependent defense in plants grown under iron deficiency before CB treatment. Transcriptional analysis of the genes encoding the root ferrous ion transporter and ferric chelate reductase, and determination of the activity of this enzyme in response to CB or deferrioxamine, showed that these compounds induce a leaf-to-root iron deficiency signal. This root response as well as ferritin gene up-regulation in the leaf were not compromised in a SA-deficient mutant line. Using the Arabidopsis-E. chrysanthemi pathosystem, we have shown that CB promotes bacterial growth in planta and can modulate plant defenses through an antagonistic mechanism between SA and jasmonic acid signaling cascades. Collectively, these data reveal a new link between two processes mediated by SA and iron in response to microbial siderophores.
Plant Physiological Adaptations to the Massive Foreign Protein Synthesis Occurring in Recombinant Chloroplasts
Authors: Bally Julia , Nadai Marie , Vitel Maxime , Rolland Anne , Dumain Raphael , Dubald Manuel 
Published: May 2009

AbstractGenetically engineered chloroplasts have an extraordinary capacity to accumulate recombinant proteins. We have investigated in tobacco (Nicotiana tabacum) the possible consequences of such additional products on several parameters of plant development and composition. Plastid transformants were analyzed that express abundantly either bacterial enzymes, alkaline phosphatase (PhoA-S and PhoA-L) and 4-hydroxyphenyl pyruvate dioxygenase (HPPD), or a green fluorescent protein (GFP). In leaves, the HPPD and GFP recombinant proteins are the major polypeptides and accumulate to higher levels than Rubisco. Nevertheless, these engineered metabolic sinks do not cause a measurable difference in growth rate or photosynthetic parameters. The total amino acid content of transgenic leaves is also not significantly affected, showing that plant cells have a limited protein biosynthetic capacity. Recombinant products are made at the expense of resident proteins. Rubisco, which constitutes the major leaf amino acid store, is the most clearly and strongly down-regulated plant protein. This reduction is even more dramatic under conditions of limited nitrogen supply, whereas recombinant proteins accumulate to even higher relative levels. These changes are regulated posttranscriptionally since transcript levels of resident plastid genes are not affected. Our results show that plants are able to produce massive amounts of recombinant proteins in chloroplasts without profound metabolic perturbation and that Rubisco, acting as a nitrogen buffer, is a key player in maintaining homeostasis and limiting pleiotropic effects.
Recognition of AvrBs3-Like Proteins Is Mediated by Specific Binding to Promoters of Matching Pepper Bs3 Alleles
Authors: Römer Patrick , Strauss Tina , Hahn Simone , Scholze Heidi , Morbitzer Robert , Grau Jan , Bonas Ulla , Lahaye Thomas 
Published: May 2009

Abstract
The pepper (Capsicum annuum) bacterial spot (Bs) resistance gene Bs3 and its allelic variant Bs3-E mediate recognition of the Xanthomonas campestris pv vesicatoria type III effector protein AvrBs3 and its deletion derivative AvrBs3Δrep16. Recognition specificity resides in the Bs3 and Bs3-E promoters and is determined by a defined promoter region, the UPA (for up-regulated by AvrBs3) box. Using site-directed mutagenesis, we defined the exact boundaries of the UPA AvrBs3 box of the Bs3 promoter and the UPA AvrBs3Δrep16 box of the Bs3-E promoter and show that both boxes overlap by at least 11 nucleotides. Despite partial sequence identity, the UPA AvrBs3 box and the UPA AvrBs3Δrep16 box were bound specifically by the corresponding AvrBs3 and AvrBs3Δrep16 proteins, respectively, suggesting that selective promoter binding of AvrBs3-like proteins is the basis for promoter activation specificity. We also demonstrate that the UPA AvrBs3 box retains its functionality at different positions within the pepper Bs3 promoter and confers AvrBs3 inducibility in a novel promoter context. Notably, the transfer of the UPA AvrBs3 box to different promoter locations is always correlated with a new transcriptional start site. The analysis of naturally occurring Bs3 alleles revealed many pepper accessions that encode a nonfunctional Bs3 variant. These accessions showed no apparent abnormalities, supporting the supposition that Bs3 functions only in disease resistance and not in other developmental or physiological processes.
Phosphorylation of SOS3-LIKE CALCIUM BINDING PROTEIN8 by SOS2 Protein Kinase Stabilizes Their Protein Complex and Regulates Salt Tolerance in Arabidopsis
Authors: Lin Huixin , Yang Yongqing , Quan Ruidang , Mendoza Imelda , Wu Yisheng , Du Wenming , Zhao Shuangshuang , Schumaker Karen S. , Pardo José M. , Guo Yan 
Published: May 2009

Abstract
The Salt Overly Sensitive (SOS) pathway plays an important role in the regulation of Na+/K+ ion homeostasis and salt tolerance in Arabidopsis thaliana. Previously, we reported that the calcium binding proteins SOS3 and SOS3-LIKE CALCIUM BINDING PROTEIN8 (SCaBP8) nonredundantly activate the protein kinase SOS2. Here, we show that SOS2 phosphorylates SCaBP8 at its C terminus but does not phosphorylate SOS3. In vitro, SOS2 phosphorylation of SCaBP8 was enhanced by the bimolecular interaction of SOS2 and SCaBP8 and did not require calcium ions. In vivo, this phosphorylation was induced by salt stress, occurred at the membrane, stabilized the SCaBP8-SOS2 interaction, and enhanced plasma membrane Na+/H+ exchange activity. When a Ser at position 237 in the SCaBP8 protein (the SOS2 phosphorylation target) was mutated to Ala, SCaBP8 was no longer phosphorylated by SOS2 and the mutant protein could not fully rescue the salt-sensitive phenotype of the scabp8 mutant. By contrast, when Ser-237 was mutated to Asp to mimic the charge of a phosphorylated Ser residue, the mutant protein rescued the scabp8 salt sensitivity. These data demonstrate that calcium sensor phosphorylation is a critical component of SOS pathway regulation of salt tolerance in Arabidopsis.
An approach to simulate cold roll‐forging of turbo‐engine thin compressor blade
Authors: Sedighi M. , Mahmoodi M. 
Published: May 2009

PurposeStudying manufacturing process of compressor blade can reduce the production cost and time in aircraft turbo‐engine industries. In the cold roll‐forging of thin compressor blades, the elastic behavior of machine structure and rolls is considerable due to the higher volume of roll separating force. Owing to this kind of elastic deformation during rolling, the adjusted gap between the rolling dies is increased and this causes unexpected flow of material, shape and thickness. The purpose of this paper is to present a new approach for simulation of cold rolling of thin blades and studying the effect of elastic behavior of the machine structure as well as rolls deflection on the material flow and roll separating force.Design/methodology/approachIn this paper, the process has been investigated using experimental test and simulation by introducing a new approach in a decision‐making flowchart. Instead of simulating of the entire system structure, a couple of virtual deformable rolls are suggested. The specifications of these rolls are selected to behave elastically during rolling same as whole roll stand. In addition, the thickness values are compared in both experiment and simulation. Also, the roll separating force is compared with and without using this approach.FindingsA decision‐making algorithm has been presented that can be used to study the process. This finding provides the basis to investigate the effect of elastic deformation of machine structure and rolls on dimensional accuracy and roll force.Originality/valueResult of this work can promote the position of simulation of the thin rolled sections to an extent more compatible with reality. For instance, the amount of increased gap between two dies during rolling can be estimated accurately. Also the influence of this gap on final blade thickness and the roll force and on the roll torque can be investigated by this approach.
Linearization in satellite attitude control with modified Rodriguez parameters
Authors: Özgür Doruk R. 
Published: May 2009

PurposeThe purpose of this paper is to analyze the results of the Jacobian matrix linearization of the satellite attitude dynamics with modified Rodriguez parameters (MRP) as attitude representation.Design/methodology/approachThe satellite dynamics is linearized using Jacobian differentiation around origin and reference values of the MRP. The controller is designed through linear quadratic regulation approach.FindingsIt is found that, for both cases the overall system converges but there exists a tracking error. The error can be reduced by increasing the controller coefficients in both cases however cannot be eliminated. In the case of linearization around zero, the torque requirements are quite higher than the case of linearization around the reference attitude trajectory.Originality/valueThe attempt of Jacobian linearization of a satellite dynamics with the MRP as the attitude representation constitutes the value of this paper. In addition, the results obtained in the derivations may be used in future research.
Effects of boundary‐layers bleeding on performance parameters of hypersonic inlets
Authors: Chang Juntao , Fan Yi 
Published: May 2009

PurposeThe purpose of this paper is to study the effects of boundary‐layers bleeding on performance parameters of hypersonic inlets.Design/methodology/approachThe inner flowfield of a hypersonic inlet at different bleeding rates is simulated with a Reynolds‐averaged Navier‐Stokes solver using a renormalization group k‐ε turbulence model.FindingsIn contrast with no bleeding, the performance parameter of hypersonic inlets without backpressure is reduced slightly, but the flow uniformity is improved. The interaction between boundary layers and shocks is weakened at the action of the bleeding, which leads to that the boundary‐layers separations at the entrance of the isolator caused by the high‐backpressure occur later, and it can improve the maximum backpressure ratio of hypersonic inlets. With the bleeding rate increasing, the maximum backpressure ratio of hypersonic inlets is added, while the total‐pressure recovery coefficient and mass‐captured coefficient are reduced.Originality/valueThis paper is a useful reference to the design and performance improvement of hypersonic inlets and propulsion systems.
A neuro‐optimal approach for thrust‐insensitive trajectory planning
Authors: Pourtakdoust S.H. , Pazooki F. , Fakhri Noushabadi M. 
Published: May 2009

PurposeThe purpose of this paper is to devise a new approach to synthesize closed‐loop feedback guidance law for online thrust‐insensitive optimal trajectory generation utilizing neural networks.Design/methodology/approachThe proposed methodology utilizes an open‐loop variational formulation that initially determines optimal launch/ascent trajectories for various scenarios of known uncertainties in the thrust profile of typical solid propellant engines. These open‐loop optimized trajectories will then provide the knowledge base needed for the subsequent training of a neural network. The trained network could eventually produce thrust‐insensitive closed‐loop optimal guidance laws and trajectories in flight.FindingsThe proposed neuro‐optimal guidance scheme is effective for online closed‐loop optimal path planning through some measurable and computable engine and flight parameters.Originality/valueDetermination of closed‐loop optimal guidance law for non‐linear dynamic systems with uncertainties in system and environment has been a challenge for researchers and engineers for many years. The problem of steering a solid propellant driven vehicle is one of these challenges. Even though a few researchers have worked in the area of non‐linear optimal control and thrust‐insensitive guidance, this paper proposes a new strategy for the determination of closed‐loop online thrust insensitive guidance laws leading to optimal flight trajectories for solid propellant launch and ascent vehicles.
Strain concentrations in notched laminates under bending
Authors: Kennedy Timothy C. , Arias Sergio G. 
Published: May 2009

PurposeThe purpose of this paper is to determine the validity of using classical laminated plate theory to predict strain concentration factors in notched laminates under bending.Design/methodology/approachThe objective was accomplished by comparing results predicted by classical theory to those from more refined theories that incorporate transverse shear and other 3D effects in the analysis. Three notch sizes and two laminate types were considered. The results were obtained through finite element analysis.FindingsStrain concentration factors predicted by the classical theory were generally found to be significantly lower than those predicted by the more refined theories. However, these differences tended to be very localized to the vicinity of the notch tip.Originality/valueThis study points out a potential deficiency in a commonly used design tool. The seriousness of this deficiency can best be determined by further research, particularly through a systematic testing program.
Mission‐based optimal control of Stewart manipulator
Authors: Omran A. , Kassem A. , El‐Bayoumi G. , Bayoumi M. 
Published: May 2009

PurposeThe purpose of this paper is to show the merit of using mission information in tuning the controller gains for Stewart manipulator instead of the generic inputs previously developed in literature.Design/methodology/approachThe paper introduces two optimization techniques based on mission information. The first technique, a partial‐information technique, uses gain scheduling that applies different controllers for different mission tracks. The second technique, a full‐information technique uses a single robust controller by considering the full mission data. For demonstrating these techniques' feasibility, a nonlinear numerical simulation for a Stewart manipulator was built and tested using a generic mission. This mission consists of two piecewise trajectories (tracks). The proposed techniques were compared with one of the previous optimization techniques in literature, no‐information technique, in which a step response is used to search for optimal controller gains without any information about the mission. Genetic algorithms were used to search for the optimal controller gain in each case with different cost functions.FindingsBased on the numerical simulations, the proposed mission‐based optimization techniques have superior performances compared with no‐information technique.Research limitations/implicationsThe proposed techniques were applied in a joint space or for a decentralized control. The work can be extended to be applied in a task space or for a centralized control.Originality/valueThe paper proposes two novel optimization techniques: partial‐ and full‐information techniques for tuning the controller gains of a Stewart manipulator, where mission information was imbedded into the cost function. These two techniques are generally applicable for other nonlinear systems such as aircraft stability and control augmentation systems.
The on‐board software architecture and distributed testbed of micro‐satellite clusters
Authors: Xiande Wu , Hui Li , Zhaowei Sun 
Published: May 2009

PurposeThe micro‐satellite clusters have been discussed for several years, however, there is not a common framework about its software, and various researches distributed at different domains. In order to conduct the future work well, the purpose of this paper is to systematically describe micro‐satellite clusters' characteristics, clusters software model, and present a distributed testbed to shorten test process, and minimize the development cost.Design/methodology/approachThe cluster characteristics and model is summarized through analyzing the past satellite cluster programs. Then the ground test system is designed to shorten micro‐satellite's development period, improve its reliability.FindingsThe clusters' characteristics are discussed, such as coverage, scalability, fault tolerance, low cost, etc. The clusters' data flow and on‐board software architecture are presented according to properties of clusters. Finally, the distributed testbed that focuses on future on‐board software and hardware technologies that aim to rapid design, build, integration, test, deployment, and operation of the future micro‐satellite is designed.Originality/valueThe presentation of software architecture of cluster member can improve the micro‐satellite's development, and the distributed testbed can improve the ground test efficiency, especially, when the micro‐satellite quantity is big.