bluuebunny/crossref_metadata_2025_split huggingface dataset:
Direct Measurement of Aluminum Uptake and Distribution in Single Cells of Chara corallina
Authors: Taylor Gregory J. , McDonald-Stephens Julie L. , Hunter Douglas B. , Bertsch Paul M. , Elmore David , Rengel Zdenko , Reid Robert J. 
Published: July 2002

Abstract
Quantitative information on the uptake and distribution of Al at the cellular level is required to understand mechanisms of Al toxicity, but direct measurement of uptake across the plasma membrane has remained elusive. We measured rates of Al transport across membranes in single cells of Chara corallina using the rare26Al isotope, an emerging technology (accelerator mass spectrometry), and a surgical technique for isolating subcellular compartments. Accumulation of Al in the cell wall dominated total uptake (71–318 μg m−2 min−1), although transport across the plasma membrane was detectable (71–540 ng m−2 min−1) within 30 min of exposure. Transport across the tonoplast was initially negligible, but accelerated to rates approximating uptake across the plasma membrane. The avacuolate protoplasm showed signs of saturation after 60 min, but continued movement across the plasma membrane was supported by sequestration in the vacuole. Saturation of all compartments was observed after 12 to 24 h. Accumulation of Al in the cell wall reflected variation in {Al3+} induced by changes in Al supply or complexing ligands, but was unaffected by pH. In contrast, transport across the plasma membrane peaked at pH 4.3 and increased when {Al3+} was reduced by complexing ligands. Cold temperature (4°C) reduced accumulation in the cell wall and protoplasm, whereas 2,4-dinitrophenol andm-chlorocarbonylcyanidephenyl hydrazone increased membrane transport by 12- to 13-fold. Our data suggest that the cell wall is the major site of Al accumulation. Nonetheless, membrane transport occurs within minutes of exposure and is supported by subsequent sequestration in the vacuole. The rapid delivery of Al to the protoplasm suggests that intracellular lesions may be possible.
Involvement of Brassinosteroids in the Gravitropic Response of Primary Root of Maize
Authors: Kim Seong-Ki , Chang Soo Chul , Lee Eun Joo , Chung Woo-Sook , Kim Young-Soo , Hwang Seongbin , Lee June Seung 
Published: July 2002

Abstract
Exogenously applied brassinolide (BL, 10−9–10−5 m) increased gravitropic curvature in maize (Zea mays) primary roots. The BL-enhanced gravitropic curvature was clearly promoted in the presence of indole-3-acetic acid (IAA, 10−10–10−8 m), indicating that BL is interactive with IAA during the gravitropic response. The interactive effect between BL and IAA was completely diminished by treatment of p-chlorophenoxy isobutric acid, an auxin action antagonist. The activation of the gravitropic response by BL in the absence and in the presence of IAA was nullified by application of 2,3,5-triiodobenzoic acid, a polar auxin transport inhibitor. The data indicate that brassinosteroids (BRs) might be involved in auxin-mediated processes for the gravitropic response. Gas chromotography-selected ion-monitoring analysis revealed that maize primary roots contained approximately 0.3 ng g−1 fresh weight castasterone as an endogenous BR. Exogenously applied castasterone also increased the gravitropic response of maize roots in an IAA-dependent manner. This study provides the first evidence, to our knowledge, for occurrence and gravitropic activity of BRs in plant roots.
Identification of a CYP84 Family of Cytochrome P450-Dependent Mono-Oxygenase Genes in Brassica napus and Perturbation of Their Expression for Engineering Sinapine Reduction in the Seeds
Authors: Nair Ramesh B. , Joy Richard W. , Kurylo Eugen , Shi Xiaohong , Schnaider Joan , Datla Raju S.S. , Keller Wilf A. , Selvaraj Gopalan 
Published: July 2002

Abstract
CYP84 is a recently identified family of cytochrome P450-dependent mono-oxygenases defined by a putative ferulate-5-hydroxylase (F5H) from Arabidopsis. Until recently F5H has been thought to catalyze the hydroxylation of ferulate to 5-OH ferulate en route to sinapic acid. Sinapine, a sinapate-derived ester in the seeds, is antinutritional and a target for elimination in canola meal. We have isolated threeF5H-like genes (BNF5H1-3) from a cultivated Brassica napus, whose amphidiploid progenitor is considered to have arisen from a fusion of the diploidsBrassica rapa and Brassica oleracea . Two cultivated varieties of the diploids were also found to contain BNF5H3 and additionally either BNF5H1 or BNF5H2, respectively. Whereas all three are &gt;90% identical in their coding sequence, BNF5H1 and BNF5H2 are closer to each other than to BNF5H3. This and additional data suggest that the two groups of genes have diverged in an ancestor of the diploids. B. napus showed maximal F5Hexpression in the stems, least in the seeds, and subtle differences among the expression profiles of the three genes elsewhere. TransgenicB. napus with cauliflower mosaic virus 35S-antisenseBNF5H contained up to 40% less sinapine, from 9.0 ± 0.3 mg in the controls to 5.3 ± 0.3 mg g−1 seed. F5H from Arabidopsis and a similar enzyme from sweetgum (Liquidamber styraciflua) has recently been shown to have coniferaldehyde hydroxylase activity instead of F5H activity. Thus the supply of 5-OH coniferaldehyde or 5-OH ferulate has a bearing on sinapine accumulation in canola seeds.
Profilin Plays a Role in Cell Elongation, Cell Shape Maintenance, and Flowering in Arabidopsis
Authors: Ramachandran Srinivasan , Christensen Hans E.M. , Ishimaru Yasuko , Dong Chun-Hai , Chao-Ming Wen , Cleary Ann L. , Chua Nam-Hai 
Published: July 2002

Abstract
Profilin (PFN) is an ubiquitous, low-M r, actin-binding protein involved in the organization of the cytoskeleton of eukaryotes including higher plants. PFNs are encoded by a multigene family in Arabidopsis. We have analyzed in vivo functions of Arabidopsis PFN by generating transgenic plants carrying a35S-PFN-1 or35S-antisense PFN-1transgene. Etiolated seedlings underexpressing PFN (PFN-U) displayed an overall dwarf phenotype with short hypocotyls whose lengths were 20% to 25% that of wild type (WT) at low temperatures. Light-grown PFN-U plants were smaller in stature and flowered early. Compared with equivalent cells in WT, most cells in PFN-U hypocotyls and roots were shorter, but more isodiametric, and microscopic observations of etiolated PFN-U hypocotyls revealed a rough epidermal surface. In contrast, light-grown seedlings overexpressing PFN had longer roots and root hair although etiolated seedlings overexpressing PFN were either the same size or slightly longer than WT seedlings. Transgenic seedlings harboring aPFN-1-GUS transgene directed expression in root and root hair and in a ring of cells at the elongating zone of the root tip. As the seedlings matured PFN-1-GUS was mainly expressed in the vascular bundles of cotyledons and leaves. Our results show that Arabidopsis PFNs play a role in cell elongation, cell shape maintenance, polarized growth of root hair, and unexpectedly, in determination of flowering time.
Membrane Lipid Biosynthesis in Chlamydomonas reinhardtii. In Vitro Biosynthesis of Diacylglyceryltrimethylhomoserine
Authors: Moore Thomas S. , Du Zhirong , Chen Zhi 
Published: July 2002

Abstract
Diacylglyceryltrimethylhomo-Ser (DGTS) is an abundant lipid in the membranes of many algae, lower plants, and fungi. It commonly has an inverse concentration relationship with phosphatidylcholine, thus seemingly capable of replacing this phospholipid in these organisms. In some places this replacement is complete; Chlamydomonas reinhardtii is such an organism, and was used for these investigations. We have assayed headgroup incorporation to form DGTS in vitro. The precursor for both the homo-Ser moiety and the methyl groups was found to be S-adenosyl-L-Met. DGTS formation was associated with microsomal fractions and is not in plastids. By analogy with phosphatidylcholine and phosphatidylethanolamine biosynthesis in higher plants, the microsomal activity probably is associated with the endoplasmic reticulum. The pH optimum for the total reaction was between 7.5 and 8.0, and the best temperature was 30°C. The apparent K m andV max forS-adenosyl-L-Met in the overall reaction were 74 and 250 μm, respectively.
LEPS2, a Phosphorus Starvation-Induced Novel Acid Phosphatase from Tomato
Authors: Baldwin James C. , Karthikeyan Athikkattuvalasu S. , Raghothama Kashchandra G. 
Published: July 2002

Abstract
Phosphate (Pi) is one of the least available plant nutrients found in the soil. A significant amount of phosphate is bound in organic forms in the rhizosphere. Phosphatases produced by plants and microbes are presumed to convert organic phosphorus into available Pi, which is absorbed by plants. In this study we describe the isolation and characterization of a novel tomato (Lycopersicon esculentum) phosphate starvation-induced gene (LePS2) representing an acid phosphatase.LePS2 is a member of a small gene family in tomato. The cDNA is 942 bp long and contains an open reading frame encoding a 269-amino acid polypeptide. The amino acid sequence of LePS2 has a significant similarity with a phosphatase from chicken. Distinct regions of the peptide also share significant identity with the members of HAD and DDDD super families of phosphohydrolases. Many plant homologs of LePS2 are found in the databases. TheLePS2 transcripts are induced rapidly in tomato plant and cell culture in the absence of Pi. However, the induction is repressible in the presence of Pi. Divided root studies indicate that internal Pi levels regulate the expression of LePS2. The enhanced expression of LePS2 is a specific response to Pi starvation, and it is not affected by starvation of other nutrients or abiotic stresses. The bacterially (Escherichia coli)expressed protein exhibits phosphatase activity against the synthetic substrate p-nitrophenyl phosphate. The pH optimum of the enzyme activity suggests that LePS2 is an acid phosphatase.
Rice Bioinformatics. Analysis of Rice Sequence Data and Leveraging the Data to Other Plant Species
Authors: Yuan Qiaoping , Quackenbush John , Sultana Razvan , Pertea Mihaela , Salzberg Steven L. , Buell C. Robin 
Published: July 2002

Abstract
Rice (Oryza sativa) is a model species for monocotyledonous plants, especially for members in the grass family. Several attributes such as small genome size, diploid nature, transformability, and establishment of genetic and molecular resources make it a tractable organism for plant biologists. With an estimated genome size of 430 Mb (Arumuganathan and Earle, 1991), it is feasible to obtain the complete genome sequence of rice using current technologies. An international effort has been established and is in the process of sequencing O. sativa spp.japonica var “Nipponbare” using a bacterial artificial chromosome/P1 artificial chromosome shotgun sequencing strategy. Annotation of the rice genome is performed using prediction-based and homology-based searches to identify genes. Annotation tools such as optimized gene prediction programs are being developed for rice to improve the quality of annotation. Resources are also being developed to leverage the rice genome sequence to partial genome projects such as expressed sequence tag projects, thereby maximizing the output from the rice genome project. To provide a low level of annotation for rice genomic sequences, we have aligned all rice bacterial artificial chromosome/P1 artificial chromosome sequences with The Institute of Genomic Research Gene Indices that are a set of nonredundant transcripts that are generated from nine public plant expressed sequence tag projects (rice, wheat, sorghum, maize, barley, Arabidopsis, tomato, potato, and barrel medic). In addition, we have used data from The Institute of Genomic Research Gene Indices and the Arabidopsis and Rice Genome Projects to identify putative orthologues and paralogues among these nine genomes.
Nonsense-Mediated Decay of MutantwaxymRNA in Rice
Authors: Isshiki Masayuki , Yamamoto Yoshiaki , Satoh Hikaru , Shimamoto Ko 
Published: July 2002

AbstractTwo rice (Oryza sativa) waxy mutations of the Japonica background were shown to contain approximately 20% of the fully spliced mRNA relative to the wild type. Sequencing analysis of the entire waxy genes of the two mutants revealed the presence of premature translation termination codons in exon 2 and exon 7. These results indicated that the lower accumulation of fully spliced RNA in the mutants was caused by nonsense-mediated decay (NMD), which is an RNA surveillance system universally found in eukaryotes. It is interesting that levels of RNA retaining intron 1 were not changed by premature nonsense codons, suggesting that splicing may be linked with NMD in plants, as previously found in mammalian cells. Measurements of the half-lives of waxy RNAs in transfected rice protoplasts indicated that the half-life of waxy RNA with a premature nonsense codon was 3.3 times shorter than that without a premature nonsense codon. Because the wild-type waxytranscripts, which are derived from the Wxbgene predominantly distributed among Japonica rice, have been shown to be less efficiently spliced and their alternative splicing has been documented, we examined whether these splicing properties influenced the efficiency of NMD. However, no effects were observed. These results established that NMD occurs in rice waxy RNA containing a premature nonsense codon.
Ectopic Expression of the Tetratricopeptide Repeat Domain of SPINDLY Causes Defects in Gibberellin Response
Authors: Tseng Tong-Seung , Swain Stephen M. , Olszewski Neil E. 
Published: July 2002

Abstract
The SPINDLY (SPY) protein of Arabidopsis is a negative regulator of gibberellin (GA) response. The SPY protein has 10 copies of the tetratricopeptide repeat (TPR) at the N terminus. TPR motifs function as protein-protein interaction domains. Several spyalleles are affected only in the TPR region suggesting that protein-protein interactions mediated by this domain are important for proper GA signaling. We have used a reverse genetics approach to further investigate the role of the TPR domain. The TPR domain of SPY was overexpressed in wild-type, gai, andspy plants. Expression of the TPR domain alone is not sufficient to rescue spy mutants. Expression of the TPR domain in a wild-type background produces phenotypes similar to those caused by loss-of-function spy mutants including resistance to GA biosynthesis inhibitors, short hypocotyl length, and early flowering. The dwarfing of the floral shoot internodes caused by the gai mutation was suppressed by expression of the TRP domain. Expression of the TPR domain had no effect on the abundance of endogenous SPY mRNA. The TPR domain was found to interact with SPY both in vitro and in yeast two-hybrid assays. These data indicate that the TPR domain of SPY can participate in protein-protein interactions and that these interactions are important for the proper functioning of SPY.
The Experimental Herbicide CGA 325′615 Inhibits Synthesis of Crystalline Cellulose and Causes Accumulation of Non-Crystalline β-1,4-Glucan Associated with CesA Protein
Authors: Peng Liangcai , Xiang Fan , Roberts Eric , Kawagoe Yasushi , Greve L. Carl , Kreuz Klaus , Delmer Deborah P. 
Published: July 2002

Abstract
Developing cotton (Gossypium hirsutum) fibers, cultured in vitro with their associated ovules, were used to compare the effects of two herbicides that inhibit cellulose synthesis: 2,6-dichlorobenzonitrile (DCB) and an experimental thiatriazine-based herbicide, CGA 325′615. CGA 325′615 in nanomolar concentrations or DCB in micromolar concentrations causes inhibition of synthesis of crystalline cellulose. Unlike DCB, CGA 325′615 also causes concomitant accumulation of non-crystalline β-1,4-glucan that can be at least partially solubilized from fiber walls with ammonium oxalate. The unusual solubility of this accumulated glucan may be explained by its strong association with protein. Treatment of the glucan fraction with protease changes its size distribution and leads to precipitation of the glucan. Treatment of the glucan fraction with cellulase digests the glucan and also releases protein that has been characterized as GhCesA-1 and GhCesA-2—proteins that are believed to represent the catalytic subunit of cellulose synthase. The fact that cellulase treatment is required to release this protein indicates an extremely tight association of the glucan with the CesA proteins. In addition, CGA 325′615, but not DCB, also causes accumulation of CesA protein and a membrane-associated cellulase in the membrane fraction of fibers. In addition to the effects of CGA 325′615 on levels of both of these proteins, the level of both also shows coordinate regulation during fiber development, further suggesting they are both important for cellulose synthesis. The accumulation of non-crystalline glucan caused by CGA 325′615 mimics the phenotype of the cellulose-deficientrsw1 mutant of Arabidopsis that also accumulates an apparently similar glucan (T. Arioli, L. Peng, A.S. Betzner, J. Burn, W. Wittke, W. Herth, C. Camilleri, H. Hofte, J. Plazinski, R. Birch et al. [1998] Science 279: 717).
Substrate entropy in enzyme enantioselectivity: An experimental and molecular modeling study of a lipase
Authors: Ottosson Jenny , Fransson Linda , Hult Karl 
Published: July 2002

AbstractThe temperature dependence of the enantioselectivity of Candida antarctica lipase B for 3‐hexanol, 2‐butanol, 3‐methyl‐2‐butanol, 3,3‐dimethyl‐2‐butanol, and 1‐bromo‐2‐butanol revealed that the differential activation entropy, ΔR−SΔS‡, was as significant as the differential activation enthalpy, ΔR−SΔH‡, to the enantiomeric ratio, E. 1‐Bromo‐2‐butanol, with isosteric substituents, displayed the largest ΔR−SΔS‡. 3‐Hexanol displayed, contrary to other sec‐alcohols, a positive ΔR−SΔS‡. In other words, for 3‐hexanol the preferred R‐enantiomer is not only favored by enthalpy but also by entropy. Molecular dynamics (MD) simulations and systematic search calculations of the substrate accessible volume within the active site revealed that the (R)‐3‐hexanol transition state (TS) accessed a larger volume within the active site than the (S)‐3‐hexanol TS. This correlates well with the higher TS entropy of (R)‐3‐hexanol. In addition, this enantiomer did also yield a higher number of allowed conformations, N, from the systematic search routines, than did the S‐enantiomer. The substrate accessible volume was greater for the enantiomer preferred by entropy also for 2‐butanol. For 3,3‐dimethyl‐2‐butanol, however, neither MD‐simulations nor systematic search calculations yielded substrate accessible volumes that correlate to TS entropy. Ambiguous results were achieved for 3‐methyl‐2‐butanol.
Lipopolysaccharide phosphorylating enzymes encoded in the genomes of Gram‐negative bacteria are related to the eukaryotic protein kinases
Authors: Krupa A. , Srinivasan N. 
Published: July 2002

AbstractBy means of profile‐matching procedures, conservation of functionally important residues, and fold‐recognition techniques, we show that two distinct families of lipopolysaccharide kinases encoded in the genomes of Gram‐negative bacteria are related to each other and to two distinct classes of proteins, namely eukaryotic protein kinases and right open reading frame (RIO1). Members of one of the lipopolysaccharide kinase families are identified only in pathogenic bacteria. Phosphorylation by these enzymes is relevant in the construction of outer membrane, immune response, and pathogenic virulence. The class of proteins called RIO1, also related to eukaryotic protein kinases and previously known to occur only in archaea and eukaryotes, are now identified in eubacteria as well. It has been suggested here that RIO1 proteins are intermediately related to lipopolysaccharide kinases and eukaryotic protein kinases implying an evolutionary relationship between the three classes of proteins.
Electrostatic properties of the anion selective porin Omp32 from Delftia acidovorans and of the arginine cluster of bacterial porins
Authors: Zachariae Ulrich , Koumanov Assen , Engelhardt Harald , Karshikoff Andrey 
Published: July 2002

AbstractThe functional properties of the anion‐selective porin Omp32 from the bacterium Delftia acidovorans, formerly Comamonas acidovorans, are determined by the particularly narrow channel constriction and the electrostatic field inside and outside the pore. A cluster of arginines (Arg 38, Arg 75, and Arg 133) determines the electrostatic field close to the constriction zone. Stacked amino acids carrying charges are prone to drastic pKa shifts. However, optimized calculations of the titration behavior of charged groups, based on the finite‐difference Poisson‐Boltzmann technique, suggest that all the arginines are charged at physiological pH. Protonation of the clustered arginines is stabilized by one buried glutamate residue (Glu 58), which is strongly interacting with Arg 75 and Arg 38. This functional arrangement of three charged amino acid residues is of general significance because it is found in the constriction zones of all known 16‐stranded porins from the α‐, β‐, and γ‐proteobacteria.
Nonlinear Transient Heat Conduction Using Similarity Groups
Authors: Becker M. 
Published: July 2002

AbstractNonlinear response is studied using similarity groups. The nonlinear solution is similar to the linear solution except with properties evaluated at the local temperature and is consistent with reported empirical observations that, near the heat source, high-temperature properties are needed to predict cooling times to high temperatures and that low temperature properties are needed to predict cooling time to low temperatures. For position-dependent characteristics of the solution away from the source, like magnitudes and locations of peak temperatures, nonlinear and linear solutions are similar if local properties are evaluated at current temperatures prevailing near the source. [S0022-1481(00)02701-8]
A Monte Carlo Solution of Heat Conduction and Poisson Equations
Authors: Grigoriu M. 
Published: July 2002

Abstract
A Monte Carlo method is developed for solving the heat conduction, Poisson, and Laplace equations. The method is based on properties of Brownian motion and Ito^ processes, the Ito^ formula for differentiable functions of these processes, and the similarities between the generator of Ito^ processes and the differential operators of these equations. The proposed method is similar to current Monte Carlo solutions, such as the fixed random walk, exodus, and floating walk methods, in the sense that it is local, that is, it determines the solution at a single point or a small set of points of the domain of definition of the heat conduction equation directly. However, the proposed and the current Monte Carlo solutions are based on different theoretical considerations. The proposed Monte Carlo method has some attractive features. The method does not require to discretize the domain of definition of the differential equation, can be applied to domains of any dimension and geometry, works for both Dirichlet and Neumann boundary conditions, and provides simple solutions for the steady-state and transient heat equations. Several examples are presented to illustrate the application of the proposed method and demonstrate its accuracy. [S0022-1481(00)02201-5]