bluuebunny/crossref_metadata_2025 huggingface dataset:
Vestibular Sensitivity and Vection Chronometry along the Spinal Axis in Erect Man
Authors: Lepecq Jean-Claude , Giannopulu Irini , Mertz Sophie , Baudonnière Pierre-Marie
Published: November 2005

A study is reported of the relations between vestibular sensitivity and vection chronometry in healthy human adults. Twenty-three subjects were examined. For both vestibular and vection investigations, the subjects were seated in an armchair with the spinal axis aligned with the earth vertical and the head normally erect. The subjects' vestibular thresholds for detection of vertical upward accelerations were assessed by a double-staircase psychophysical method. The subjects' vection onset latencies were measured for both upward and downward directions. Since the vection onset latencies are presumed to be shortened by the decrease of the conflict between visual and vestibular afferents, the less-vestibular-sensitive subjects were hypothesised to have shorter vection onset latencies than the more-vestibular-sensitive ones. As expected, the results indicate a negative correlation between vestibular thresholds and vection onset latencies: the higher the vestibular thresholds, the lower the vection onset latencies.
The ‘Ecological’ Probability Density Function for Linear Optic Flow: Implications for Neurophysiology
Authors: Ivins Jim , Porrill John , Frisby John , Orban Guy
Published: November 2005

A theoretical analysis of the recovery of shape from optic flow highlights the importance of the deformation components; however, pure deforming stimuli elicit few responses from flow-sensitive neurons in the medial superior temporal (MST) area of the cerebral cortex. This finding has prompted the conclusion that MST cells are not involved in shape recovery. However, this conclusion may be unjustified in view of the emerging consensus that MST cells perform nonlinear pattern matching, rather than linear projection as implicitly assumed in many neurophysiological studies. Artificial neural models suggest that the input probability density function (PDF) is crucial in determining the distribution of responses shown by pattern-matching cells. This paper therefore describes a Monte-Carlo study of the joint PDF for linear optic-flow components produced by ego-motion in a simulated planar environment. The recent search for deformation-selective cells in MST is then used to illustrate the importance of the input PDF in determining cell characteristics. The results are consistent with the finding that MST cells exhibit a continuum of responses to translation, rotation, and divergence. In addition, there are negative correlations between the deformation and conformal components of optic flow. Consequently, if cells responsible for shape analysis are present in the MST area, they should respond best to combinations of deformation with other first-order flow components, rather than to the pure stimuli used in previous neurophysiological studies.
Inferring the
in vivo
looping properties of DNA
Authors: Saiz Leonor , Rubi J. Miguel , Vilar Jose M. G.
Published: November 2005

The free energy of looping DNA by proteins and protein complexes determines to what extent distal DNA sites can affect each other. We inferred its
in vivo
value through a combined computational–experimental approach for different lengths of the loop and found that, in addition to the intrinsic periodicity of the DNA double helix, the free energy has an oscillatory component of about half the helical period. Moreover, the oscillations have such an amplitude that the effects of regulatory molecules become strongly dependent on their precise DNA positioning and yet easily tunable by their cooperative interactions. These unexpected results can confer to the physical properties of DNA a more prominent role at shaping the properties of gene regulation than previously thought.
The expression of the pituitary growth hormone-releasing hormone receptor and its splice variants in normal and neoplastic human tissues
Authors: Havt Alexandre , Schally Andrew V. , Halmos Gabor , Varga Jozsef L. , Toller Gabor L. , Horvath Judit E. , Szepeshazi Karoly , Köster Frank , Kovitz Kevin , Groot Kate , Zarandi Marta , Kanashiro Celia A.
Published: November 2005

Various attempts to detect human pituitary growth hormone-releasing hormone receptor (pGHRH-R) in neoplastic extrapituitary tissues have thus far failed. Recently, four splice variants (SVs) of GHRH-R have been described, of which SV1 has the highest structural homology to pGHRH-R and likely plays a role in tumor growth. The aim of this study was to reinvestigate whether human tumors and normal human extrapituitary tissues express the pGHRH-R and to corroborate our previous findings on its SVs. Thus, we developed a real-time PCR method for the detection of the mRNA for the pGHRH-R, its SVs, and the GHRH peptide. Using real-time PCR, Western blotting, and radioligand-binding assays, we detected the mRNA for pGHRH-R and pGHRH-R protein in various human cancer cell lines grown in nude mice and in surgical specimens of human lung cancers. The expression of mRNA for SVs of pGHRH-R and GHRH was likewise found in xenografts of human non-Hodgkin's lymphomas, pancreatic cancer, glioblastoma, small-cell lung carcinomas, and in human nonmalignant prostate, liver, lung, kidney, and pituitary. Western blots showed that these normal and malignant human tissues contain SV1 protein and immunoreactive GHRH. Our results demonstrate that some normal human tissues and tumors express mRNA and protein for the pGHRH-R and its splice variants. These findings confirm and extend the concept that GHRH and its receptors play an important role in the pathophysiology of human cancers.
Myosin light chain kinase and myosin phosphorylation effect frequency-dependent potentiation of skeletal muscle contraction
Authors: Zhi Gang , Ryder Jeffrey W. , Huang Jian , Ding Peiguo , Chen Yue , Zhao Yingming , Kamm Kristine E. , Stull James T.
Published: November 2005

Repetitive stimulation potentiates contractile tension of fast-twitch skeletal muscle. We examined the role of myosin regulatory light chain (RLC) phosphorylation in this physiological response by ablating Ca
2+
/calmodulin-dependent skeletal muscle myosin light chain kinase (MLCK) gene expression. Western blot and quantitative-PCR showed that MLCK is expressed predominantly in fast-twitch skeletal muscle fibers with insignificant amounts in heart and smooth muscle. In contrast, smooth muscle MLCK had a more ubiquitous tissue distribution, with the greatest expression observed in smooth muscle tissue. Ablation of the MYLK2 gene in mice resulted in loss of skeletal muscle MLCK expression, with no change in smooth muscle MLCK expression. In isolated fast-twitch skeletal muscles from these knockout mice, there was no significant increase in RLC phosphorylation in response to repetitive electrical stimulation. Furthermore, isometric twitch-tension potentiation after a brief tetanus (posttetanic twitch potentiation) or low-frequency twitch potentiation (staircase) was attenuated relative to responses in muscles from wild-type mice. Interestingly, the site of phosphorylation of the small amount of monophosphorylated RLC in the knockout mice was the same site phosphorylated by MLCK, indicating a potential alternative signaling pathway affecting contractile potentiation. Loss of skeletal muscle MLCK expression had no effect on cardiac RLC phosphorylation. These results identify myosin light chain phosphorylation by the dedicated skeletal muscle Ca
2+
/calmodulin-dependent MLCK as a primary biochemical mechanism for tension potentiation due to repetitive stimulation in fast-twitch skeletal muscle.
Modeling genome evolution with a diffusion approximation of a birth-and-death process
Authors: Karev Georgy P. , Berezovskaya Faina S. , Koonin Eugene V.
Published: November 2005

Motivation: In our previous studies, we developed discrete-space birth, death and innovation models (BDIMs) of genome evolution. These models explain the origin of the characteristic Pareto distribution of paralogous gene family sizes in genomes, and model parameters that provide for the evolution of these distributions within a realistic time frame have been identified. However, extracting the temporal dynamics of genome evolution from discrete-space BDIM was not technically feasible. We were interested in obtaining dynamic portraits of the genome evolution process by developing a diffusion approximation of BDIM.

Results: The diffusion version of BDIM belongs to a class of continuous-state models whose dynamics is described by the Fokker–Plank equation and the stationary solution could be any specified Pareto function. The diffusion models have time-dependent solutions of a special kind, namely, generalized self-similar solutions, which describe the transition from one stationary distribution of the system to another; this provides for the possibility of examining the temporal dynamics of genome evolution. Analysis of the generalized self-similar solutions of the diffusion BDIM reveals a biphasic curve of genome growth in which the initial, relatively short, self-accelerating phase is followed by a prolonged phase of slow deceleration. This evolutionary dynamics was observed both when genome growth started from zero and proceeded via innovation (a potential model of primordial evolution), and when evolution proceeded from one stationary state to another. In biological terms, this regime of evolution can be tentatively interpreted as a punctuated-equilibrium-like phenomenon whereby evolutionary transitions are accompanied by rapid gene amplification and innovation, followed by slow relaxation to a new stationary state.

Contact:  koonin@ncbi.nlm.nih.gov
Describing ancient horizontal gene transfers at the nucleotide and gene levels by comparative pathogenicity island genometrics
Authors: Collyn F. , Guy L. , Marceau M. , Simonet M. , Roten C.-A. H.
Published: November 2005

Motivation: Lateral gene transfer is a major mechanism contributing to bacterial genome dynamics and pathovar emergence via pathogenicity island (PAI) spreading. However, since few of these genomic exchanges are experimentally reproducible, it is difficult to establish evolutionary scenarios for the successive PAI transmissions between bacterial genera. Methods initially developed at the gene and/or nucleotide level for genomics, i.e. comparisons of concatenated sequences, ortholog frequency, gene order or dinucleotide usage, were combined and applied here to homologous PAIs: we call this approach comparative PAI genometrics.

Results: YAPI, a Yersinia PAI, and related islands were compared with measure evolutionary relationships between related modules. Through use of our genometric approach designed for tracking codon usage adaptation and gene phylogeny, an ancient inter-genus PAI transfer was oriented for the first time by characterizing the genomic environment in which the ancestral island emerged and its subsequent transfers to other bacterial genera.

Contact:  claude-alain.roten@unil.ch

Supplementary information:
THE IMPACT OF HIGH‐TECH CAPITAL ON PRODUCTIVITY: EVIDENCE FROM AUSTRALIA
Authors: CONNOLLY ELLIS , FOX KEVIN J.
Published: November 2005

This article examines the relationship between high‐tech capital use and productivity. Using Australian data, some evidence is found of a positive relationship between high‐tech capital use and productivity in the market sector, but there is much less evidence of excess returns. These results are robust to the use of a variety of different measures of high‐tech capital. At the industry level however, the relationship is significant and positive for only some industries. This suggests that the benefits of investment in high‐tech capital are not spread evenly across the economy. (JEL O3)
A CHANGE POINT ANALYSIS OF THE IMPACT OF “ENVIRONMENTAL FEDERALISM” ON AGGREGATE AIR QUALITY IN THE UNITED STATES: 1940–98
Authors: FOMBY THOMAS B. , LIN LIMIN
Published: November 2005

During President Reagan's administration, environmental policy making was substantially shifted from the federal level to the state and local levels. We use techniques in Bai (1997a, 1997b) to determine change points in the trends of three important air pollution series. We find that the beneficial trends in the emission series began with federal legislation and were not due to the Reagan devolution. However, second‐round change point tests indicate that the beneficial trends in the emissions series that began with federal legislation continued unabated following the Reagan devolution. (JEL Q20, C50)
HEALTH CARE, INSURANCE, AND THE CONTRACT CHOICE EFFECT
Authors: DUSANSKY RICHARD , KOÇ ÇAGATAY
Published: November 2005

This article explores the interdependence between the individual consumer's demand for medical care and choice of health insurance coverage, with emphasis on its implications for demand behavior and empirical analysis. We show that an increase in the price of medical care has two effects on demand, the usual response of reduced quantity demanded and a health insurance contract choice effect resulting from the consumer's incentive to change insurance plan. The contract choice effect, widely neglected in studies of medical care demand, alters both the quantitative and qualitative predictive properties of the consumer's demand for medical services. (JEL D11, D81, I11)
MEDIA CONCENTRATION AND CONSUMER PRODUCT PRICES
Authors: DUKES ANTHONY J.
Published: November 2005

This article examines the interaction of commercial media and retail producers of well‐known consumer products when advertising is used to differentiate brands. In particular, I address how competition in the media market affects choices of advertising and program quality. The results suggest counterintuitively that advertisers may actually prefer media markets with less competition for audiences. Product differentiation through advertising is more effective when media markets are less competitive, leading to higher prices for advertised products. As a result, media concentration may lead to higher profits for advertising firms if the additional revenue exceeds the higher advertising costs associated with media concentration. (JEL L11, L82, M37)
BIRTH ORDER AND RISKY ADOLESCENT BEHAVIOR
Authors: ARGYS LAURA M. , REES DANIEL I. , AVERETT SUSAN L. , WITOONCHART BENJAMA
Published: November 2005

It is commonly believed that birth order is an important determinant of success. However, previous studies in this area have failed to provide convincing evidence that birth order is related to test scores, education, or earnings. Using data from the National Longitudinal Survey of Youth–1979, we investigate the association between birth order and adolescent behaviors such as smoking, drinking, marijuana use, sexual activity, and crime. Our estimates show that middle borns and last borns are much more likely to use substances and be sexually active than their firstborn counterparts. These results provide the strongest evidence to date that birth order is related to measurable behaviors. (JEL I12, J12, J13)
A TIME SERIES TEST OF INNOVATION‐DRIVEN ENDOGENOUS GROWTH
Authors: SEDGLEY NORMAN H.
Published: November 2005

This article finds evidence that ideas and innovation are a key force explaining postwar growth in the U.S. economy. Utilizing data on patents issued since 1851, I construct a measure of the growth rate of knowledge. Capital stock estimates, human capital estimates, and real gross domestic product per worker growth rates are combined with the knowledge growth series to construct a time series test of endogenous innovation growth models. The results support the endogenous innovation approach but suggest that the accumulation of the per worker capital stock and changes in average human capital per worker are at least as important. (JEL030,C32)
SIMULTANEOUS EQUATION ECONOMETRICS: THE MISSING EXAMPLE
Authors: EPPLE DENNIS , MCCALLUM BENNETT T.
Published: November 2005

For introductory presentation of issues involving simultaneous equation systems, a natural vehicle consists of supply and demand relationships for a single good. One would expect to find in econometrics textbooks a supply‐demand example featuring actual data in which structural estimation methods yield more satisfactory results than does ordinary least squares. But a search of 26 existing textbooks finds no example with actual data in which all crucial parameter estimates are of the proper sign and are statistically significant. The present article accordingly develops a simple but satisfying example, for broiler chickens, based on U.S. annual data from 1960 to 1999. (JEL C30)
DO NEWLY RETIRED WORKERS IN THE UNITED STATES HAVE SUFFICIENT RESOURCES TO MAINTAIN WELL‐BEING?
Authors: HAVEMAN ROBERT , HOLDEN KAREN , WOLFE BARBARA , SHERLUND SHANE
Published: November 2005

A current policy issue is the extent to which savings are sufficient to sustain economic well‐being in retirement. We compare annuitized wealth at retirement to three preretirement consumption estimates. About one‐half of new retirees have insufficient resources to enable the full maintenance of estimated preretirement consumption in retirement, and about 40% fail to meet the “0.7 of earnings” standard that is used in many studies. Using standards reflecting social (poverty) norms we find a less serious problem. About 5% (25%) of new retirees have insufficient resources to enable an above‐poverty (near‐poverty) level of living during retirement. (JEL J14, J26)
Evaluation of the Antimicrobial Activities of Plant Oxylipins Supports Their Involvement in Defense against Pathogens
Authors: Prost Isabelle , Dhondt Sandrine , Rothe Grit , Vicente Jorge , Rodriguez Maria José , Kift Neil , Carbonne Francis , Griffiths Gareth , Esquerré-Tugayé Marie-Thérèse , Rosahl Sabine , Castresana Carmen , Hamberg Mats , Fournier Joëlle
Published: November 2005

Plant oxylipins are a large family of metabolites derived from polyunsaturated fatty acids. The characterization of mutants or transgenic plants affected in the biosynthesis or perception of oxylipins has recently emphasized the role of the so-called oxylipin pathway in plant defense against pests and pathogens. In this context, presumed functions of oxylipins include direct antimicrobial effect, stimulation of plant defense gene expression, and regulation of plant cell death. However, the precise contribution of individual oxylipins to plant defense remains essentially unknown. To get a better insight into the biological activities of oxylipins, in vitro growth inhibition assays were used to investigate the direct antimicrobial activities of 43 natural oxylipins against a set of 13 plant pathogenic microorganisms including bacteria, oomycetes, and fungi. This study showed unequivocally that most oxylipins are able to impair growth of some plant microbial pathogens, with only two out of 43 oxylipins being completely inactive against all the tested organisms, and 26 oxylipins showing inhibitory activity toward at least three different microbes. Six oxylipins strongly inhibited mycelial growth and spore germination of eukaryotic microbes, including compounds that had not previously been ascribed an antimicrobial activity, such as 13-keto-9(Z),11(E),15(Z)-octadecatrienoic acid and 12-oxo-10,15(Z)-phytodienoic acid. Interestingly, this first large-scale comparative assessment of the antimicrobial effects of oxylipins reveals that regulators of plant defense responses are also the most active oxylipins against eukaryotic microorganisms, suggesting that such oxylipins might contribute to plant defense through their effects both on the plant and on pathogens, possibly through related mechanisms.
A Wound-Responsive and Phospholipid-Regulated Maize Calcium-Dependent Protein Kinase
Authors: Szczegielniak Jadwiga , Klimecka Maria , Liwosz Aneta , Ciesielski Arkadiusz , Kaczanowski Szymon , Dobrowolska Grażyna , Harmon Alice C. , Muszyńska Grażyna
Published: November 2005

Using protein sequence data obtained from a calcium- and phospholipid-regulated protein kinase purified from maize (Zea mays), we isolated a cDNA encoding a calcium-dependent protein kinase (CDPK), which we designated ZmCPK11. The deduced amino acid sequence of ZmCPK11 includes the sequences of all the peptides obtained from the native protein. The ZmCPK11 sequence contains the kinase, autoregulatory, and calmodulin-like domains typical of CDPKs. Transcripts for ZmCPK11 were present in every tested organ of the plant, relatively high in seeds and seedlings and lower in stems, roots, and leaves. In leaves, kinase activity and ZmCPK11 mRNA accumulation were stimulated by wounding. The level of ZmCPK11 is also increased in noninjured neighboring leaves. The results suggest that the maize protein kinase is involved in a systemic response to wounding. Bacterially expressed glutathione S-transferase (GST)-ZmCPK11 was catalytically active in a calcium-dependent manner. Like the native enzyme, GST-ZmCPK11 was able to phosphorylate histone III-S and Syntide 2. Phosphorylation of histone was stimulated by phosphatidylserine, phosphatidylinositol, and phosphatidic acid, whereas phosphatidylcholine, lysophosphatidylcholine, phosphatidylethanolamine, diolein, and cardiolipin did not increase the enzymatic activity. Autophosphorylation of GST-ZmCPK11 was stimulated by calcium and by phosphatidic acid and, to a lesser extent, by phosphatidylserine. Phosphatidylcholine did not affect autophosphorylation. These data unequivocally identify the maize phospholipid- and calcium-regulated protein kinase, which has protein kinase C-like activity, as a CDPK, and emphasize the potential that other CDPKs are regulated by phospholipids in addition to calcium.
Sucrose-Specific Induction of Anthocyanin Biosynthesis in Arabidopsis Requires the MYB75/PAP1 Gene
Authors: Teng Sheng , Keurentjes Joost , Bentsink Leónie , Koornneef Maarten , Smeekens Sjef
Published: November 2005

Sugar-induced anthocyanin accumulation has been observed in many plant species. We observed that sucrose (Suc) is the most effective inducer of anthocyanin biosynthesis in Arabidopsis (Arabidopsis thaliana) seedlings. Other sugars and osmotic controls are either less effective or ineffective. Analysis of Suc-induced anthocyanin accumulation in 43 Arabidopsis accessions shows that considerable natural variation exists for this trait. The Cape Verde Islands (Cvi) accession essentially does not respond to Suc, whereas Landsberg erecta is an intermediate responder. The existing Landsberg erecta/Cvi recombinant inbred line population was used in a quantitative trait loci analysis for Suc-induced anthocyanin accumulation (SIAA). A total of four quantitative trait loci for SIAA were identified in this way. The locus with the largest contribution to the trait, SIAA1, was fine mapped and using a candidate gene approach, it was shown that the MYB75/PAP1 gene encodes SIAA1. Genetic complementation studies and analysis of a laboratory-generated knockout mutation in this gene confirmed this conclusion. Suc, in a concentration-dependent way, induces MYB75/PAP1 mRNA accumulation. Moreover, MYB75/PAP1 is essential for the Suc-mediated expression of the dihydroflavonol reductase gene. The SIAA1 locus in Cvi probably is a weak or loss-of-function MYB75/PAP1 allele. The C24 accession similarly shows a very weak response to Suc-induced anthocyanin accumulation encoded by the same locus. Sequence analysis showed that the Cvi and C24 accessions harbor mutations both inside and downstream of the DNA-binding domain of the MYB75/PAP1 protein, which most likely result in loss of activity.
A Cellular Timetable of Autumn Senescence
Authors: Keskitalo Johanna , Bergquist Gustaf , Gardeström Per , Jansson Stefan
Published: November 2005

We have studied autumn leaf senescence in a free-growing aspen (Populus tremula) by following changes in pigment, metabolite and nutrient content, photosynthesis, and cell and organelle integrity. The senescence process started on September 11, 2003, apparently initiated solely by the photoperiod, and progressed steadily without any obvious influence of other environmental signals. For example, after this date, senescing leaves accumulated anthocyanins in response to conditions inducing photooxidative stress, but at the beginning of September the leaves did not. Degradation of leaf constituents took place over an 18-d period, and, although the cells in each leaf did not all senesce in parallel, senescence in the tree as a whole was synchronous. Lutein and β-carotene were degraded in parallel with chlorophyll, whereas neoxanthin and the xanthophyll cycle pigments were retained longer. Chloroplasts in each cell were rapidly converted to gerontoplasts and many, although not all, cells died. From September 19, when chlorophyll levels had dropped by 50%, mitochondrial respiration provided the energy for nutrient remobilization. Remobilization seemed to stop on September 29, probably due to the cessation of phloem transport, but, up to abscission of the last leaves (over 1 week later), some cells were metabolically active and had chlorophyll-containing gerontoplasts. About 80% of the nitrogen and phosphorus was remobilized, and on September 29 a sudden change occurred in the δ15n of the cellular content, indicating that volatile compounds may have been released.
Analysis of the Female Gametophyte Transcriptome of Arabidopsis by Comparative Expression Profiling
Authors: Yu Hee-Ju , Hogan Pat , Sundaresan Venkatesan
Published: November 2005

The extensive data on the transcription of the plant genome are derived primarily from the sporophytic generation. There currently is little information on genes that are expressed during female gametophyte development in angiosperms, and it is not known whether the female gametophyte transcriptome contains a major set of genes that are not expressed in the sporophyte or whether it is primarily a subset of the sporophytic transcriptome. Because the embryo sac is embedded within the maternal ovule tissue, we have utilized the Arabidopsis (Arabidopsis thaliana) mutant sporocyteless that produces ovules without embryo sacs, together with the ATH1 Arabidopsis whole-genome oligonucleotide array, to identify genes that are preferentially or specifically expressed in female gametophyte development. From analysis of the datasets, 225 genes are identified as female gametophyte genes, likely a lower limit as stringent criteria were used for the analysis, eliminating many low expressed genes. Nearly 45% of the identified genes were not previously detected by sporophytic expression profiling, suggesting that the embryo sac transcriptome may contain a significant fraction of transcripts restricted to the gametophyte. Validation of six candidate genes was performed using promoter∷β-glucuronidase fusions, and all of these showed embryo sac-specific expression in the ovule. The unfiltered expression data from this study can be used to evaluate the possibility of female gametophytic expression for any gene in the ATH1 array, and contribute to identification of the functions of the component of the Arabidopsis genome not represented in studies of sporophytic expression and function.
The Diphenylether Herbicide Lactofen Induces Cell Death and Expression of Defense-Related Genes in Soybean
Authors: Graham Madge Y.
Published: November 2005

Lactofen belongs to the diphenylether class of herbicides, which targets protoporphyrinogen oxidase, which in turn causes singlet oxygen generation. In tolerant plants like soybean (Glycine max), the chemical nonetheless causes necrotic patches called “bronzing” in contact areas. Here it is shown that such bronzing is accompanied by cell death, which was quantified from digital microscopic images using Assess Software. Cellular autofluorescence accompanied cell death, and a homolog of the cell death marker gene, Hsr203j, was induced by lactofen in treated soybean tissues. Thus, this form of chemically induced cell death shares some hallmarks of certain types of programmed cell death. In addition to the cell death phenotype, lactofen caused enhanced expressions of chalcone synthase and chalcone reductase genes, mainly in the exposed and immediately adjacent (proximal) cells. Furthermore, isoflavone synthase genes, which are wound inducible in soybean, were up-regulated by lactofen in both proximal and distal cell zones in minimally wounded cotyledons and further enhanced in wounded tissues. Moreover, if the wall glucan elicitor from Phytophthora sojae was present during lactofen treatment, the induction of isoflavone synthase was even more rapid. These results are consistent with the fact that lactofen triggers massive isoflavone accumulations and activates the capacity for glyceollin elicitation competency. In addition, lactofen induces late expression of a selective set of pathogenesis-related (PR) protein genes, including PR-1a, PR-5, and PR-10, mainly in treated proximal tissues. These various results are discussed in the context of singlet oxygen-induced responses and lactofen's potential as a disease resistance-inducing agent.
Effects of Brefeldin A on Pollen Germination and Tube Growth. Antagonistic Effects on Endocytosis and Secretion
Authors: Wang Qinli , Kong Lingan , Hao Huaiqing , Wang Xiaohua , Lin Jinxing , Šamaj Jozef , Baluška František
Published: November 2005

We assessed the effects of brefeldin A (BFA) on pollen tube development in Picea meyeri using fluorescent marker FM4-64 as a membrane-inserted endocytic/recycling marker, together with ultrastructural studies and Fourier transform infrared analysis of cell walls. BFA inhibited pollen germination and pollen tube growth, causing morphological changes in a dose-dependent manner, and pollen tube tip growth recovered after transferring into BFA-free medium. FM4-64 labeling showed typical bright apical staining in normally growing P. meyeri pollen tubes; this apical staining pattern differed from the V-formation pattern found in angiosperm pollen tubes. Confocal microscopy revealed that exocytosis was greatly inhibited in the presence of BFA. In contrast, the overall uptake of FM4-64 dye was about 2-fold that in the control after BFA (5 μg mL−1) treatment, revealing that BFA stimulated endocytosis in a manner opposite to the induced changes in exocytosis. Transmission electron microscopic observation showed that the number of secretory vesicles at the apical zone dramatically decreased, together with the disappearance of paramural bodies, while the number of vacuoles and other larger organelles increased. An acid phosphatase assay confirmed that the addition of BFA significantly inhibited secretory pathways. Importantly, Fourier transform infrared microspectroscopy documented significant changes in the cell wall composition of pollen tubes growing in the presence of BFA. These results suggest that enhanced endocytosis, together with inhibited secretion, is responsible for the retarded growth of pollen tubes induced by BFA.
Biotin Synthesis in Plants. The First Committed Step of the Pathway Is Catalyzed by a Cytosolic 7-Keto-8-Aminopelargonic Acid Synthase
Authors: Pinon Violaine , Ravanel Stéphane , Douce Roland , Alban Claude
Published: November 2005

Biochemical and molecular characterization of the biotin biosynthetic pathway in plants has dealt primarily with biotin synthase. This enzyme catalyzing the last step of the pathway is localized in mitochondria. Other enzymes of the pathway are however largely unknown. In this study, a genomic-based approach allowed us to clone an Arabidopsis (Arabidopsis thaliana) cDNA coding 7-keto-8-aminopelargonic acid (KAPA) synthase, the first committed enzyme of the biotin synthesis pathway, which we named AtbioF. The function of the enzyme was demonstrated by functional complementation of an Escherichia coli mutant deficient in KAPA synthase reaction, and by measuring in vitro activity. Overproduction and purification of recombinant AtbioF protein enabled a thorough characterization of the kinetic properties of the enzyme and a spectroscopic study of the enzyme interaction with its substrates and product. This is the first characterization of a KAPA synthase reaction in eukaryotes. Finally, both green fluorescent protein-targeting experiments and western-blot analyses showed that the Arabidopsis KAPA synthase is present in cytosol, thus revealing a unique compartmentation of the plant biotin synthesis, split between cytosol and mitochondria. The significance of the complex compartmentation of biotin synthesis and utilization in the plant cell and its potential importance in the regulation of biotin metabolism are also discussed.
Premature Leaf Senescence Modulated by the Arabidopsis PHYTOALEXIN DEFICIENT4 Gene Is Associated with Defense against the Phloem-Feeding Green Peach Aphid
Authors: Pegadaraju Venkatramana , Knepper Caleb , Reese John , Shah Jyoti
Published: November 2005

Aphids, which are phloem-feeding insects, cause extensive loss of plant productivity and are vectors of plant viruses. Aphid feeding causes changes in resource allocation in the host, resulting in an increase in flow of nutrients to the insect-infested tissue. We hypothesized that leaf senescence, which is involved in the programmed degradation of cellular components and the export of nutrients out of the senescing leaf, could be utilized by plants to limit aphid growth. Using Arabidopsis (Arabidopsis thaliana) and green peach aphid (GPA; Myzus persicae Sulzer), we found that GPA feeding induced premature chlorosis and cell death, and increased the expression of SENESCENCE ASSOCIATED GENES (SAGs), all hallmarks of leaf senescence. Hypersenescence was accompanied by enhanced resistance against GPA in the Arabidopsis constitutive expresser of PR genes5 and suppressor of SA insensitivity2 mutant plants. In contrast, resistance against GPA was compromised in the phytoalexin deficient4 (pad4) mutant plant. The PAD4 gene, which is expressed at elevated level in response to GPA feeding, modulates the GPA feeding-induced leaf senescence. In comparison to the wild-type plant, GPA feeding-induced chlorophyll loss, cell death, and SAG expression were delayed in the pad4 mutant. Although PAD4 is associated with camalexin synthesis and salicylic acid (SA) signaling, camalexin and SA signaling are not important for restricting GPA growth; growth of GPA on the camalexin-biosynthesis mutant, pad3, and the SA deficient2 and NahG plants and the SA-signaling mutant, nonexpresser of PR genes1, were comparable to that on the wild-type plant. Our results suggest that PAD4 modulates the activation of senescence in the aphid-infested leaves, which contributes to basal resistance to GPA.
Characterization of Transformed Arabidopsis with Altered Alternative Oxidase Levels and Analysis of Effects on Reactive Oxygen Species in Tissue
Authors: Umbach Ann L. , Fiorani Fabio , Siedow James N.
Published: November 2005

The alternative oxidase (AOX) of plant mitochondria transfers electrons from the ubiquinone pool to oxygen without energy conservation. AOX can use reductant in excess of cytochrome pathway capacity, preventing reactive oxygen species (ROS) formation from an over-reduced ubiquinone pool, and thus may be involved in acclimation to oxidative stresses. The AOX connection with mitochondrial ROS has been investigated only in isolated mitochondria and suspension culture cells. To study ROS and AOX in whole plants, transformed lines of Arabidopsis (Arabidopsis thaliana) were generated: AtAOX1a overexpressors, AtAOX1a anti-sense plants, and overexpressors of a mutated, constitutively active AtAOX1a. In the presence of KCN, leaf tissue of either mutant or wild-type AOX overexpressors showed no increase in oxidative damage, whereas anti-sense lines had levels of damage greater than those observed for untransformed leaves. Similarly, ROS production increased markedly in anti-sense and untransformed, but not overexpressor, roots with KCN treatment. Thus, AOX functions in leaves and roots, as in suspension cells, to ameliorate ROS production when the cytochrome pathway is chemically inhibited. However, in contrast with suspension culture cells, no changes in leaf transcript levels of selected electron transport components or oxidative stress-related enzymes were detected under nonlimiting growth conditions, regardless of transformation type. Further, a microarray study using an anti-sense line showed AOX influences outside mitochondria, particularly in chloroplasts and on several carbon metabolism pathways. These results illustrate the value of expanding AOX transformant studies to whole tissues.
The Alternative Oxidase of Plant Mitochondria Is Involved in the Acclimation of Shoot Growth at Low Temperature. A Study of Arabidopsis AOX1a Transgenic Plants
Authors: Fiorani Fabio , Umbach Ann L. , Siedow James N.
Published: November 2005

The alternative oxidase (AOX) pathway of plant mitochondria uncouples respiration from mitochondrial ATP production and may ameliorate plant performance under stressful environmental conditions, such as cold temperatures, by preventing excess accumulation of reactive oxygen species. We tested this model in whole tissues by growing AtAOX1a-transformed Arabidopsis (Arabidopsis thaliana) plants at 12°C. For the first time, to our knowledge, in plants genetically engineered for AOX, we identified a vegetative shoot growth phenotype. Compared with wild type at day 21 after sowing, anti-sense and overexpressing lines showed, on average, 27% reduced leaf area and 25% smaller rosettes versus 30% increased leaf area and 33% larger rosette size, respectively. Lines overexpressing a mutated, constitutively active AOX1a showed smaller phenotypic effects. These phenotypic differences were not the result of a major alteration of the tissue redox state because the changes in levels of lipid peroxidation products, reflecting oxidative damage, and the expression of genes encoding antioxidant and electron transfer chain redox enzymes did not correspond with the shoot phenotypes. However, the observed phenotypes were correlated with the amount of total shoot anthocyanin at low temperature and with the transcription of the flavonoid pathway genes PAL1 and CHS. These results demonstrate that (1) AOX activity plays a role in shoot acclimation to low temperature in Arabidopsis, and that (2) AOX not only functions to prevent excess reactive oxygen species formation in whole tissues under stressful environmental conditions but also affects metabolism through more pervasive effects, including some that are extramitochondrial.
Cuticular Lipid Composition, Surface Structure, and Gene Expression in Arabidopsis Stem Epidermis
Authors: Suh Mi Chung , Samuels A. Lacey , Jetter Reinhard , Kunst Ljerka , Pollard Mike , Ohlrogge John , Beisson Fred
Published: November 2005

All vascular plants are protected from the environment by a cuticle, a lipophilic layer synthesized by epidermal cells and composed of a cutin polymer matrix and waxes. The mechanism by which epidermal cells accumulate and assemble cuticle components in rapidly expanding organs is largely unknown. We have begun to address this question by analyzing the lipid compositional variance, the surface micromorphology, and the transcriptome of epidermal cells in elongating Arabidopsis (Arabidopsis thaliana) stems. The rate of cell elongation is maximal near the apical meristem and decreases steeply toward the middle of the stem, where it is 10 times slower. During and after this elongation, the cuticular wax load and composition remain remarkably constant (32 μg/cm2), indicating that the biosynthetic flux into waxes is closely matched to surface area expansion. By contrast, the load of polyester monomers per unit surface area decreases more than 2-fold from the upper (8 μg/cm2) to the lower (3 μg/cm2) portion of the stem, although the compositional variance is minor. To aid identification of proteins involved in the biosynthesis of waxes and cutin, we have isolated epidermal peels from Arabidopsis stems and determined transcript profiles in both rapidly expanding and nonexpanding cells. This transcriptome analysis was validated by the correct classification of known epidermis-specific genes. The 15% transcripts preferentially expressed in the epidermis were enriched in genes encoding proteins predicted to be membrane associated and involved in lipid metabolism. An analysis of the lipid-related subset is presented.
Inhibition of Target of Rapamycin Signaling by Rapamycin in the Unicellular Green Alga Chlamydomonas reinhardtii
Authors: Crespo José L. , Díaz-Troya Sandra , Florencio Francisco J.
Published: November 2005

The macrolide rapamycin specifically binds the 12-kD FK506-binding protein (FKBP12), and this complex potently inhibits the target of rapamycin (TOR) kinase. The identification of TOR in Arabidopsis (Arabidopsis thaliana) revealed that TOR is conserved in photosynthetic eukaryotes. However, research on TOR signaling in plants has been hampered by the natural resistance of plants to rapamycin. Here, we report TOR inactivation by rapamycin treatment in a photosynthetic organism. We identified and characterized TOR and FKBP12 homologs in the unicellular green alga Chlamydomonas reinhardtii. Whereas growth of wild-type Chlamydomonas cells is sensitive to rapamycin, cells lacking FKBP12 are fully resistant to the drug, indicating that this protein mediates rapamycin action to inhibit cell growth. Unlike its plant homolog, Chlamydomonas FKBP12 exhibits high affinity to rapamycin in vivo, which was increased by mutation of conserved residues in the drug-binding pocket. Furthermore, pull-down assays demonstrated that TOR binds FKBP12 in the presence of rapamycin. Finally, rapamycin treatment resulted in a pronounced increase of vacuole size that resembled autophagic-like processes. Thus, our findings suggest that Chlamydomonas cell growth is positively controlled by a conserved TOR kinase and establish this unicellular alga as a useful model system for studying TOR signaling in photosynthetic eukaryotes.
The Rice Dwarf Virus P2 Protein Interacts with ent-Kaurene Oxidases in Vivo, Leading to Reduced Biosynthesis of Gibberellins and Rice Dwarf Symptoms
Authors: Zhu Shifeng , Gao Feng , Cao Xuesong , Chen Mao , Ye Gongyin , Wei Chunhong , Li Yi
Published: November 2005

The mechanisms of viral diseases are a major focus of biology. Despite intensive investigations, how a plant virus interacts with host factors to cause diseases remains poorly understood. The Rice dwarf virus (RDV), a member of the genus Phytoreovirus, causes dwarfed growth phenotypes in infected rice (Oryza sativa) plants. The outer capsid protein P2 is essential during RDV infection of insects and thus influences transmission of RDV by the insect vector. However, its role during RDV infection within the rice host is unknown. By yeast two-hybrid and coimmunoprecipitation assays, we report that P2 of RDV interacts with ent-kaurene oxidases, which play a key role in the biosynthesis of plant growth hormones gibberellins, in infected plants. Furthermore, the expression of ent-kaurene oxidases was reduced in the infected plants. The level of endogenous GA1 (a major active gibberellin in rice vegetative tissues) in the RDV-infected plants was lower than that in healthy plants. Exogenous application of GA3 to RDV-infected rice plants restored the normal growth phenotypes. These results provide evidence that the P2 protein of RDV interferes with the function of a cellular factor, through direct physical interactions, that is important for the biosynthesis of a growth hormone leading to symptom expression. In addition, the interaction between P2 and rice ent-kaurene oxidase-like proteins may decrease phytoalexin biosynthesis and make plants more competent for virus replication. Moreover, P2 may provide a novel tool to investigate the regulation of GA metabolism for plant growth and development.
Sugars and Circadian Regulation Make Major Contributions to the Global Regulation of Diurnal Gene Expression inArabidopsis
Authors: Bläsing Oliver E. , Gibon Yves , Günther Manuela , Höhne Melanie , Morcuende Rosa , Osuna Daniel , Thimm Oliver , Usadel Björn , Scheible Wolf-Rüdiger , Stitt Mark
Published: November 2005

The diurnal cycle strongly influences many plant metabolic and physiological processes. Arabidopsis thaliana rosettes were harvested six times during 12-h-light/12-h-dark treatments to investigate changes in gene expression using ATH1 arrays. Diagnostic gene sets were identified from published or in-house expression profiles of the response to light, sugar, nitrogen, and water deficit in seedlings and 4 h of darkness or illumination at ambient or compensation point [CO2]. Many sugar-responsive genes showed large diurnal expression changes, whose timing matched that of the diurnal changes of sugars. A set of circadian-regulated genes also showed large diurnal changes in expression. Comparison of published results from a free-running cycle with the diurnal changes in Columbia-0 (Col-0) and the starchless phosphoglucomutase (pgm) mutant indicated that sugars modify the expression of up to half of the clock-regulated genes. Principle component analysis identified genes that make large contributions to diurnal changes and confirmed that sugar and circadian regulation are the major inputs in Col-0 but that sugars dominate the response in pgm. Most of the changes in pgm are triggered by low sugar levels during the night rather than high levels in the light, highlighting the importance of responses to low sugar in diurnal gene regulation. We identified a set of candidate regulatory genes that show robust responses to alterations in sugar levels and change markedly during the diurnal cycle.
Structure and intermolecular interactions of glipizide from laboratory X-ray powder diffraction
Authors: Burley Jonathan C.
Published: November 2005

The crystal structure of glipizide, used as a major treatment of type-2 diabetes, has been determined ab initio using variable-temperature laboratory X-ray powder diffraction combined with a direct-space Monte Carlo/simulated annealing methodology. The strengths of the intermolecular interactions (van der Waals, π–π stacking, hydrogen bonding and steric interlock) were quantitatively estimated using the thermal expansion data, which were collected in the same set of experiments as those used to determine the structure.
Structural characterization of Cd3(O3PC2H4CO2)2·2H2O from in-house X-ray powder data and NMR
Authors: Bestaoui Naima , Ouyang Xiang , Fredoueil Florence , Bujoli Bruno , Clearfield Abraham
Published: November 2005

The title compound poly[[bis(μ-2-carboxylatoethylphosphonato)cadmium] dihydrate], Cd3(O3PC2H4CO2)2·2H2O, was prepared by a hydrothermal reaction and its crystal structure determined from in-house powder data. The structure was solved in both P21/c and P21 space groups. The refinement converged with Rp
= 0.1046, R
wp = 0.1378 and Rf
= 0.0763 in P21/c. However, the solid-state NMR data could not be explained. The structure was then solved in P21 and the refinement converged with Rp
= 0.0750, R
wp = 0.1022 and Rf
= 0.0409 and satisfied the NMR requirements.
X-ray diffraction study for one-dimensional ionic conductors K
x
(Ga1 − y
Aly)2 + x
Ti2 − x
O7 (x ≃ 0.14, y ≃ 0.10, 0.23, 0.39)
Authors: Michiue Yuichi , Yoshikado Shinzo
Published: November 2005

The structures of one-dimensional ionic conductors K
x
(Ga1 − y
Al
y
)2 + x
Ti2 − x
O7 (x ≃ 0.14, y ≃ 0.10, 0.23, 0.39) were refined by single-crystal X-ray diffraction. A one-dimensional tunnel-like space with a large cross section is formed by the linkage of coordination polyhedra of the metal and oxygen ions; K ions are distributed in the tunnel. Significant differences were seen in structures with different Al content; these differences could be explained by considerations in crystal chemistry. The probability density functions (PDFs) of the K ion were obtained using up to fourth-order terms of the atomic displacement parameters. The joint PDFs for the K ion have clarified that a K conduction path deviates slightly from the central axis of the tunnel in all the samples. In contrast with the usual one-dimensional ionic conductors, no distinct bottleneck effect was observed from the joint-PDFs and one-particle potentials.