bluuebunny/crossref_metadata_2025 huggingface dataset:
Formation of the Z1,2 deep-level defects in 4H-SiC epitaxial layers: Evidence for nitrogen participation
Authors: Pintilie I. , Pintilie L. , Irmscher K. , Thomas B.
Published: December 2002

As-grown 4H-SiC epitaxial layers were investigated by deep-level transient spectroscopy to study the formation of the well-known Z1,2 defect with energy levels normally detected at about EC−0.7 eV. Chemical vapor deposition, applying various nitrogen-doping concentrations and C/Si ratios (1.2–3) in the gas phase, was used to prepare the samples. The Z1,2 defect concentration was observed to increase with the incorporated nitrogen concentration. The dependence was linear for medium C/Si ratios (1.5–2.5). The highest and lowest applied C/Si ratios (3 and 1.2) enhanced and suppressed the Z1,2 defect formation, respectively. This behavior tentatively suggests a complex of nitrogen with interstitial carbon atoms or, less probably, silicon vacancies. In particular, the correlation between the Z1,2 defect formation and the nitrogen incorporation was clearly shown in the present investigation, in contradiction to conclusions of other authors. Previously reported negative-U properties of the Z1,2 deep-level defects could be confirmed. A 1:1 relation between the concentrations of Z1 and Z2 was obtained for the present as-grown epitaxial layers.
Carbon-nanotube-reinforced Zr52.5Cu17.9Ni14.6Al10Ti5 bulk metallic glass composites
Authors: Bian Zan , Pan Ming Xiang , Zhang Yun , Wang Wei Hua
Published: December 2002

Carbon-nanotube (CNT) reinforced Zr-based bulk metallic glass composites are prepared by the conventional die cast method. A large amount of CNTs still keep their seamless cylindrical morphology in the glassy matrix, even though some CNTs react with Zr, resulting in the formation of ZrC phase. Investigation shows that the elastic moduli, Vicker’s hardness, density, and Debye temperature of the composite are markedly changed by introducing CNTs into the glass. Our results suggest that CNTs are promising materials for preparing reinforced, lightweight bulk metallic glass composites with improved mechanical and physical properties relative to the undoped glass.
Dielectric response of semiconducting carbon nanotubes
Authors: Léonard François , Tersoff J.
Published: December 2002

The dielectric response of semiconducting carbon nanotubes is studied within a tight-binding theory. We focus on “zigzag” tubes, finding that the induced charge exhibits large oscillations within the unit cell. The spatial extent of the response function is roughly equal to the nanotube radius, for any radius. We point out that the dielectric constant of undoped tubes (or any low-dimensional semiconductor) is 1. Our results are confirmed by direct numerical calculations.
Influence of strain on diffusion at Ge(111) surfaces
Authors: Cherepanov Vasily , Voigtländer Bert
Published: December 2002

The measurement of the density of two-dimensional islands by scanning tunneling microscopy after submonolayer growth is used to determine the strain dependence of surface diffusion. Templates of strained and relaxed Ge surfaces with the same surface reconstruction are prepared for comparison. The diffusion barrier for Ge and Si adatoms is found to increase with increasing compressive strain of the Ge(111) substrate. When the strain increases from relaxed Ge to Ge strained to the Si lattice constant, the diffusion barrier is estimated to increase by ∼60 meV.
Acoustic cavity polariton in multilayer piezoelectric structures
Authors: Chen Jing , Khurgin Jacob B.
Published: December 2002

Coupling between the transverse electromagnetic mode of the coplanar strips and transverse acoustic phonon mode in the multilayer piezoelectric structures is considered. It is shown that it leads to the formation of a coupled entity—acoustic cavity polariton, whose frequency and velocity can be adjusted within a very broad range by the proper design of the piezoelectric cavity. The acoustic cavity polaritons can be used in filters, delay lines, and solid-state traveling wave devices for frequencies of up to 100 GHz.
Reduction of interfacial recombination in GaInAsSb/GaSb double heterostructures
Authors: Donetsky D. , Anikeev S. , Belenky G. , Luryi S. , Wang C. A. , Nichols G.
Published: December 2002

Minority carrier lifetimes in 0.55 eV band-gap GaInAsSb epitaxial layers that are double capped with GaSb or AlGaAsSb layers were determined using time-resolved photoluminescence. It was found that accumulation of electrons at the p-doped GaInAsSb/GaSb type-II interface contributes significantly to the interfacial recombination velocity S, which was measured to be 3100 cm/s. The use of heavily p-doped GaSb cap layers was proposed to eliminate the potential well of electrons and barrier for holes at the interface. Increasing the GaSb cap doping level from 1×1016 to 2×1018 cm−3 resulted in a 2.7 times reduction of S down to 1140 cm/s. The smallest value of S was determined to be 720 cm/s, which was obtained for structures with AlGaAsSb cap layers that have no valence band offset.
Fabrication of an InGaN multiple-quantum-well laser diode featuring high reflectivity semiconductor/air distributed Bragg reflectors
Authors: Wang Hailong , Kumagai Masami , Tawara Takehiko , Nishida Toshio , Akasaka Tetsuya , Kobayashi Naoki , Saitoh Tadashi
Published: December 2002

High-quality deeply-etched GaN-based semiconductor/air distributed Bragg reflectors (DBRs) have been fabricated. A 50% reduction relative to the value for reflectors of Fabry–Perot type in the threshold pump intensity was realized by the introduction of such DBRs at the ends of the laser cavity. The reflectivity of the grating was evaluated between 44% and 62%. Finite-difference time-domain simulation had earlier been used to obtain a design for the semiconductor/air DBRs, which provides high values for reflectivity despite a significant inclination from the vertical of the sidewalls of the structure.
Statewide Prevalences of Concern about Enough Food, 1996–1999
Authors: Evenson Kelly R. , Laraia Barbara A. , Welch Verna L. Lamar , Perry April L.
Published: December 2002

Objective.

Food insecurity is defined as not having access at all times to enough food for an active and healthy life-style. A Healthy People 2010 objective is to increase food security and reduce the risk of hunger for all households. The objective of this study was to characterize the prevalence of concern about enough food and its association with other sociodemographic and health characteristics at the state level.

Methods.

Adult respondents participating in the Behavioral Risk Factor Surveillance System survey provided information on concern about enough food from nine states from 1996 through 1999.

Results.

Overall, the prevalence of concern about enough food ranged from 3.1% to 11.8% for individual states. Across states, low household income was the strongest predictor of concern about enough food. The odds of being concerned about enough food were generally higher among respondents who were female, younger, and without health care coverage. The odds were generally lower among those reporting excellent or very good general health and among non-Hispanic whites.

Conclusion.

Food security scales could be used at the state level to track progress for the Healthy People 2010 objective of reducing food insecurity and hunger across American households.
Ectopic Expression of Carpel-Specific MADS Box Genes from Lily and Lisianthus Causes Similar Homeotic Conversion of Sepal and Petal in Arabidopsis
Authors: Tzeng Tsai-Yu , Chen Hsing-Yu , Yang Chang-Hsien
Published: December 2002

Two MADS box genes, Lily MADS Box Gene 2(LMADS2) and Eustoma grandiflorum MADS Box Gene 1 (EgMADS1), with an extensive similarity to the petunia (Petunia hybrida) FLORAL BINDING PROTEIN 7/11 and Arabidopsis AGL11, were characterized from the lily (Lilium longiflorum) and lisianthus (Eustoma grandiflorum). The expression ofLMADS2 and EgMADS1 mRNA was restricted to the carpel and was absent in the other flower organs or vegetative leaves. LMADS2 mRNA was detected mainly in ovules and weakly in style tissues of the carpel, whereas EgMADS1mRNA was only expressed in the ovules. Transgenic Arabidopsis plants ectopically expressing LMADS2 or EgMADS1showed similar novel phenotypes resembling35S::AGAMOUS plants by significantly reducing plant size, flowering early, and losing inflorescence indeterminacy. Ectopic expression of these two genes also generated similar ap2-like flowers by inducing homeotic conversion of the sepals into carpel-like structures in which stigmatic papillae and ovules were observed. In addition, the petals were converted into stamen-like structures in the second whorl of 35S::LMADS2 and35S::EgMADS1 transgenic Arabidopsis. Our data indicated that LMADS2 andEgMADS1 are putative D functional MADS box genes in lily and lisianthus with a function similar to C functional genes once ectopically expressed in Arabidopsis.
Control of Demand-Driven Biosynthesis of Glutathione in Green Arabidopsis Suspension Culture Cells
Authors: Meyer Andreas J. , Fricker Mark D.
Published: December 2002

We have investigated what limits demand-driven de novo glutathione (GSH) biosynthesis in green Arabidopsis suspension culture cells. GSH is the most abundant low-molecular weight thiol in most plants and can be quantified using monochlorobimane to fluorescently label GSH in live cells. Progress curves for labeling reached a plateau as all the cytoplasmic GSH was conjugated. In the presence of excess monochlorobimane, a second, almost linear phase of labeling was observed, after a lag of 2 to 3 h, that was then maintained for an extended period. The increase in fluorescence was shown to be because of de novo GSH biosynthesis by high-performance liquid chromatography analysis and was eliminated bydl-buthionine-[S,R]-sulfoximine, a specific inhibitor of GSH biosynthesis, or reduced by inhibitors of transcription and translation. The rate of GSH biosynthesis during the linear phase was 8.9 ± 1.4 nmol g fresh weight−1min−1 and was not affected by addition of glutamate, glycine, or cysteine, the immediate precursors needed for GSH biosynthesis. Likewise, the synthesis rate was not affected by pretreatment with aminotriazole, menadione, jasmonic acid, or cadmium, all of which cause oxidative stress and up-regulate expression of GSH biosynthetic genes. The lag phase was markedly reduced by aminotriazole and menadione and marginally by jasmonic acid, suggesting the system was primed to react faster after mild stress. In contrast to the other feeding experiments, exclusion of SO4  2− from the medium abolished the second phase completely. This suggests demand-driven GSH biosynthesis is directly coupled to uptake of SO4  2− and that the linear increase in fluorescence reflects flux through the entire SO4  2− assimilation pathway.
The Maize Geneterpene synthase 1Encodes a Sesquiterpene Synthase Catalyzing the Formation of (E)-β-Farnesene, (E)-Nerolidol, and (E,E)-Farnesol after Herbivore Damage
Authors: Schnee Christiane , Köllner Tobias G. , Gershenzon Jonathan , Degenhardt Jörg
Published: December 2002

Maize (Zea mays) emits a mixture of volatile compounds upon attack by the Egyptian cotton leafworm (Spodoptera littoralis). These substances, primarily mono- and sesquiterpenes, are used by parasitic wasps to locate the lepidopteran larvae, which are their natural hosts. This interaction among plant, lepidopteran larvae, and hymenopteran parasitoids benefits the plant and has been termed indirect defense. The committed step in the biosynthesis of the different skeletal types of mono- and sesquiterpenes is catalyzed by terpene synthases, a class of enzymes that forms a large variety of mono- and sesquiterpene products from prenyl diphosphate precursors. We isolated a terpene synthase gene,terpene synthase 1 (tps1), from maize that exhibits only a low degree of sequence identity to previously identified terpene synthases. Upon expression in a bacterial system, the encoded enzyme produced the acyclic sesquiterpenes, (E)-β-farnesene, (E,E)-farnesol, and (3R)-(E)-nerolidol, the last an intermediate in the formation of (3E)-4,8-dimethyl-1,3,7-nonatriene. Both (E)-β-farnesene and (3E)-4,8-dimethyl-1,3,7-nonatriene are prominent compounds of the maize volatile blend that is emitted after herbivore damage. The biochemical characteristics of the encoded enzyme are similar to those of terpene synthases from both gymnosperms and dicotyledonous angiosperms, suggesting that catalysis involves a similar electrophilic reaction mechanism. The transcript level oftps1 in the maize cv B73 was elevated after herbivory, mechanical damage, and treatment with elicitors. In contrast, the increase in the transcript level of the tps1 gene or gene homolog in the maize cv Delprim after herbivory was less pronounced, suggesting that the regulation of terpene synthase expression may vary among maize varieties.
Light-Dependent Death of Maize lls1 Cells Is Mediated by Mature Chloroplasts
Authors: Gray John , Janick-Buckner Diane , Buckner Brent , Close Pam S. , Johal Gurmukh S.
Published: December 2002

We reported previously the isolation of a novel cell death-suppressing gene from maize (Zea mays) encoded by the Lls1 (Lethal leaf spot-1) gene. Although the exact metabolic function of LLS1 remains elusive, here we provide insight into mechanisms that underlie the initiation and propagation of cell death associated withlls1 lesions. Our data indicate that lls1lesions are triggered in response to a cell-damaging event caused by any biotic or abiotic agent or intrinsic metabolic imbalance—as long as the leaf tissue is developmentally competent to developlls1 lesions. Continued expansion of these lesions, however, depends on the availability of light, with fluence rate being more important than spectral quality. Double-mutant analysis oflls1 with two maize mutants oil-yellowand iojap, both compromised photosynthetically and unable to accumulate normal levels of chlorophyll, indicated that it was the light harvested by the plant that energized lls1lesion development. Chloroplasts appear to be the key mediators oflls1 cell death; their swelling and distortion occurs before any other changes normally associated with dying cells. In agreement with these results are indications that LLS1 is a chloroplast-localized protein whose transcript was detected only in green tissues. The propagative nature of light-dependentlls1 lesions predicts that cell death associated with these lesions is caused by a mobile agent such as reactive oxidative species. LLS1 may act to prevent reactive oxidative species formation or serve to remove a cell death mediator so as to maintain chloroplast integrity and cell survival.
Plasma Membrane Aquaporins Play a Significant Role during Recovery from Water Deficit
Authors: Martre Pierre , Morillon Raphaël , Barrieu François , North Gretchen B. , Nobel Park S. , Chrispeels Maarten J.
Published: December 2002

The role of plasma membrane aquaporins (PIPs) in water relations of Arabidopsis was studied by examining plants with reduced expression of PIP1 and PIP2 aquaporins, produced by crossing two different antisense lines. Compared with controls, the double antisense (dAS) plants had reduced amounts of PIP1 and PIP2 aquaporins, and the osmotic hydraulic conductivity of isolated root and leaf protoplasts was reduced 5- to 30-fold. The dAS plants had a 3-fold decrease in the root hydraulic conductivity expressed on a root dry mass basis, but a compensating 2.5-fold increase in the root to leaf dry mass ratio. The leaf hydraulic conductance expressed on a leaf area basis was similar for the dAS compared with the control plants. As a result, the hydraulic conductance of the whole plant was unchanged. Under sufficient and under water-deficient conditions, stomatal conductance, transpiration rate, plant hydraulic conductance, leaf water potential, osmotic pressure, and turgor pressure were similar for the dAS compared with the control plants. However, after 4 d of rewatering following 8 d of drying, the control plants recovered their hydraulic conductance and their transpiration rates faster than the dAS plants. Moreover, after rewatering, the leaf water potential was significantly higher for the control than for the dAS plants. From these results, we conclude that the PIPs play an important role in the recovery of Arabidopsis from the water-deficient condition.
An Endoplasmic Reticulum-Derived Structure That Is Induced under Stress Conditions in Arabidopsis
Authors: Matsushima Ryo , Hayashi Yasuko , Kondo Maki , Shimada Tomoo , Nishimura Mikio , Hara-Nishimura Ikuko
Published: December 2002

The endoplasmic reticulum (ER) body is a characteristic structure derived from ER and is referred to as a proteinase-sorting system that assists the plant cell under various stress conditions. Fluorescent ER bodies were observed in transgenic plants of Arabidopsis expressing green fluorescent protein fused with an ER retention signal. ER bodies were widely distributed in the epidermal cells of whole seedlings. In contrast, rosette leaves had no ER bodies. We found that wound stress induced the formation of many ER bodies in rosette leaves. ER bodies were also induced by treatment with methyl jasmonate (MeJA), a plant hormone involved in the defense against wounding and chewing by insects. The induction of ER bodies was suppressed by ethylene. An electron microscopic analysis showed that typical ER bodies were induced in the non-transgenic rosette leaves treated with MeJA. An experiment using coi1 and etr1-4 mutant plants showed that the induction of ER bodies was strictly coupled with the signal transduction of MeJA and ethylene. These results suggested that the formation of ER bodies is a novel and unique type of endomembrane system in the response of plant cells to environmental stresses. It is possible that the biological function of ER bodies is related to defense systems in higher plants.
Proteomics of Light-Harvesting Proteins in Different Plant Species. Analysis and Comparison by Liquid Chromatography-Electrospray Ionization Mass Spectrometry. Photosystem I
Authors: Zolla Lello , Rinalducci Sara , Timperio Anna Maria , Huber Christian G.
Published: December 2002

The light-harvesting proteins (Lhca) of photosystem I (PSI) from four monocot and five dicot species were extracted from plant material, separated by reversed-phase high-performance liquid chromatography (HPLC) and subsequently identified on the basis of their intact molecular masses upon on-line hyphenation with electrospray ionization mass spectrometry. Although their migration behavior in gel electrophoresis was very similar, the elution times among the four antenna types in reversed-phase-HPLC differed significantly, even more than those observed for the light-harvesting proteins of photosystem II. Identification of proteins is based on the good agreement between the measured intact molecular masses and the values calculated on the basis of their nucleotide-derived amino acid sequences, which makes the intact molecular masses applicable as intact mass tags. These values match excellently for Arabidopsis, most probably because of the availability of high-quality DNA sequence data. In all species examined, the four antennae eluted in the same order, namely Lhca1 > Lhca3 > Lhca4 > Lhca2. These characteristic patterns enabled an unequivocal assignment of the proteins in preparations from different species. Interestingly, in all species examined, Lhca1 and Lhca2 were present in two or three isoforms. A fifth antenna protein, corresponding to the Lhca6 gene, was found in tomato (Lycopersicon esculentum). However PSI showed a lower heterogeneity than photosystem II. In most plant species, Lhca2 and Lhca4 proteins are the most abundant PSI antenna proteins. The HPLC method used in this study was found to be highly reproducible, and the chromatograms may serve as a highly confident fingerprint for comparison within a single and among different species for future studies of the PSI antenna.
Cloning and Sequencing of cDNAs for Hypothetical Genes from Chromosome 2 of Arabidopsis,
Authors: Xiao Yong-Li , Malik Mukesh , Whitelaw Catherine A. , Town Christopher D.
Published: December 2002

About 25% of the genes in the fully sequenced and annotated Arabidopsis genome have structures that are predicted solely by computer algorithms with no support from either nucleic acid or protein homologs from other species or expressed sequence matches from Arabidopsis. These are referred to as “hypothetical genes.” On chromosome 2, sequenced by The Institute for Genomic Research, there are approximately 800 hypothetical genes among a total of approximately 4,100 genes. To test their expression under various growth conditions and in specific tissues, we used six cDNA populations prepared from cold-treated, heat-treated, and pathogen (Xanthomonas campestris pv campestris)-infected plants, callus, roots, and young seedlings. To date, 169 hypothetical genes were tested, and 138 of them are found to be expressed in one or more of the six cDNA populations. By sequencing multiple clones from each 5′- and 3′-rapid amplification of cDNA ends (RACE) product and assembling the sequences, we generated full-length sequences for 16 of these genes. For 14 genes, there was one full-length assembly that precisely supported the intron-exon boundaries of their gene predictions, adding only 5′- and 3′-untranslated region sequences. However, for three of these genes, the other assemblies represent additional exons and alternatively spliced or unspliced introns. For the remaining two genes, the cDNA sequences reveal major differences with predicted gene structures. In addition, a total of six genes displayed more than one polyadenylation site. These data will be used to update gene models in The Institute for Genomic Research annotation database ATH1.
Cloning and Expression of the Gene for Soybean Hydroxyisourate Hydrolase. Localization and Implications for Function and Mechanism
Authors: Raychaudhuri Aniruddha , Tipton Peter A.
Published: December 2002

The gene encoding hydroxyisourate hydrolase, a novel ureide-metabolizing enzyme, has been cloned from soybean (Glycine max). The gene encodes a protein that is 560 amino acids in length and contains a 31-amino acid signal sequence at the N terminus that is not present in the mature protein. The presence of two SKL motifs near the C terminus suggests that the protein resides in the peroxisome. This expectation is borne out by results from immunogold electron microscopy, which revealed that hydroxyisourate hydrolase was localized in the peroxisomes of uninfected root nodules. The gene encoding hydroxyisourate hydrolase was expressed inEscherichia coli, and soluble, catalytically active enzyme was purified to homogeneity. Sequence analysis revealed considerable homology with members of the β-glucosidase family of enzymes. Two glutamate residues, E199 and E408, align with the conserved glutamates that play catalytic roles in the β-glucosidases. However, the other residues that have been identified by crystallography to interact directly with the substrates in β-glucosidases are not conserved in hydroxyisourate hydrolase. The E199A and E408A hydroxyisourate hydrolase mutants were devoid of detectable catalytic activity. Analysis of transcripts for hydroxyisourate hydrolase demonstrated that its level of expression was highest in the nodule; mRNA was detectable 12 d after infection and increased until 21 d postinfection, then declined. In a similar manner, immunodetection of hydroxyisourate hydrolase indicated preferential localization in the nodule; the amount of protein detected was maximal at 21 d postinfection. The pattern of expression of hydroxyisourate hydrolase matched that of urate oxidase, and supports the hypothesis that hydroxyisourate hydrolase plays a role in ureide metabolism.
Polyphenolic Allelochemicals from the Aquatic Angiosperm Myriophyllum spicatumInhibit Photosystem II
Authors: Leu Eva , Krieger-Liszkay Anja , Goussias Charilaos , Gross Elisabeth M.
Published: December 2002

Myriophyllum spicatum (Haloragaceae) is a highly competitive freshwater macrophyte that produces and releases algicidal and cyanobactericidal polyphenols. Among them, β-1,2,3-tri-O-galloyl-4,6-(S)-hexahydroxydiphenoyl-d-glucose (tellimagrandin II) is the major active substance and is an effective inhibitor of microalgal exoenzymes. However, this mode of action does not fully explain the strong allelopathic activity observed in bioassays. Lipophilic extracts of M. spicatum inhibit photosynthetic oxygen evolution of intact cyanobacteria and other photoautotrophs. Fractionation of the extract provided evidence for tellimagrandin II as the active compound. Separate measurements of photosystem I and II activity with spinach (Spinacia oleracea) thylakoid membranes indicated that the site of inhibition is located at photosystem II (PSII). In thermoluminescence measurements with thylakoid membranes and PSII-enriched membrane fragments M. spicatum extracts shifted the maximum temperature of the B-band (S2QB  −recombination) to higher temperatures. Purified tellimagrandin II in concentrations as low as 3 μm caused a comparable shift of the B-band. This demonstrates that the target site of this inhibitor is different from the QB-binding site, a common target of commercial herbicides like 3-(3,4-dichlorophenyl)-1,1-dimethylurea. Measurements with electron paramagnetic resonance spectroscopy suggest a higher redox midpoint potential for the non-heme iron, located between the primary and the secondary quinone electron acceptors, QA and QB. Thus, tellimagrandin II has at least two modes of action, inhibition of exoenzymes and inhibition of PSII. Multiple target sites are a common characteristic of many potent allelochemicals.
Rapid Structural Phenotyping of Plant Cell Wall Mutants by Enzymatic Oligosaccharide Fingerprinting
Authors: Lerouxel Olivier , Choo Tze Siang , Séveno Martial , Usadel Björn , Faye Loı̈c , Lerouge Patrice , Pauly Markus
Published: December 2002

Various biochemical, chemical, and microspectroscopic methods have been developed throughout the years for the screening and identification of mutants with altered cell wall structure. However, these procedures fail to provide the insight into structural aspects of the cell wall polymers. In this paper, we present various methods for rapidly screening Arabidopsis cell wall mutants. The enzymatic fingerprinting procedures using high-performance anion-exchange-pulsed-amperometric detection liquid chromatography, fluorophore-assisted carbohydrate electrophoresis, and matrix-assisted laser-desorption ionization time of flight (MALDI-TOF) mass spectrometry (MS) were exemplified by the structural analysis of the hemicellulose xyloglucan. All three techniques are able to identify structural alterations of wall xyloglucans in mur1,mur2, and mur3, which in comparison with the wild type have side chain defects in their xyloglucan structure. The quickest analysis was provided by MALDI-TOF MS. Although MALDI-TOF MS per se is not quantitative, it is possible to reproducibly obtain relative abundance information of the various oligosaccharides present in the extract. The lack of absolute quantitation by MALDI-TOF MS was compensated for with a xyloglucan-specific endoglucanase and simple colorimetric assay. In view of the potential for mass screening using MALDI-TOF MS, a PERL-based program was developed to process the spectra obtained from MALDI-TOF MS automatically. Outliers can be identified very rapidly according to a set of defined parameters based on data collected from the wild-type plants. The methods presented here can easily be adopted for the analysis of other wall polysaccharides. MALDI-TOF MS offers a powerful tool to screen and identify cell wall mutants rapidly and efficiently and, more importantly, is able to give initial insights into the structural composition and/or modification that occurs in these mutants.
Contiguous Genomic DNA Sequence Comprising the 19-kD Zein Gene Family from Maize
Authors: Song Rentao , Messing Joachim
Published: December 2002

A new approach has been undertaken to analyze the sequences and linear organization of the 19-kD zein genes in maize (Zea mays). A high-coverage, large-insert genomic library of the inbred line B73 based on bacterial artificial chromosomes was used to isolate a redundant set of clones containing members of the 19-kD zein gene family, which previously had been estimated to consist of 50 members. The redundant set of clones was used to create bins of overlapping clones that represented five distinct genomic regions. Representative clones containing the entire set of 19-kD zein genes were chosen from each region and sequenced. Seven bacterial artificial chromosome clones yielded 1,160 kb of genomic DNA. Three of them formed a contiguous sequence of 478 kb, the longest contiguous sequenced region of the maize genome. Altogether, these DNA sequences provide the linear organization of 25 19-kD zein genes, one-half the number previously estimated. It is suggested that the difference is because of haplotypes exhibiting different degrees of gene amplification in the zein multigene family. About one-half the genes present in B73 appear to be expressed. Because some active genes have only been duplicated recently, they are so conserved in their sequence that previous cDNA sequence analysis resulted in “unigenes” that were actually derived from different gene copies. This analysis also shows that the 22- and 19-kD zein gene families shared a common ancestor. Although both ancestral genes had the same incremental gene amplification, the 19-kD zein branch exhibited a greater degree of far-distance gene translocations than the 22-kD zein gene family.
Functional Specialization of Maize Mitochondrial Aldehyde Dehydrogenases
Authors: Liu Feng , Schnable Patrick S.
Published: December 2002

The maize (Zea mays) rf2a andrf2b genes both encode homotetrameric aldehyde dehydrogenases (ALDHs). The RF2A protein was shown previously to accumulate in the mitochondria. In vitro import experiments and ALDH assays on mitochondrial extracts from rf2a mutant plants established that the RF2B protein also accumulates in the mitochondria. RNA gel-blot analyses and immunohistolocation experiments revealed that these two proteins have only partially redundant expression patterns in organs and cell types. For example, RF2A, but not RF2B, accumulates to high levels in the tapetal cells of anthers. Kinetic analyses established that RF2A and RF2B have quite different substrate specificities; although RF2A can oxidize a broad range of aldehydes, including aliphatic aldehydes and aromatic aldehydes, RF2B can oxidize only short-chain aliphatic aldehydes. These two enzymes also have different pH optima and responses to changes in substrate concentration. In addition, RF2A, but not RF2B or any other natural ALDHs, exhibits positive cooperativity. These functional specializations may explain why many species have two mitochondrial ALDHs. This study provides data that serve as a basis for identifying the physiological pathway by which the rf2a gene participates in normal anther development and the restoration of Texas cytoplasm-based male sterility. For example, the observations that Texas cytoplasm anthers do not accumulate elevated levels of reactive oxygen species or lipid peroxidation and the kinetic features of RF2A make it unlikely that rf2a restores fertility by preventing premature programmed cell death.
The Involvement of a Multicopper Oxidase in Iron Uptake by the Green Algae Chlamydomonas reinhardtii
Authors: Herbik Alexandra , Bölling Christian , Buckhout Thomas J.
Published: December 2002

In the unicellular green algae Chlamydomonas reinhardtii, high-affinity uptake of iron (Fe) requires an Fe3+-chelate reductase and an Fe transporter. Neither of these proteins nor their corresponding genes have been isolated. We previously identified, by analysis of differentially expressed plasma membrane proteins, an approximately 150-kD protein whose synthesis was induced under conditions of Fe-deficient growth. Based on homology of internal peptide sequences to the multicopper oxidase hephaestin, this protein was proposed to be a ferroxidase. A nucleotide sequence to the full-length cDNA clone for this ferroxidase-like protein has been obtained. Analysis of the primary amino acid sequence revealed a putative transmembrane domain near the amino terminus of the protein and signature sequences for two multicopper oxidase I motifs and one multicopper oxidase II motif. The ferroxidase-like gene was transcribed under conditions of Fe deficiency. Consistent with the role of a copper (Cu)-containing protein in Fe homeostasis, growth of cells in Cu-depleted media eliminated high-affinity Fe uptake, and Cu-deficient cells that were grown in optimal Fe showed greatly reduced Fe accumulation compared with control, Cu-sufficient cells. Reapplication of Cu resulted in the recovery of Fe transport activity. Together, these results were consistent with the participation of a ferroxidase in high-affinity Fe uptake in C. reinhardtii.
Phosphorylation of the D1 Photosystem II Reaction Center Protein Is Controlled by an Endogenous Circadian Rhythm
Authors: Booij-James Isabelle S. , Swegle W. Mark , Edelman Marvin , Mattoo Autar K.
Published: December 2002

The light dependence of D1 phosphorylation is unique to higher plants, being constitutive in cyanobacteria and algae. In a photoautotrophic higher plant, Spirodela oligorrhiza, grown in greenhouse conditions under natural diurnal cycles of solar irradiation, the ratio of phosphorylated versus total D1 protein (D1-P index: [D1-P]/[D1] + [D1-P]) of photosystem II is shown to undergo reproducible diurnal oscillation. These oscillations were clearly out of phase with the period of maximum in light intensity. The timing of the D1-P index maximum was not affected by changes in temperature, the amount of D1 kinase activity present in the thylakoid membranes, the rate of D1 protein synthesis, or photoinhibition. However, when the dark period in a normal diurnal cycle was cut short artificially by transferring plants to continuous light conditions, the D1-P index timing shifted and reached a maximum within 4 to 5 h of light illumination. The resultant diurnal oscillation persisted for at least two cycles in continuous light, suggesting that the rhythm is endogenous (circadian) and is entrained by an external signal.
Both Vegetative and Reproductive Actin Isovariants Complement the Stunted Root Hair Phenotype of the Arabidopsisact2-1 Mutation
Authors: Gilliland Laura U. , Kandasamy Muthugapatti K. , Pawloski Lucia C. , Meagher Richard B.
Published: December 2002

The ACT2 gene, encoding one of eight actin isovariants in Arabidopsis, is the most strongly expressed actin gene in vegetative tissues. A search was conducted for physical defects inact2-1 mutant plants to account for their reduced fitness compared with wild type in population studies. Theact2-1 insertion fully disrupted expression ofACT2 RNA and significantly lowered the level of total actin protein in vegetative organs. The root hairs of theact2-1 mutants were 10% to 70% the length of wild-type root hairs, and they bulged severely at the base. The length of the mutant root hairs and degree of bulging at the base were affected by adjusting the osmolarity and gelling agent of the growth medium. Theact2-1 mutant phenotypes were fully rescued by anACT2 genomic transgene. When the act2-1mutation was combined with another vegetative actin mutation,act7-1, the resulting double mutant exhibited extensive synergistic phenotypes ranging from developmental lethality to severe dwarfism. Transgenic overexpression of the ACT7 vegetative isovariant and ectopic expression of the ACT1 reproductive actin isovariant also rescued the root hair elongation defects of the act2-1mutant. These results suggest normal ACT2 gene regulation is essential to proper root hair elongation and that even minor differences may cause root defects. However, differences in the actin protein isovariant are not significant to root hair elongation, in sharp contrast to recent reports on the functional nonequivalency of plant actin isovariants. Impairment of root hair functions such as nutrient mining, water uptake, and physical anchoring are the likely cause of the reduced fitness seen for act2-1 mutants in multigenerational studies.
T-DNA Insertional Mutagenesis for Activation Tagging in Rice
Authors: Jeong Dong-Hoon , An Suyoung , Kang Hong-Gyu , Moon Sunok , Han Jong-Jin , Park Sunhee , Lee Hyun Sook , An Kyungsook , An Gynheung
Published: December 2002

We have developed a new T-DNA vector, pGA2715, which can be used for promoter trapping and activation tagging of rice (Oryza sativa) genes. The binary vector contains the promoterlessβ-glucuronidase (GUS) reporter gene next to the right border. In addition, the multimerized transcriptional enhancers from the cauliflower mosaic virus 35S promoter are located next to the left border. A total of 13,450 T-DNA insertional lines have been generated using pGA2715. Histochemical GUS assays have revealed that the GUS-staining frequency from those lines is about twice as high as that from lines transformed with the binary vector pGA2707, which lacks the enhancer element. This result suggests that the enhancer sequence present in the T-DNA improves the GUS-tagging efficiency. Reverse transcriptase-PCR analysis of a subset of randomly selected pGA2715 lines shows that expression of the genes immediately adjacent to the inserted enhancer is increased significantly. Therefore, the large population of T-DNA-tagged lines transformed with pGA2715 could be used to screen for promoter activity using the gusreporter, as well as for creating gain-of-function mutants.
DashengandRIRE2. A Nonautonomous Long Terminal Repeat Element and Its Putative Autonomous Partner in the Rice Genome
Authors: Jiang Ning , Jordan I. King , Wessler Susan R.
Published: December 2002

Dasheng is one of the highest copy number long terminal repeat elements and one of the most recent elements to amplify in the rice (Oryza sativa) genome. However, the absence of any significant coding capacity for retroviral proteins, including gag and pol, suggests that Dasheng is a nonautonomous element. Here, we have exploited the availability of 360 Mb of rice genomic sequence to identify a candidate autonomous element. RIRE2 is a previously described gypsy-like long terminal repeat retrotransposon with significant sequence similarity toDasheng in the regions where putative cis factors for retrotransposition are thought to be located. Dashengand RIRE2 elements have similar chromosomal distribution patterns and similar target site sequences, suggesting that they use the same transposition machinery. In addition, the presence of severalRIRE2-Dasheng element chimeras in the genome is consistent with the copackaging of element mRNAs in the same virus-like particle. Finally, both families have recently amplified members, suggesting that they could have been co-expressed, a necessary prerequisite for RIRE2 to serve as the source of transposition machinery for Dasheng. Consistent with this hypothesis, transcripts from both elements were found in the same expressed sequence tag library.
Molecular Analysis of a Bifunctional Fatty Acid Conjugase/Desaturase from Tung. Implications for the Evolution of Plant Fatty Acid Diversity
Authors: Dyer John M. , Chapital Dorselyn C. , Kuan Jui-Chang W. , Mullen Robert T. , Turner Charlotta , McKeon Thomas A. , Pepperman Armand B.
Published: December 2002

The seed oil derived from the tung (Aleurites fordiiHemsl.) tree contains approximately 80% α-eleostearic acid (18:3Δ9cis,11trans,13trans), an unusual conjugated fatty acid that imparts industrially important drying qualities to tung oil. Here, we describe the cloning and functional analysis of two closely related Δ12 oleate desaturase-like enzymes that constitute consecutive steps in the biosynthetic pathway of eleostearic acid. Polymerase chain reaction screening of a tung seed cDNA library using degenerate oligonucleotide primers resulted in identification of two desaturases, FAD2 and FADX, that shared 73% amino acid identity. Both enzymes were localized to the endoplasmic reticulum of tobacco (Nicotiana tabacumcv Bright-Yellow 2) cells, and reverse transcriptase-polymerase chain reaction revealed that FADX was expressed exclusively within developing tung seeds. Expression of the cDNAs encoding these enzymes in yeast (Saccharomyces cerevisiae) revealed that FAD2 converted oleic acid (18:1Δ9cis) into linoleic acid (18:2Δ9cis,12cis) and that FADX converted linoleic acid into α-eleostearic acid. Additional characterization revealed that FADX exhibited remarkable enzymatic plasticity, capable of generating a variety of alternative conjugated and Δ12-desaturated fatty acid products in yeast cells cultured in the presence of exogenously supplied fatty acid substrates. Unlike other desaturases reported to date, the double bond introduced by FADX during fatty acid desaturation was in the trans, rather than cis, configuration. Phylogenetic analysis revealed that tung FADX is grouped with Δ12 fatty acid desaturases and hydroxylases rather than conjugases, which is consistent with its desaturase activity. Comparison of FADX and other lipid-modifying enzymes (desaturase, hydroxylase, epoxygenase, acetylenase, and conjugase) revealed several amino acid positions near the active site that may be important determinants of enzymatic activity.
Resist distribution effect of spin coating
Authors: Kim Sang-Kon , Yoo Ji-Yong , Oh Hye-Keun
Published: December 2002

The thin-film formation of the spin coating is one of the important factors in the fabrication of microelectronic devices. In this study, the theoretical models for thickness variation during spin coating and nanotopography impact are analyzed. The finite-difference–time-domain method and the finite-element method are used to solve the convective diffusion equation for solvent distribution and the Navier–Stokes equation including solvent evaporation for the film thickness change. These numerical calculations are in good agreement with experimental results for 193 nm chemically amplified resist (CAR) and i-line non-CAR resists. Solvent distributions of nonspin coating are described through mesoscale modeling by using the Monte Carlo method. Nanotopography impact on the variation of resist distribution after spin coating is investigated quantitatively. The reason for the similarity in the transfer functions for different types of wafers is due to solvent diffusion and evaporation.
Simulations and experiments of etching of silicon in HBr plasmas for high aspect ratio features
Authors: Hwang Helen H. , Meyyappan M. , Mathad G. S. , Ranade R.
Published: December 2002

Etching in semiconductor processing typically involves using halides because of the relatively fast rates. Bromine-containing plasmas can generate high aspect ratio trenches, desirable for dynamic random access memory and microelectromechanical system applications, with relatively straight sidewalls. We present scanning electron microscope images for silicon-etched trenches in a HBr plasma. Using a feature profile simulation, we show that the removal yield parameter, or number of neutrals removed per incident ion due to all processes (sputtering, spontaneous desorption, etc.), dictates the profile shape. We find that the profile becomes pinched off when the removal yield is a constant, with a maximum aspect ratio (AR) of about 5 to 1 (depth to height). When the removal yield decreases with increasing ion angle, the etch rate increases at the corners and the trench bottom broadens. The profiles have ARs of over 9:1 for yields that vary with ion angle. To match the experimentally observed etched time of 250 s for an AR of 9:1 with a trench width of 0.135 μm, we find that the neutral flux must be 3.336×1017 cm2 s−1.
Initial oxidation phenomena of heavily phosphorus-doped silicon in dry oxygen
Authors: Kamiura Y. , Hasegawa K. , Sano Y. , Mizokawa Y. , Kawamoto K.
Published: December 2002

The oxidation of heavily phosphorus-doped Si(100) and polycrystalline Si in the room temperature (RT) to 800 °C range in dry oxygen was studied by Auger electron spectroscopy (AÉS) and quadrupole mass spectrometry. The oxidation rate of the phosphorus-doped (P-doped) Si(100) was larger than the P-doped poly-Si at RT. In thermal oxidation at 650 °C in the P-doped Si(100), the delay of the dioxide formation was found above 5×105 L. The AES measurements in the range of 97–137 eV showed that phosphorus oxidized in the initial stages of the oxidation of both samples. In the thermal oxidation of both samples at 800 °C, oxygen uptake on the silicon surfaces did not take place under 104 L. And dioxide formation took place rapidly above 104 L for both samples. Then, a large amount of phosphorus piled up at the interfaces due to the formation of SiO2. We gave explanations for these initial stages of oxidation of P-doped Si by the competition process between the oxidation of silicon and the desorption of SiO and P2O5.
Nanopipe fabrication using vertically aligned carbon nanofiber templates
Authors: Melechko A. V. , McKnight T. E. , Guillorn M. A. , Austin D. W. , Ilic B. , Merkulov V. I. , Doktycz M. J. , Lowndes D. H. , Simpson M. L.
Published: December 2002

We report a method to fabricate tubular nanostructures using vertically aligned carbon nanofibers grown by plasma-enhanced chemical vapor deposition as templates. The resulting nanopipes are oriented perpendicular to the substrate and have internal diameters ranging from 30 to 200 nm and can be up to several micrometers in length. These nanopipes can be deterministically positioned on a substrate and arranged into singular devices or arrays.
High-resolution organic polymer light-emitting pixels fabricated by imprinting technique
Authors: Cheng Xing , Hong Yongtaek , Kanicki Jerzy , Guo L. Jay
Published: December 2002

We have developed an approach to fabricate pixelated organic polymer light-emitting devices (OPLED) using an imprinting technique. The pixel array pattern was first defined in an insulating polymer layer on indium tin oxide glass by direct imprinting, followed by the spin-coating of OPLED polymers and cathode metal deposition. We demonstrated successful fabrication and operation of OPLED pixels of sizes from 50 μm down to 2 μm. Optoelectronic characterization is performed on these devices, and measured results show comparable device performance with OPLED pixels patterned by other methods. This fabrication scheme holds many merits such as easy to process, low-cost, high yield, expandable to flexible substrate, capable of repeated imprinting for large area arrays, and the potential to pattern submicron and nanoscale organic polymer light emitters.
Polymer thickness effects on Bosch etch profiles
Authors: Craigie C. J. D. , Sheehan T. , Johnson V. N. , Burkett S. L. , Moll A. J. , Knowlton W. B.
Published: December 2002

Time-multiplexed etching, the Bosch process, is a technique consisting of alternating etch and deposition cycles to produce high aspect-ratio etched features. The Bosch process uses SF6 and C4F8 as etch and polymer deposition gases, respectively. In these experiments, polymer thickness is controlled by both C4F8 gas flow rates and by deposition cycle time. The authors show that polymer thickness can be used to control wall angle and curvature at the base of feature walls. Wall angle is found to be independent of trench width under thin-polymer deposition conditions. Experimental results are compared to results obtained by other researchers using the more conventional simultaneous etch/deposition technique.