bluuebunny/crossref_metadata_2025_split huggingface dataset:
Loss of Tonoplast Integrity Programmed in Tracheary Element Differentiation
Authors: Kuriyama Hideo 
Published: July 2002

Abstract
A tracheary element (TE) is a typical example of a cell type that undergoes programmed cell death in the developmental processes of vascular plants. The loss of the selective permeability of the tonoplast, which corresponds to tonoplast disintegration, occurred after the cells commenced secondary wall thickening and played a pivotal role in the programmed cell death of TEs in a zinnia (Zinnia elegans L.) cell culture. A search for events specifically associated with the TE vacuole provided an important clue to the understanding of the cell death mechanism. The transport of fluorescein, a fluorescent organic anion, across the tonoplast declined drastically in differentiating TEs. The capacity of the vacuole to accumulate the probe was also impaired. Treatment with probenecid, an inhibitor of organic anion transport, caused rapid cell death of TEs and led to the ultimate disruption of the vacuole even in other types of cultured cells. These changes in vacuolar properties during TE development were suppressed by cycloheximide. Specific mRNA accumulation in cells cultured in a TE differentiation-inductive condition was abolished by probenecid. These results suggest that a change in vacuolar membrane permeability promotes programmed cell death in TEs.
High Throughput Cellular Localization of Specific Plant mRNAs by Liquid-Phase in Situ Reverse Transcription-Polymerase Chain Reaction of Tissue Sections
Authors: Koltai Hinanit , Bird David McKenzie 
Published: July 2002

Abstract
Advances in high throughput DNA sequencing and bioinformatic gene discovery far outpace our ability to analyze gene function, necessitating development of more efficient means to examine expression at the cellular level. Here we present a polymerase chain reaction-based method to detect mRNA species in situ in which essentially all of the steps are carried out in liquid phase in a 96-well microtiter tray and only the final signal detection is performed on a microscope slide. We demonstrate the sensitivity of the method by the cellular localization of mRNA for the Tkn2transcription factor in a wide variety of plant tissues, and its selectivity in discriminating a single gene family member by the in situ localization of rbcs3 transcripts. Furthermore, we demonstrate the utility of the in-well in situ method in detectingFDL and IFL1 transcripts in Arabidopsis sections, thus establishing the method as a tool to determine spatial expression pattern of sequences obtained from genomic sequencing projects. Being amenable to robotic processing, in-well in situ reverse transcription-polymerase chain reaction permits a great enhancement in the number of tissue samples that can be processed. Consequently, this method may become a powerful tool for functional genomics studies, permitting the cellular site of transcription of large numbers of sequences obtained from databases to be rapidly established.
LEFPS1, a Tomato Farnesyl Pyrophosphate Gene Highly Expressed during Early Fruit Development
Authors: Gaffe Joel , Bru Jean-Philippe , Causse Mathilde , Vidal Alain , Stamitti-Bert Linda , Carde Jean-Pierre , Gallusci Philippe 
Published: July 2002

Abstract
Farnesyl pyrophosphate synthase (FPS) catalyzes the synthesis of farnesyl pyrophosphate, a key intermediate in sterol and sesquiterpene biosynthesis. Using a polymerase chain reaction-based approach, we have characterized LeFPS1, a tomato (Lycoperscion esculentum cv Wva 106) fruit cDNA, which encodes a functional FPS. We demonstrate that tomato FPSs are encoded by a small multigenic family with genes located on chromosomes 10 and 12. Consistent with farnesyl pyrophosphate requirement in sterol biosynthesis,FPS genes are ubiquitously expressed in tomato plants. Using an LeFPS1 specific probe, we show that the corresponding gene can account for most of FPS mRNA in most plant organs, but not during young seedling development, indicating a differential regulation of FPS genes in tomato. FPS gene expression is also under strict developmental control: FPS mRNA was mainly abundant in young organs and decreased as organs matured with the exception of fruits that presented a biphasic accumulation pattern. In this latter case in situ hybridization studies have shown that FPSmRNA is similarly abundant in all tissues of young fruit. Taken together our results suggest that several FPS isoforms are involved in tomato farnesyl pyrophosphate metabolism and that FPSgenes are mostly expressed in relation to cell division and enlargement.
Oligandrin. A Proteinaceous Molecule Produced by the MycoparasitePythium oligandrum Induces Resistance to Phytophthora parasitica Infection in Tomato Plants
Authors: Picard Karine , Ponchet Michel , Blein Jean-Pierre , Rey Patrice , Tirilly Yves , Benhamou Nicole 
Published: July 2002

Abstract
A low-molecular weight protein, termed oligandrin, was purified to homogeneity from the culture filtrate of the mycoparasitic fungusPythium oligandrum. When applied to decapitated tomato (Lycopersicon esculentum Mill. var. Prisca) plants, this protein displayed the ability to induce plant defense reactions that contributed to restrict stem cell invasion by the pathogenic fungus Phytophthora parasitica. According to its N-terminal sequence, low-molecular weight, acidic isoelectric point, ultraviolet spectrum, and migration profile, the P. oligandrum-produced oligandrin was found to share some similarities with several elicitins from otherPhytophthora spp. and Pythium spp. However, oligandrin did not induce hypersensitive reactions. A significant decrease in disease incidence was monitored in oligandrin-treated plants as compared with water-treated plants. Ultrastructural investigations of the infected tomato stem tissues from non-treated plants showed a rapid colonization of all tissues associated with a marked host cell disorganization. In stems from oligandrin-treated plants, restriction of fungal growth to the outermost tissues and decrease in pathogen viability were the main features of the host-pathogen interaction. Invading fungal cells were markedly damaged at a time when the cellulose component of their cell walls was quite well preserved. Host reactions included the plugging of intercellular spaces as well as the occasional formation of wall appositions at sites of potential pathogen entry. In addition, pathogen ingress in the epidermis was associated with the deposition of an electron-opaque material in most invaded intercellular spaces. This material, lining the primary walls, usually extended toward the inside to form deposits that frequently interacted with the wall of invading hyphae. In the absence of fungal challenge, host reactions were not detected.
Effects of Iron Deficiency on the Composition of the Leaf Apoplastic Fluid and Xylem Sap in Sugar Beet. Implications for Iron and Carbon Transport
Authors: López-Millán Ana Flor , Morales Fermı́n , Abadı́a Anunciación , Abadı́a Javier 
Published: July 2002

Abstract
The effects of iron deficiency on the composition of the xylem sap and leaf apoplastic fluid have been characterized in sugar beet (Beta vulgaris Monohil hybrid). pH was estimated from direct measurements in apoplastic fluid and xylem sap obtained by centrifugation and by fluorescence of leaves incubated with 5-carboxyfluorescein and fluorescein isothiocyanate-dextran. Iron deficiency caused a slight decrease in the pH of the leaf apoplast (from 6.3 down to 5.9) and xylem sap (from 6.0 down to 5.7) of sugar beet. Major organic acids found in leaf apoplastic fluid and xylem sap were malate and citrate. Total organic acid concentration in control plants was 4.3 mm in apoplastic fluid and 9.4 mm in xylem sap and increased to 12.2 and 50.4 mm, respectively, in iron-deficient plants. Inorganic cation and anion concentrations also changed with iron deficiency both in apoplastic fluid and xylem sap. Iron decreased with iron deficiency from 5.5 to 2.5 μm in apoplastic fluid and xylem sap. Major predicted iron species in both compartments were [FeCitOH]−1 in the controls and [FeCit2]−3 in the iron-deficient plants. Data suggest the existence of an influx of organic acids from the roots to the leaves via xylem, probably associated to an anaplerotic carbon dioxide fixation by roots.
A Simple Procedure for the Analysis of Single Nucleotide Polymorphisms Facilitates Map-Based Cloning in Arabidopsis
Authors: Drenkard Eliana , Richter Brent G. , Rozen Steve , Stutius Lisa M. , Angell Nathaniel A. , Mindrinos Michael , Cho Raymond J. , Oefner Peter J. , Davis Ronald W. , Ausubel Frederick M. 
Published: July 2002

Abstract
We developed a modified allele-specific PCR procedure for assaying single nucleotide polymorphisms (SNPs) and used the procedure (called SNAP for single-nucleotide amplified polymorphisms) to generate 62 Arabidopsis mapping markers. SNAP primers contain a single base pair mismatch within three nucleotides from the 3′ end of one allele (the specific allele) and in addition have a 3′ mismatch with the nonspecific allele. A computer program called SNAPER was used to facilitate the design of primers that generate at least a 1,000-fold difference in the quantity of the amplification products from the specific and nonspecific SNP alleles. Because SNAP markers can be readily assayed by electrophoresis on standard agarose gels and because a public database of over 25,000 SNPs is available between the Arabidopsis Columbia and Landsberg erecta ecotypes, the SNAP method greatly facilitates the map-based cloning of Arabidopsis genes defined by a mutant phenotype.
Characterization of Maize Cytochrome P450 Monooxygenases Induced in Response to Safeners and Bacterial Pathogens
Authors: Persans Michael W. , Wang Jian , Schuler Mary A. 
Published: July 2002

Abstract
Plants use a diverse array of cytochrome P450 monooxygenases in their biosynthetic and detoxification pathways. To determine the extent to which various maize P450s are induced in response to chemical inducers, such as naphthalic anhydride (NA), triasulfuron (T), phenobarbital, and bacterial pathogens (Erwinia stuartii, Acidovorax avenae), we have analyzed the response patterns of seven P450 transcripts after treatment of seedlings with these inducers. Each of these P450 transcripts has distinct developmental, tissue-specific, and chemical cues regulating their expression even when they encode P450s within the same biosynthetic pathway. Most notably, the CYP71C1 andCYP71C3 transcripts, encoding P450s in the DIMBOA biosynthetic pathway, are induced to the same level in response to wounding and NA treatment of younger seedlings and differentially in response to NA/T treatment of younger seedlings and NA and NA/T treatment of older seedlings. NA and T induce expression of bothCYP92A1 and CYP72A5 transcripts in older seedling shoots, whereas phenobarbital induces CYP92A1expression in older seedling shoots and highly inducesCYP72A5 expression in young and older seedling roots. Expressed sequence tag (EST) 6c06b11 transcripts, encoding an undefined P450 activity, are highly induced in seedling shoots infected with bacterial pathogens.
Genetic Analysis of Amino Acid Accumulation inopaque-2 Maize Endosperm
Authors: Wang Xuelu , Larkins Brian A. 
Published: July 2002

Abstract
The opaque-2 mutation in maize (Zea mays) is associated with an increased level of free amino acids (FAA) in the mature endosperm. In particular, there is a high concentration of lysine, the most limiting essential amino acid. To investigate the basis for the high-FAA phenotype ofopaque-2 maize, we characterized amino acid accumulation during endosperm development of several wild-type andopaque-2 inbreds. Oh545o2 was found to have an exceptionally high level of FAA, in particular those derived from aspartate (Asp) and intermediates of glycolysis. The FAA content in Oh545o2 is 12 times greater than its wild-type counterpart, and three and 10 times greater than in Oh51Ao2 and W64Ao2, respectively. We crossed Oh545o2 to Oh51Ao2 and analyzed the F2:3 progeny to identify genetic loci linked with the high FAA level in these mutants. Quantitative trait locus mapping identified four significant loci that account for about 46% of the phenotypic variance. One locus on the long arm of chromosome 2 is coincident with genes encoding a monofunctional Asp kinase 2 and a bifunctional Asp kinase-homo-Ser dehydrogenase-2, whereas another locus on the short arm of chromosome 3 is linked with a cytosolic triose phosphate isomerase 4. The results suggest an alternation of amino acid and carbon metabolism leads to overproduction and accumulation of FAA in opaque-2 mutants.
Isolation of a CONSTANS Ortholog from Pharbitis nil and Its Role in Flowering
Authors: Liu Jiayou , Yu Jianping , McIntosh Lee , Kende Hans , Zeevaart Jan A.D. 
Published: July 2002

Abstract
The short-day plant Pharbitis nil is a model plant for the study of photoperiodic control of floral initiation. Flower formation can be induced at the cotyledon stage by a single long night of at least 14 h in duration. Using differential display of mRNA we identified a P. nil ortholog of the ArabidopsisCONSTANS (CO) gene, which will be referred to as PnCO. Expression of PnCOwas high after a 14-h night, but low when the dark period was 12 h or less. Our results indicate that the level of the PnCOtranscript is photoperiodically regulated. After transfer from continuous light to darkness, PnCO showed a circadian pattern of expression. Expression of the CAB gene, which is a molecular marker for the circadian clock, exhibited a different pattern of expression than did PnCO and was not subject to the same photoperiodic control. A major portion of thePnCO transcripts contained an unspliced intron. Only the intron-free PnCO was able to complement theco mutant of Arabidopsis by shortening the time to flower.
Signaling Events in the Hypoxic Induction of Alcohol Dehydrogenase Gene in Arabidopsis
Authors: Peng Hsiao-Ping , Chan Chui-Sien , Shih Ming-Che , Yang Shang Fa 
Published: July 2002

Abstract
Expression of the alcohol dehydrogenase gene (ADH) of Arabidopsis is induced during hypoxia. Because many plants increase their ethylene production in response to hypoxic stress, we examined in this report whether ethylene is involved in the hypoxic induction ofADH in Arabidopsis. We found that the hypoxic induction of ADH can be partially inhibited by aminooxy acetic acid, an inhibitor of ethylene biosynthesis. This partial inhibition can be reversed by the addition of 1-aminocyclopropane-1-carboxylic acid, a direct precursor of ethylene. In addition, the hypoxic induction of the ADH gene is also reduced inetr1-1 and ein2-1, two ethylene insensitive mutants in ethylene-signaling pathways, whereas the addition of exogenous ethylene or an increase in cellular ethylene alone does not induce ADH under normoxic conditions. Kinetic analyses of ADH mRNA accumulation indicated that an ethylene signal is required for the induction of ADHduring later stages of hypoxia. Therefore, we conclude that ethylene is needed, but not sufficient for, the induction of ADH in Arabidopsis during hypoxia.
The TASTY Locus on Chromosome 1 of Arabidopsis Affects Feeding of the Insect Herbivore Trichoplusia ni
Authors: Jander Georg , Cui Jianping , Nhan Betty , Pierce Naomi E. , Ausubel Frederick M. 
Published: July 2002

Abstract
The generalist insect herbivore Trichoplusia ni(cabbage looper) readily consumes Arabidopsis and can complete its entire life cycle on this plant. Natural isolates (ecotypes) of Arabidopsis are not equally susceptible to T. ni feeding. While some are hardly touched by T. ni, others are eaten completely to the ground. Comparison of two commonly studied Arabidopsis ecotypes in choice experiments showed that Columbia is considerably more resistant than Landsberg erecta. In no-choice experiments, where larvae were confined on one or the other ecotype, weight gain was more rapid on Landsberg erectathan on Columbia. Genetic mapping of this difference in insect susceptibility using recombinant inbred lines resulted in the discovery of the TASTY locus near 85 cM on chromosome 1 of Arabidopsis. The resistant allele of this locus is in the Columbia ecotype, and an F1 hybrid has a sensitive phenotype that is similar to that of Landsberg erecta. TheTASTY locus is distinct from known genetic differences between Columbia and Landsberg erecta that affect glucosinolate content, trichome density, disease resistance, and flowering time.
Frequencies of amino acid strings in globular protein sequences indicate suppression of blocks of consecutive hydrophobic residues
Authors: Schwartz Russell , Istrail Sorin , King Jonathan 
Published: July 2002

AbstractPatterns of hydrophobic and hydrophilic residues play a major role in protein folding and function. Long, predominantly hydrophobic strings of 20–22 amino acids each are associated with transmembrane helices and have been used to identify such sequences. Much less attention has been paid to hydrophobic sequences within globular proteins. In prior work on computer simulations of the competition between on‐pathway folding and off‐pathway aggregate formation, we found that long sequences of consecutive hydrophobic residues promoted aggregation within the model, even controlling for overall hydrophobic content. We report here on an analysis of the frequencies of different lengths of contiguous blocks of hydrophobic residues in a database of amino acid sequences of proteins of known structure. Sequences of three or more consecutive hydrophobic residues are found to be significantly less common in actual globular proteins than would be predicted if residues were selected independently. The result may reflect selection against long blocks of hydrophobic residues within globular proteins relative to what would be expected if residue hydrophobicities were independent of those of nearby residues in the sequence.
Probing protein conformation with a minimal photochemical reagent
Authors: Craig Patricio O. , Ureta Daniela B. , Delfino José M. 
Published: July 2002

Abstract3H‐diazirine (3H‐DZN), a photoreactive gas similar in size to water, was used to probe the topography of the surface and inner space of proteins. On photolysis 3H‐DZN generates 3H‐methylene carbene, which reacts unselectively with its molecular cage, inserting even into C‐H bonds. Labeling of bovine α‐lactalbumin (α‐LA, MW: 14,200) with 1 mM 3H‐DZN yielded 0.0041 mol CH2/mol of protein, in agreement with the expectation for an unspecific surface‐labeling phenomenon. The cooperative urea‐induced unfolding of α‐LA, as monitored by the extent of 3H‐methylene labeling, agrees with that measured by circular dichroism spectroscopy in the far and near ultraviolet regions. At 8 M urea, the unfolded state U was labeled 25–30% more than the native state N primarily because of the increase in the accessible surface area (ASA) of the protein occurring upon unfolding. However, this result lies below the ∼100% increment expected from theoretical estimates of ASA of state U. Among other factors, most likely the existence of a residual structure in U, that involves helices H2 and H4 of the α subdomain, might account for this fact, as shown by a comparative analysis of peptide labeling patterns of N and U samples. In this paper, we demonstrate the usefulness of the 3H‐methylene labeling method to monitor conformational transitions and map solvent accessibility along the polypeptide sequence, thus opening the possibility of outlining structural features of nonnative states (i.e., denatured states, molten globule). We anticipate that this technique also would help to identify ligand binding and oligomerization sites in proteins.
Angular Distributions of Secondary Electrons Originating from Thin Films of Different Metals in Re-emission and Transmission
Authors: Jahrreiss H. , Oppel W. 
Published: July 2002

Continuing preceding research on this field, angular distributions of η and δ electrons from thin films of Al and Au have been investigated by means of a considerably improved apparatus. Measurements have been made in forward and backward directions with primary energies in the interval 1 to 20 keV with normal as well as oblique incidence of the primaries. In addition, the angular distributions in reemission of bulk probes of Al and Au as well as other metals (Ag, Cu, In, Ni, Ta, W) have been investigated. There are several characteristic differences between the measured curves and the cosine distribution which are discussed in respect to the generating processes within these metals.
Im Anschluss an frühere Arbeiten wurden Winkelverteilungen von η- und δ-Elektronen aus dünnen Al- und Au-Schichten mittels einer wesentlich verbesserten Apparatur untersucht. Die Messungen wurden in Vorwärts- und Rückwärtsrichtung mit Primäirelektronenenergien zwischen 1 und 20 keV bei senkrechtem und schrägem Einfall der Primärelektronen ausgeführt. Zusätzlich wurden die Winkelverteilungen in Rückwärtsrichtung aus massiven Proben von Al und Au wie auch von weiteren Metallen (Ag, Cu, In, Ni, Ta, W) untersucht. Man beobachtet einige charakteristische Unterschiede zwischen den gemessenen Kurven und der Kosinus-Verteilung, die im Hinblick auf die zugrunde liegenden Prozesse innerhalb dieser Metalle diskutiert werden.
Effects of annealing and surface preparation on the properties of polycrystalline CdZnTe films grown by molecular beam epitaxy
Authors: Ringel S. A. , Sudharsanan R. , Rohatgi A. , Owens M. S. , Gillis H. P. 
Published: July 2002

The effects of annealing and chemical etching on the chemical, compositional, and electrical properties of polycrystalline molecular-beam epitaxy (MBE)-grown Cd1−xZnxTe thin films were investigated in detail for the first time to identify and eliminate some of the undesirable process-induced side effects resulting from the CdZnTe/CdS solar cell fabrication procedure. Depth-resolved x-ray photoelectron and Auger electron spectroscopies on processed surfaces along with current-voltage and capacitance-voltage measurements on In/Cd1−xZnxTe Schottky diodes were used to characterize the treated Cd1−xZnxTe surface. Films were annealed in air at 200–400 °C and etched in Br:CH3OH and K2Cr2O7:H2SO4 solutions, similar to processes used to achieve high efficiency CdTe/CdS solar cells. Air annealing was found to enhance the uniformity of the p-type conductivity within the film, yielding a doping value of ∼3×1015 cm−3. However, the air anneal resulted in a highly Zn-rich surface compared to hydrogen and argon anneals. Furthermore, the air anneal resulted in the oxidation of ∼80% of the Zn at the surface which was found to extend ∼0.1 μm into the bulk. This is in contrast to Cd and Te oxides which were detected only at the surface.
A model is proposed to explain the Zn pileup near the surface. According to this model, the oxygen diffuses into the film to oxidize Zn resulting in a concentration gradient and outdiffusion of Zn. Subsequent etching of the annealed films by the standard Br2:CH3OH etch used for CdTe processing removed the surface Te and Cd oxides but failed to remove the Zn-rich surface region and Zn–O and did not result in a p+ Te-rich surface which is required to facilitate ohmic contacts. In contrast, etching of the annealed Cd1−xZnxTe surfaces with a concentrated K2Cr2O7:H2SO4 solution removed all oxides and left a surface completely depleted in Cd and Zn. Subsequently fabricated In/Cd1−xZnxTe Schottky barrier diodes on etched surfaces confirmed a significant reduction in effective barrier height, from ∼1.2 eV for the Br:CH3OH surface to ∼0.65 eV for the K2Cr2O7:H2SO4 etched surface due to a Te-rich surface layer with a p-type doping concentration of ∼3×1017 cm−3. It is expected that these results will provide guidelines to increase present-day Cd1−xZnxTe cell performance by reducing the resistance of ‘‘ohmic’’ contacts.