bluuebunny/crossref_metadata_2025_split huggingface dataset:
Transgenic Tobacco Plants Expressing Pea Chloroplast Nmdh cDNA in Sense and Antisense Orientation (Effects on NADP-Malate Dehydrogenase Level, Stability of Transformants, and Plant Growth)
Authors: Faske M. , Backhausen J. E. , Sendker M. , Singer-Bayrle M. , Scheibe R. , von Schaewen A. 
Published: July 2002

Abstract
A full-length cDNA encoding light-activated chloroplast NADP-malate dehydrogenase (NADP-MDH) (EC 1.1.1.82) from pea (Pisum sativum L.) was introduced in the sense and antisense orientation into tobacco (Nicotiana tabacum L.). Transgenic plants with decreased or increased expression levels were obtained. Because of substantial age-dependent differences in individual leaves of a single plant, standardization of NADP-MDH levels was required first. Then, extent and stability of over- or under-expression of Nmdh, the gene encoding NADP-MDH, was characterized in the various transformants. Frequently, cosuppression effects were observed, indicating sufficient homology between the endogenous tobacco and the heterologous pea gene. Analysis of the T1 and T2 progeny of a series of independent transgenic lines revealed that NADP-MDH capacity ranged between 10% and [greater than or equal to]10-fold compared with the wild type. Under ambient conditions whole-plant development, growth period, and fertility were unaffected by NADP-MDH reduction to 20% of the wild-type level; below this threshold plant growth was retarded. A positive growth effect was registered in young plants with stably enhanced NADP-MDH levels within a defined developmental window.
Metabolism ofd-Glycero-d-Manno-Heptitol, Volemitol, in Polyanthus. Discovery of a Novel Ketose Reductase1
Authors: Häfliger Beat , Kindhauser Elsbeth , Keller Felix 
Published: July 2002

AbstractVolemitol (d-glycero-d-manno-heptitol, α-sedoheptitol) is an unusual seven-carbon sugar alcohol that fulfills several important physiological functions in certain species of the genus Primula. Using the horticultural hybrid polyanthus (Primula × polyantha) as our model plant, we found that volemitol is the major nonstructural carbohydrate in leaves of all stages of development, with concentrations of up to 50 mg/g fresh weight in source leaves (about 25% of the dry weight), followed by sedoheptulose (d-altro-2-heptulose, 36 mg/g fresh weight), and sucrose (4 mg/g fresh weight). Volemitol was shown by the ethylenediaminetetraacetate-exudation technique to be a prominent phloem-mobile carbohydrate. It accounted for about 24% (mol/mol) of the phloem sap carbohydrates, surpassed only by sucrose (63%). Preliminary 14CO2 pulse-chase radiolabeling experiments showed that volemitol was a major photosynthetic product, preceded by the structurally related ketose sedoheptulose. Finally, we present evidence for a novel NADPH-dependent ketose reductase, tentatively called sedoheptulose reductase, in volemitol-containingPrimula species, and propose it as responsible for the biosynthesis of volemitol in planta. Using enzyme extracts from polyanthus leaves, we determined that sedoheptulose reductase has a pH optimum between 7.0 and 8.0, a very high substrate specificity, and displays saturable concentration dependence for both sedoheptulose (apparent Km = 21 mm) and NADPH (apparent Km = 0.4 mm). Our results suggest that volemitol is important in certainPrimula species as a photosynthetic product, phloem translocate, and storage carbohydrate.
The Relationship between Photosynthesis and a Mastoparan-Induced Hypersensitive Response in Isolated Mesophyll Cells1
Authors: Allen Lisa J. , MacGregor Kennaway B. , Koop Randall S. , Bruce Doug H. , Karner Julie , Bown Alan W. 
Published: July 2002

Abstract
The G-protein activator mastoparan (MP) was found to elicit the hypersensitive response (HR) in isolatedAsparagus sprengeri mesophyll cells at micromolar concentrations. The HR was characterized by cell death, extracellular alkalinization, and an oxidative burst, indicated by the reduction of molecular O2 to O2⋅−. To our knowledge, this study was the first to monitor photosynthesis during the HR. MP had rapid and dramatic effects on photosynthetic electron transport and excitation energy transfer as determined by variable chlorophyll a fluorescence measurements. A large increase in nonphotochemical quenching of chlorophylla fluorescence accompanied the initial stages of the oxidative burst. The minimal level of fluorescence was also quenched, which suggests the origin of this nonphotochemical quenching to be a decrease in the antenna size of photosystem II. In contrast, photochemical quenching of fluorescence decreased dramatically during the latter stages of the oxidative burst, indicating a somewhat slower inhibition of photosystem II electron transport. The net consumption of O2 and the initial rate of O2 uptake, elicited by MP, were higher in the light than in the dark. These data indicate that light enhances the oxidative burst and suggest a complex relationship between photosynthesis and the HR.
Cucumber Cotyledon Lipoxygenase during Postgerminative Growth. Its Expression and Action on Lipid Bodies
Authors: Matsui Kenji , Hijiya Kohko , Tabuchi Yutaka , Kajiwara Tadahiko 
Published: July 2002

Abstract
In cucumber (Cucumis sativus), high lipoxygenase-1 (LOX-1) activity has been detected in the soluble fraction prepared from cotyledons of germinating seeds, and the involvement of this enzyme in lipid turnover has been suggested (K. Matsui, M. Irie, T. Kajiwara, A. Hatanaka [1992] Plant Sci 85: 23–32; I. Fuessner, C. Wasternack, H. Kindl, H. Kühn [1995] Proc Natl Acad Sci USA 92: 11849–11853). In this study we have investigated the expression of the gene lox-1, corresponding to the LOX-1 enzyme. LOX-1 expression is highly coordinated with that of a typical glyoxysomal enzyme, isocitrate lyase, during the postgerminative stage of cotyledon development. In contrast, although icl transcripts accumulated in tissue during in vitro senescence, no accumulation oflox-1 mRNA could be observed, suggesting thatlox-1 plays a specialized role in fat mobilization. LOX-1 is also known to be a major lipid body protein. The partial peptide sequences of purified LOX-1 and lipid body LOX-1 entirely coincided with that deduced from the lox-1 cDNA sequence. The data strongly suggest that LOX-1 and lipid body LOX-1 are derived from a single gene and that LOX-1 can exist both in the cytosol and on the lipid bodies. We constructed an in vitro oxygenation system to address the mechanism of this dual localization and to investigate the action of LOX-1 on lipids in the lipid bodies. LOX-1 cannot act on the lipids in intact lipid bodies, although degradation of lipid body proteins, either during seedling growth or by treatment with trypsin, allows lipid bodies to become susceptible to LOX-1. We discuss the role of LOX-1 in fat mobilization and its mechanism of action.
Roles of Cellulose and Xyloglucan in Determining the Mechanical Properties of Primary Plant Cell Walls
Authors: Whitney Sarah E.C. , Gothard Michelle G.E. , Mitchell John T. , Gidley Michael J. 
Published: July 2002

AbstractThe primary cell walls of growing and fleshy plant tissue mostly share a common set of molecular components, cellulose, xyloglucan (XyG), and pectin, that are required for both inherent strength and the ability to respond to cell expansion during growth. To probe molecular mechanisms underlying material properties, cell walls and analog composites from Acetobacter xylinus have been measured under small deformation and uniaxial extension conditions as a function of molecular composition. Small deformation oscillatory rheology shows a common frequency response for homogenized native cell walls, their sequential extraction residues, and bacterial cellulose alone. This behavior is characteristic of structuring via entanglement of cellulosic rods and is more important than cross-linking with XyG in determining shear moduli. Compared with cellulose alone, composites with XyG have lower stiffness and greater extensibility in uniaxial tension, despite being highly cross-linked at the molecular level. It is proposed that this is due to domains of cross-linked cellulose behaving as mechanical elements, whereas cellulose alone behaves as a mat of individual fibrils. The implication from this work is that XyG/cellulose networks provide a balance of extensibility and strength required by primary cell walls, which is not achievable with cellulose alone.
Light-Dependent Osmoregulation in Pea Stem Protoplasts. Photoreceptors, Tissue Specificity, Ion Relationships, and Physiological Implications
Authors: Long Cheng , Iino Moritoshi 
Published: July 2002

Abstract
Light-induced changes in the volume of protoplasts bathed in a medium of constant osmolarity are useful indications of light-dependent cellular osmoregulation. With this in mind, we investigated the effect of light on the volume of protoplasts isolated from the elongating stems of pea (Pisum sativum) seedlings raised under red light. The protoplasts were isolated separately from epidermal peels and the remaining peeled stems. Under continuous red light, the protoplasts of peeled stems swelled steadily, but those of epidermal peels maintained a constant volume. Experiments employing far-red light and phytochrome-deficient mutants revealed that the observed swelling is a light-induced response mediated mainly by phytochromes A and B with a little greater contribution by phytochrome A. Protoplasts of epidermal peels and peeled stems shrank transiently in response to a pulse of blue light. The blue light responsiveness in this shrinking response, which itself is probably mediated by cryptochrome, is under the strict control of phytochromes A and B with equal contributions by these phytochromes. We suggest that the swelling response participates in the maintenance of high tissue tension of elongating stems and that the shrinking response is involved in stem growth inhibition. Other findings include the following: The swelling is caused by uptake of K+ and Cl−. The presence of Ca2+in the bathing medium is required for phytochrome signaling in the swelling response, but not in the response establishing blue light responsiveness. Phytochrome A mediates the two responses in a totally red/far-red light reversible manner, as does phytochrome B.
Differential mRNA Degradation of Two β-Tubulin Isoforms Correlates with Cytosolic Ca2+ Changes in Glucan-Elicited Soybean Cells
Authors: Ebel Chantal , Gómez Lourdes Gómez , Schmit Anne-Catherine , Neuhaus-Url Gabriele , Boller Thomas 
Published: July 2002

Abstract
Transgenic soybean (Glycine max) culture cells expressing apoaequorin, a Ca2+ indicator, were exposed to glucan fragments derived from Phytophthora sojae or to chitin oligomers. The effects of these elicitors on cytosolic Ca2+ concentrations and on mRNA levels of two β-tubulin isoforms, tubB1 and tubB2, were investigated. The glucan elicitors, to which the cells are known to react with a biphasic cytosolic Ca2+ increase, induced a down-regulation of the tubB1 mRNA levels while the tubB2 mRNA level remained constant. The decrease of tubB1 mRNA level was observed after 1 hour of glucan treatment. In contrast, chitin oligomers, known to provoke a monophasic Ca2+ increase of short duration, did not affect the tubB1 mRNA level. Pre-incubation with 10 mm1,2-bis(o-aminophenoxy)ethane-N,N,N′,N′-tetraacetic acid, an extracellular Ca2+ chelator, blocked the cytosolic Ca2+ increase as well as the decrease of tubB1 mRNA levels induced by glucan elicitors. Likewise, pre-incubation with 1 mm neomycin, which reduced only the second glucan-induced Ca2+ peak, blocked the decrease of tubB1 mRNA level. Experiments with cordycepin, a transcription inhibitor, indicated that glucan fragments induced the degradation of tubB1 mRNA. In conclusion, the glucan-induced cytosolic Ca2+ changes are correlated with a strong increase in tubB1 mRNA degradation.
Application of photoaffinity labeling with [3H] all trans‐ and 9‐cis‐retinoic acids for characterization of cellular retinoic acid–binding proteins I and II
Authors: Radominska‐Pandya Anna , Chen Guangping , Samokyszyn Victor M. , Little Joanna M. , Gall Walter E. , Zawada Gregory , Terrier Nadege , Magdalou Jacques , Czernik Piotr 
Published: July 2002

AbstractCellular retinoic acid–binding proteins (CRABPs) are carrier proteins thought to play a crucial role in the transport and metabolism of all‐trans‐retinoic acid (atRA) and its derivatives within the cell. This report describes a novel photoaffinity‐based binding assay involving competition between potential ligands of CRABP and [3H]atRA or [3H]‐9‐cis‐RA for binding to the atRA‐binding sites of CRABP I and II. Photoaffinity labeling of purified CRABPs with [3H]atRA was light‐ and concentration‐dependent, saturable, and protected by several retinoids in a concentration‐dependent manner, indicating that binding occurred in the CRABP atRA‐binding site. Structure–function relationship studies demonstrated that oxidative changes to the atRA β‐ionone ring did not affect ligand potency. However, derivatives lacking a terminal carboxyl group and some cis isomers did not bind to CRABPs. These studies also identified two novel ligands for CRABPs: 5,6‐epoxy‐RA and retinoyl‐β‐D‐glucuronide (RAG). The labeling of both CRABPs with 9‐cis‐RA occurred with much lower affinity. Experimental evidence excluded nonspecific binding of RAG to CRABPs and UDP‐glucuronosyltransferases, the enzymes responsible for RAG synthesis. These results established that RAG is an effective ligand of CRABPs. Therefore, photoaffinity labeling with [3H]atRA can be used to identify new ligands for CRABP and retinoid nuclear receptors and also provide information concerning the identity of amino acid(s) localized in the atRA‐binding site of these proteins.
Computational stabilization of human growth hormone
Authors: Filikov Anton V. , Hayes Robert J. , Luo Peizhi , Stark Diane M. , Chan Cheryl , Kundu Anirban , Dahiyat Bassil I. 
Published: July 2002

AbstractRecombinant human growth hormone (hGH) is used worldwide for the treatment of pediatric hypopituitary dwarfism and in children suffering from low levels of hGH. It has limited stability in solution, and because of poor oral absorption, is administered by injection, typically several times a week. Development has therefore focused on more stable or sustained‐release formulations and alternatives to injectable delivery that would increase bioavailability and make it easier for patients to use. We redesigned hGH computationally to improve its thermostability. A more stable variant of hGH could have improved pharmacokinetics or enhanced shelf‐life, or be more amenable to use in alternate delivery systems and formulations. The computational design was performed using a previously developed combinatorial optimization algorithm based on the dead‐end elimination theorem. The algorithm uses an empirical free energy function for scoring designed sequences. This function was augmented with a term that accounts for the loss of backbone and side‐chain conformational entropy. The weighting factors for this term, the electrostatic interaction term, and the polar hydrogen burial term were optimized by minimizing the number of mutations designed by the algorithm relative to wild‐type. Forty‐five residues in the core of the protein were selected for optimization with the modified potential function. The proteins designed using the developed scoring function contained six to 10 mutations, showed enhancement in the melting temperature of up to 16°C, and were biologically active in cell proliferation studies. These results show the utility of our free energy function in automated protein design.
Replacement of Asp‐162 by Ala prevents the cooperative transition by the substrates while enhancing the effect of the allosteric activator ATP on E. coli aspartate transcarbamoylase
Authors: Fetler L. , Tauc P. , Baker D.P. , Macol C.P. , Kantrowitz E.R. , Vachette P. 
Published: July 2002

AbstractThe available crystal structures of Escherichia coli aspartate transcarbamoylase (ATCase) show that the conserved residue Asp‐162 from the catalytic chain interacts with essentially the same residues in both the T‐ and R‐states. To study the role of Asp‐162 in the regulatory properties of the enzyme, this residue has been replaced by alanine. The mutant D162A shows a 7700‐fold reduction in the maximal observed specific activity, a twofold decrease in the affinity for aspartate, a loss of homotropic cooperativity, and decreased activation by the nucleotide effector adenosine triphosphate (ATP) compared with the wild‐type enzyme. Small‐angle X‐ray scattering (SAXS) measurements reveal that the unliganded mutant enzyme adopts the T‐quaternary structure of the wild‐type enzyme. Most strikingly, the bisubstrate analog N‐phosphonacetyl‐L‐aspartate (PALA) is unable to induce the T to R quaternary structural transition, causing only a small alteration of the scattering pattern. In contrast, addition of the activator ATP in the presence of PALA causes a significant increase in the scattering amplitude, indicating a large quaternary structural change, although the mutant does not entirely convert to the wild‐type R structure. Attempts at modeling this new conformation using rigid body movements of the catalytic trimers and regulatory dimers did not yield a satisfactory solution. This indicates that intra‐ and/or interchain rearrangements resulting from the mutation bring about domain movements not accounted for in the simple model. Therefore, Asp‐162 appears to play a crucial role in the cooperative structural transition and the heterotropic regulatory properties of ATCase.
Scaling of Si and GaAs trench etch rates with aspect ratio, feature width, and substrate temperature
Authors: Bailey A. D. , van de Sanden M. C. M. , Gregus J. A. , Gottscho R. A. 
Published: July 2002

The scaling of etch rates with feature dimensions is an important issue in the fabrication of microelectronic and photonic devices. Because etch rates depend on circuit layouts and design rules, considerable effort is spent to modify processes each time changes in design are made. Knowing how etch rates scale with design parameters should accelerate the introduction of new designs into manufacturing while minimizing the cost of doing so. Recently it has been shown that etch rates for a variety of conditions scale with the depth/width or aspect ratio and not on width or depth alone. While various mechanisms might be responsible for such scaling, isolating one mechanism from another is not straight forward. Nonetheless, it is important to understand the underlying mechanisms so that differences in etch chemistry and etch reactor design can be accounted for when scaling plasma processes from one design or reactor to another. To assess the effects of etch chemistry alone, the trench etch rates of Si and GaAs are compared under constant plasma conditions. Substrate temperature is varied to further assess the relative importance of surface vs transport phenomena during the etching process.
At higher temperatures, both Si and GaAs trench etch rates scale only with aspect ratio in an Ar/Cl2 electron cyclotron resonance plasma. The results are consistent with an ion-neutral synergy model based on Langmuir adsorption kinetics where the scaling can be explained by the aspect ratio dependence of the neutral reactant transport into the trench: charging effects, ion shadowing, and Knudsen transport are not consistent with the data. At −45 °C, the etch rate no longer scales with aspect ratio alone, but now also depends on trench width. The data at this lower temperature are well described by a model incorporating the deposition of an etch inhibiting layer. While the trench etch rates for GaAs and Si scale in similar ways with aspect ratio and trench width, the dependence on feature dimensions of the Si etch rate is much stronger than that for GaAs at all substrate temperatures because the steady-state surface coverage of Cl is smaller for Si. This results in a greater sensitivity to the incoming, aspect ratio dependent, neutral fluxes. The implications of the models on the goal of aspect ratio independent etching are also discussed.
Chemical vapor deposition TiN process for contact/via barrier applications
Authors: Paranjpe Ajit , IslamRaja Mazhar 
Published: July 2002

Chemical vapor deposition (CVD) TiN is an attractive replacement for PVD TiN as a barrier and glue layer for subhalf-micron contacts and vias. CVD TiN films have been deposited in a commercial reactor via the thermal decomposition of tetrakis-dimethyl-amino-titanium (TDMAT) precursor in an N2 ambient. The deposition can be characterized by a simple Arrhenius rate expression with a half-order dependence on TDMAT concentration and an activation energy of 0.53 eV. Designed experiments show that the deposition transitions from being kinetically limited at high TDMAT flow rates and low temperatures to transport limited at the other extreme. In the kinetically limited regime, the deposition rate increases with increasing TDMAT mole fraction and increasing temperature. Step coverage simulations have been performed by coupling SPEEDIE (a profile evolution program) with the Arrhenius rate expression. Experimental and simulated step coverages show good agreement over a wide range of process conditions. Step coverage improves with increasing deposition rate and decreasing temperature. Adequate deposition rates (≳400 Å/min) with good deposition uniformity and high step coverage (50%–85%) can be achieved. Film stress and roughness are mostly invariant with process conditions. These films are close to stoichiometric (i.e., 1:1 Ti:N ratio), but contain up to 30% carbon. Exposure of these films to air causes rapid oxidation with a steady state concentration of 15%–20% oxygen after 24 h of air exposure.
The high carbon concentration results in high film resistivity (5000 μΩ cm), which doubles after 24 h of air exposure due to oxidation of the film. Film resistivity decreases and film stability improves with increasing N2 flow rate. Electrical characterization of two process variants have been performed. The first provides a film with 85% step coverage with a resistivity of 5600 μΩ cm, while the second process achieves a lower resistivity of 3700 μΩ cm and a lower step coverage of 50%. Electrical performance of both films is similar. Contact induced diode leakage is lower for CVD TiN compared to PVD TiN. Contact resistance for 100–200 Å CVD TiN is comparable or lower than 500 Å PVD TiN. A 100 Å CVD TiN barrier is adequate; 300 Å CVD TiN is too thick because of high film resistivity. An Al–Cu/100–300 Å CVD TiN/Si stack shows lower resistance increase after 450–500 °C, 30 min N2 anneal compared to a Al–Cu/200 Å PVD TiN/Si stack indicating that CVD TiN is a superior barrier and is more inert than PVD TiN.
Nota Bene: Why Did the Penguins Gasp?
Authors: Ash Caroline , Croft Samuel Ash 
Published: July 2002

The Blue Planet
A Natural History of the Oceans. Andrew Byatt, Alastair Fothergill, and Martha Holmes. BBC One, Fall, 2001. Discovery Channel, January, 2002. Eight 50-minute episodes.

BBC Worldwide, London, 2001. 384 pp. £24.99. ISBN 0-563-38498-0. DK, New York, 2002. $40. ISBN 0-7894-8265-7.
This eight-part series from the BBC Natural History Unit is filled with breathtaking sequences that depict the ocean life and habitats from pole to pole and from high tide to the abyss.
Two Efflux Systems Expressed Simultaneously in Multidrug-Resistant
Pseudomonas aeruginosa
Authors: Pumbwe Lilian , Piddock Laura J. V. 
Published: July 2002

ABSTRACT

Simultaneous overexpression of MexAB-OprM and MexEF-OprN was demonstrated for a multiply antibiotic-resistant clinical isolate of
Pseudomonas aeruginosa
(G49). G49 also had decreased expression of OprF. No mutations in
mexR
or its upstream promoter region,
mexT
,
oprM
,
oprF
, or
sigX
were revealed, suggesting regulation by a hitherto undescribed locus.