bluuebunny/crossref_metadata_2025_split huggingface dataset:
Issues facing clinical trials of the future
Authors: Califf R. M. 
Published: October 2003

Abstract. Califf RM (Duke University Medical Center, Durham, NC, USA). Issues facing clinical trials of the future (Clinical Trials). J Intern Med 2003; 254: 426–433.Diagnostic and therapeutic technology continues to advance rapidly, as does our knowledge of therapeutics and of clinical research methods. Unfortunately, these advances have been only poorly coupled with our knowledge of therapeutic principles, leading to increasing uncertainty about which technologies are truly effective and, amongst those that are effective, which are most effective for the cost. This article presents general principles derived from several investigators’ experiences with clinical trials, and uses them to suggest how future clinical trials may differ from current approaches. A proposed organization for future trials also is elucidated.
Mass spectrometric approach for identifying putative plasma membrane proteins of Arabidopsis leaves associated with cold acclimation
Authors: Kawamura Yukio , Uemura Matsuo 
Published: October 2003

SummaryAlthough enhancement of freezing tolerance in plants during cold acclimation is closely associated with an increase in the cryostability of plasma membrane, the molecular mechanism for the increased cryostability of plasma membrane is still to be elucidated. In Arabidopsis, enhanced freezing tolerance was detectable after cold acclimation at 2°C for as short as 1 day, and maximum freezing tolerance was attained after 1 week. To identify the plasma membrane proteins that change in quantity in response to cold acclimation, a highly purified plasma membrane fraction was isolated from leaves before and during cold acclimation, and the proteins in the fraction were separated with gel electrophoresis. We found that there were substantial changes in the protein profiles after as short as 1 day of cold acclimation. Subsequently, using matrix‐assisted laser desorption–ionization time‐of‐flight mass spectrometry (MALDI‐TOF MS), we identified 38 proteins that changed in quantity during cold acclimation. The proteins that changed in quantity during the first day of cold acclimation include those that are associated with membrane repair by membrane fusion, protection of the membrane against osmotic stress, enhancement of CO2 fixation, and proteolysis.
Formation of plant cuticle: evidence for the occurrence of the peroxygenase pathway
Authors: Lequeu José , Fauconnier Marie‐Laure , Chammaï Antoine , Bronner Roberte , Blée Elizabeth 
Published: October 2003

SummaryCuticle plays a major role as a protective barrier in plants. Despite its physiological importance, the mode of formation of this complex structure remains poorly understood. In particular, none of the putative enzymes involved in the biosynthesis of the cutin, the matrix of cuticle, have been cloned. We have shown previously that peroxygenase is able to catalyze in vitro the epoxidation step required for the biosynthesis of C18 cutin monomers. In the present work, we have confirmed in planta that this oxidase is indeed a key enzyme involved in the formation of cutin. Thus, in maize leaves, the specific inactivation of peroxygenase by organophosphorothioates resulted in a dramatic decrease of cuticular epoxide content, as visualized by a specific histochemical technique that was accompanied by a reduced thickness of the cuticle. A strict correlation could also be established between the extent of inhibition of the peroxygenase and the modification of the cuticle triggered by a family of structurally related inhibitors. Importantly, these effects were restricted to plants that contain a cutin originating from C18 monomers. The altered cuticle of maize, treated with the peroxygenase inhibitor, was characterized by an increased permeability to pesticides. In addition, such plants became largely susceptible to infection by fungi, implying that the cuticle represents a crucial target for the modulation of the response in plant–pathogen interactions.
Roles of OsCKI1, a rice casein kinase I, in root development and plant hormone sensitivity
Authors: Liu Wei , Xu Zhi‐Hong , Luo Da , Xue Hong‐Wei 
Published: October 2003

SummaryCasein kinases are critical in cell division and differentiation across species. A rice cDNA fragment encoding a putative casein kinase I (CKI) was identified via cDNA macroarray under brassinosteroid (BR) treatment, and a 1939‐bp full‐length cDNA, OsCKI1, was isolated and found to encode a putative 463‐aa protein. RT‐PCR and Northern blot analysis indicated that OsCKI1 was constitutively expressed in various rice tissues and upregulated by treatments with BR and abscisic acid (ABA). Enzymatic assay of recombinant OsCKI1 proteins expressed in Escherichia coli showed that the protein was capable of phosphorylating casein. The physiological roles of OsCKI1 were studied through antisense transgenic approaches, and homozygous transgenic plants showed abnormal root development, including fewer lateral and adventitious roots, and shortened primary roots as a result of reduced cell elongation. Treatment of wild‐type plants with CKI‐7, a specific inhibitor of CKI, also confirmed these functions of OsCKI1. Interestingly, in transgenic and CKI‐7‐treated plants, exogenously supplied IAA could restore normal root development, and measurement of free IAA content in CKI‐deficient primary and adventitious roots revealed altered auxin content, indicating that OsCKI1 is involved in auxin metabolism or that it may affect auxin levels. Transgenic plants were less sensitive than control plants to ABA or BR treatment during germination, suggesting that OsCKI1 may be involved in various hormone‐signaling pathways. OsCKI1‐GFP fusion studies revealed the localization of OsCKI1 to the nucleus, suggesting a possible involvement in regulation of gene expression. In OsCKI1‐deficient plants, differential gene expression was investigated using cDNA chip technology, and results indicated that genes related to signal transduction and hormone metabolism were indeed with altered expression.
Transcriptome analysis of Arabidopsis colonized by a plant‐growth promoting rhizobacterium reveals a general effect on disease resistance
Authors: Cartieaux Fabienne , Thibaud Marie‐Christine , Zimmerli Laurent , Lessard Philippe , Sarrobert Catherine , David Pascale , Gerbaud Alain , Robaglia Christophe , Somerville Shauna , Nussaume Laurent 
Published: October 2003

SummaryRNA transcript levels of Arabidopsis plants, infected by the rhizobacterium Pseudomonas thivervalensis (strain MLG45), and axenic control plants were compared using cDNA microarrays representing approximately 14 300 genes. The analysis revealed an increase of defence‐related transcripts in the shoots of bacterized plants relative to control (axenic) plants. These modifications of transcript levels were confirmed by physiological experiments. Plants infected with P. thivervalensis were more resistant to subsequent infections by the virulent pathogen P. syringae pv. tomato (strain DC3000) than control plants. In addition, photosynthesis rates were repressed consistently with the reduced growth of plants colonized by P. thivervalensis. These results highlight the value of molecular phenotyping to predict physiological changes.
Genomic and physiological studies of early cryptochrome 1 action demonstrate roles for auxin and gibberellin in the control of hypocotyl growth by blue light
Authors: Folta Kevin M. , Pontin Mariela A. , Karlin‐Neumann George , Bottini Rubén , Spalding Edgar P. 
Published: October 2003

SummaryBlue light inhibits elongation of etiolated Arabidopsis thaliana hypocotyls during the first 30 min of irradiation by a mechanism that depends on the phototropin 1 (phot1) photoreceptor. The cryptochrome 1 (cry1) photoreceptor begins to exert control after 30 min. To identify genes responsible for the cry1 phase of growth inhibition, mRNA expression profiles of cry1 and wild‐type seedlings were compared using DNA microarrays. Of the roughly 420 genes found to be differentially expressed at the point of cry1 response incipience, approximately half were expressed higher and half lower in cry1 relative to the wild type. Many of the cry1‐dependent genes encoded kinases, transcription factors, cell cycle regulators, cell wall metabolism enzymes, gibberellic acid (GA) biosynthesis enzymes, and auxin response factors. High‐resolution growth studies supported the hypothesis that genes in the last two categories were indeed relevant to cry1‐mediated growth control. Inhibiting GA4 biosynthesis with a 3β‐hydroxylase inhibitor (Ca‐prohexadione) restored wild‐type response kinetics in cry1 and completely suppressed its long‐hypocotyl phenotype in blue light. Co‐treatment of cry1 seedlings with Ca‐prohexadione plus GA4 completely reversed the effects of the inhibitor, restoring the long‐hypocotyl phenotype typical of the mutant. Treatment of wild‐type seedlings with GA4 was not sufficient to phenocopy cry1 seedlings, but co‐treatment with IAA plus GA4 produced cry1‐like growth kinetics for a period of approximately 5 h. The genomic and physiological data together indicate that blue light acting through cry1 quickly affects the expression of many genes, a subset of which suppresses stem growth by repressing GA and auxin levels and/or sensitivity.
Vacuolar cation/H+ exchange, ion homeostasis, and leaf development are altered in a T‐DNA insertional mutant of AtNHX1, the Arabidopsis vacuolar Na+/H+ antiporter
Authors: Apse Maris P. , Sottosanto Jordan B. , Blumwald Eduardo 
Published: October 2003

SummaryThe function of vacuolar Na+/H+ antiporter(s) in plants has been studied primarily in the context of salinity tolerance. By facilitating the accumulation of Na+ away from the cytosol, plant cells can avert ion toxicity and also utilize vacuolar Na+ as osmoticum to maintain turgor. As many genes encoding these antiporters have been cloned from salt‐sensitive plants, it is likely that they function in some capacity other than salinity tolerance. The wide expression pattern of Arabidopsis thaliana sodium proton exchanger 1 (AtNHX1) in this study supports this hypothesis. Here, we report the isolation of a T‐DNA insertional mutant of AtNHX1, a vacuolar Na+/H+ antiporter in Arabidopsis. Vacuoles isolated from leaves of the nhx1 plants had a much lower Na+/H+ and K+/H+ exchange activity. nhx1 plants also showed an altered leaf development, with reduction in the frequency of large epidermal cells and a reduction in overall leaf area compared to wild‐type plants. The overexpression of AtNHX1 in the nhx1 background complemented these phenotypes. In the presence of NaCl, nhx1 seedling establishment was impaired. These results place AtNHX1 as the dominant K+ and Na+/H+ antiporter in leaf vacuoles in Arabidopsis and also suggest that its contribution to ion homeostasis is important for not only salinity tolerance but development as well.
Stress memory in plants: a negative regulation of stomatal response and transient induction of rd22 gene to light in abscisic acid‐entrained Arabidopsis plants
Authors: Goh Chang‐Hyo , Nam Hong Gil , Park Yu Shin 
Published: October 2003

SummaryAll organisms, including plants, perceive environmental stress, and they use this information to modify their behavior or development. Here, we demonstrate that Arabidopsis plants have memory functions related to repeated exposure to stressful concentrations of the phytohormone abscisic acid (ABA), which acts as a chemical signal. Repeated exposure of plants to ABA (40 µm for 2 h) impaired light‐induced stomatal opening or inhibited the response to a light stimulus after ABA‐entrainment under both dark/light cycle and continuous light. Moreover, there were transient expressions of the rd22 gene during the same periods under both the growing conditions. Such acquired information in ABA‐entrained plants produced a long‐term sensitization. When the time of light application was changed, a transient induction of the rd22 gene in plants after ABA‐entrainment indicated that these were light‐associated responses. These transient effects were also observed in kin1, rab18, and rd29B. The transient expression of AtNCED3, causing the accumulation of endogenous ABA, indicated a possible regulation by ABA‐dependent pathways in ABA‐entrained plants. An ABA immunoassay supported this hypothesis: ABA‐entrained plants showed a transient increase in endogenous ABA level from 220 to 250 pmol g−1 fresh mass at 1–2 h of the training period, whereas ABA‐deficient (aba2) mutants did not. Taking into account these results, we propose that plants have the ability to memorize stressful environmental experiences, and discuss the molecular events in ABA‐entrained plants.
Enhanced formation of flowers in salt‐stressed Arabidopsis after genetic engineering of the synthesis of glycine betaine
Authors: Sulpice Ronan , Tsukaya Hirokazu , Nonaka Hideko , Mustardy Laszlo , Chen Tony H. H. , Murata Norio 
Published: October 2003

SummaryPreviously, we showed that transformation with the codA gene for choline oxidase allows plants to synthesize glycine betaine (GB) and enhances their ability to tolerate various kinds of stress during germination and vegetative growth. In this study, we examined the tolerance of transformed plants to salt stress at the reproductive stage, which is the stage at which plants are most sensitive to environmental stress. Salt‐shock treatment of wild‐type plants for 3 days resulted in the abortion of flower buds and decreased the number of seeds per silique. These deleterious effects were clearly visible 6 days after the termination of salt‐shock treatment. Microscopic examination of floral structures revealed that salt stress inhibited the development of anthers, pistils, and petals. In particular, the production of pollen grains and ovules was dramatically inhibited. These effects of salt stress were significantly reduced by transformation with the codA gene, and our observations suggested that the enhanced tolerance of the transgenic plants was a result of the accumulation of GB in the reproductive organs. Indeed, levels of GB in flowers, siliques, and inflorescence apices were about five times higher than in leaves.
AtAGP30, an arabinogalactan‐protein in the cell walls of the primary root, plays a role in root regeneration and seed germination
Authors: Van Hengel Arjon J. , Roberts Keith 
Published: October 2003

SummaryArabinogalactan‐proteins (AGPs) are extracellular proteoglycans that are implicated in many plant growth and developmental processes, but in no case has a biological function been assigned to a particular AGP. AtAGP30 is a non‐classical AGP core protein from Arabidopsis that is expressed only in roots. Analysis of the corresponding mutant, agp30, has revealed that the wild‐type gene product is required in vitro for root regeneration and in planta for the timing of seed germination. The mutant shows a suppression of the abscisic acid (ABA)‐induced delay in germination and altered expression of some ABA‐regulated genes. This suggests that AtAGP30 functions in the ABA response. By analogy to proteoglycan‐mediated regulation of growth‐factor‐signalling pathways in animals, our data indicate that phytohormone activity in plants can be modulated by AGPs.
Molecular Characterization of a Strain ofSquash Leaf Curl China Virusfrom the Philippines
Authors: Kon T. , Dolores L. M. , Bajet N. B. , Hase S. , Takahashi H. , Ikegami M. 
Published: October 2003

AbstractThe complete nucleotide sequence of infectious cloned DNA components (A and B) of the causal agent of squash leaf curl disease in the Philippines was determined. DNA‐A and DNA‐B comprise 2739 and 2705 nucleotides, respectively; the common region is 174 bases in length. Five ORFs were found in DNA‐A and two in DNA‐B. Partial dimeric clones containing DNA‐A and DNA‐B, constructed in a binary vector and transformed intoAgrobacterium tumefaciens, induced systemic infection in agro‐inoculated pumpkin plants (Cucurbita moschata). The total DNA‐A sequence was most closely related to that ofSquash leaf curl China virus(SLCCNV) (88% identity), although the existence of B component of SLCCNV has not been reported. The deduced coat protein was like that of SLCCNV (98% amino acid sequence identity) and the Philippines virus has low sequence identity toSquash leaf curl virus(SLCV) andSquash mild leaf curl virus(SMLCV) (63 and 64% total nucleotide sequence identities, respectively). From these results, we propose that the Philippines virus be designatedSquash leaf curl China virus‐[Philippines] (SLCCNV‐[PH]).
Survival and Responses of Botrytis cinerea after Exposure to Ethanol and Heat
Authors: Lichter A. , Zhou H.‐W. , Vaknin M. , Dvir O. , Zutchi Y. , Kaplunov T. , Lurie S. 
Published: October 2003

AbstractDipping of table grapes in ethanol was previously shown to control bunch decay caused by Botrytis cinerea and further studies were conducted in order to quantify the effect of ethanol on the fungus. Different methods were used to determine that 30% ethanol prevented spore germination. Spores exposed to a range of temperatures, up to 49.5°C for 30 s, survived but were killed at the lethal heat dose of 46.3°C for 2 min. The combined application of ethanol and heat to ungerminated spores caused retardation of subsequent mycelial development. Ethanol or heat treatment of mature berries did not alter the expression of the gene that encodes the heat‐shock protein, HSP101 or grape berry alcohol dehydrogenase. Transcription of the heat‐shock gene, HSP104 of B. cinerea in mycelia was elevated 4 h after exposure to ethanol or heat, but not 18 h after such exposure. It is suggested that tolerance of spores to ethanol or heat may be correlated with their ability to repair damage through the action of chaperones such as HSP104.
Simplified 13C‐urea breath test with a new infrared spectrometer for diagnosis of Helicobacter pylori infection
Authors: CHEN TSENG‐SHING , CHANG FULL‐YOUNG , CHEN PANG‐CHI , HUANG THOMAS W , OU JONATHAN T , TSAI MING‐HUNG , WU MING‐SHIANG , LIN JAW‐TOWN 
Published: October 2003

AbstractBackground and Aim:  Infrared spectrometry has correlated excellently with mass spectrometry in detecting the ratio of 13CO2 to 12CO2 in breath samples. The present study aimed to evaluate the accuracy of the 13C‐urea breath test (13C‐UBT) using a new model of infrared analyzer.Methods:  A total of 600 patients who were undergoing upper endoscopy without receiving eradication therapy were entered into the study. Culture, histology, and rapid urease test on biopsies from the antrum and corpus of the stomach were used for the determination of Helicobacter pylori infection. Breath samples were collected before and 20 min after drinking 100 mg 13C‐urea in 100 mL water. The optimal cutoff value was determined by the receiver operating characteristic curve.Results:  Of the 586 patients who were eligible for analysis, 369 were positive for H. pylori infection, 185 were negative for H. pylori infection, and 32 were indeterminate. When the appropriate cutoff value was set at 3.5‰, a sensitivity of 97.8%, a specificity of 96.8% and an accuracy of 97.5% were obtained using the 13C‐UBT. The accuracy of the 13C‐UBT decreased when CO2 concentration in the breath sample was <2%, as compared with ≥2% (93.6%vs 97.7%), mainly because of a decrease in specificity (81.8%vs 97.7%). There were 2.7% of patients with Δ13CO2 values that fell between 3.0–4.5‰, in whom the risk of error was 47%.Conclusions:  The 13C‐UBT performed with infrared spectrometry is a highly sensitive, specific, and non‐invasive method for the detection of H. pylori infection. The immediate availability of the test result and technical simplicity make it particularly effective in routine clinical practice.
Effect of Helicobacter pylori eradicated therapy on water gastric emptying in patients with active duodenal ulcer
Authors: CHANG FULL‐YOUNG , LU CHING‐LIANG , CHEN CHIH‐YEN , LUO JIING‐CHYUAN , JIUM KANG LIH , LEE SHOU‐DONG 
Published: October 2003

AbstractBackground and Aims:  It remains debatable if duodenal ulcer (DU) or Helicobacter pylori infection has a definite impact on human gastric emptying (GE). We explored the nature of water GE in active DU patients before and after ulcer healing and the influence of H. pylori eradication on GE.Methods:  A home made applied potential tomography (APT) was used to measure liquid GE. Twelve electrodes were placed in a circular array around the upper abdomen of studied subjects. After drinking 500 mL of ion‐free water, paired electrodes injected electrical current and the remaining 10 electrodes recorded signals, one‐by‐one in a rotating order. Based on tomographical calculation, the serial changes of averaged signals from altered resistivities were constructed to display GE. Initially, 64 H. pylori infected active DU patients were enrolled. After APT measurement, one‐week triple therapy (omeprazole, amoxicillin and clarithromycin) was dispensed. Patients were asked back to determine ulcer/H. pylori status and GE on a scheduled date 3 months later. Finally, 58 patients finished the trial with valid and readable GE data obtained.Results:  The ulcer healing and H. pylori eradicated rates were 91.4% and 82.8%, respectively. In general, liquid GE was prolonged in all DU patients at follow up. Of 48 eradicated patients, 35.4% manifested either enhanced or delayed GE before treatment, whereas only five (10.4%) had abnormal GE after treatment (P < 0.0001). In contrast, this characteristically normalized GE was not found in non‐eradicated patients.Conclusions:  Water GE of active DU patients ranges from enhanced to delayed, while an effective H. pylori triple therapy is useful not only for healing ulcers, but also for restoring abnormal GE.
Differential diagnosis of intrahepatic bile duct dilatation without demonstrable mass on ultrasonography or CT: Benign versus malignancy
Authors: KIM HONG JOO , LEE KYU TAEK , KIM SEUNG HOON , LEE JONG KYUN , LIM JAE HOON , PAIK SEUNG WOON , RHEE JONG CHUL 
Published: October 2003

AbstractBackground:  The purpose of the present study was to define the differential diagnostic markers of benign and malignant bile duct strictures without demonstrable mass on ultrasonography (US) or computed tomography (CT) using aspects of clinical, laboratory and imaging findings.Methods:  Between February 1995 and February 2001, 24 patients who underwent surgical resection for dilations of the bile duct (peripheral and hilar) without visible mass lesion on US or CT were included in our study. Hospital records, laboratory results, findings of imaging studies and pathological findings were reviewed retrospectively.Results:  For laboratory results, levels of alkaline phosphatase (benign 163.9 ± 145.1 vs malignant 407.25 ± 481.7; p < 0.05) and CA 19–9 (benign 25.0 ± 41.1 vs malignant 614.6 ± 818.5; p < 0.05) levels were significantly elevated in the malignant group compared with that of the benign group. Findings such as thickening of the bile duct wall ≥ 5 mm (P < 0.05) on radiological examination, significant regional lymph node enlargement (> 1 cm, p = 0.01) on CT scan and abrupt cut‐off (P < 0.01), and separation of bile ducts (P < 0.05) on cholangiogram were differential diagnostic markers between the two groups.Conclusions:  Preoperative laboratory data such as alkaline phosphatase and CA 19–9, and imaging findings such as significant wall thickening and regional lymph node enlargement on CT, abrupt cut‐off and separation of bile duct on cholangiogram are useful differential diagnostic markers for benign and malignant bile duct strictures without demonstrable mass on US or CT.