Showing papers by "Ghent University published in 2002"

PlantCARE, a database of plant cis-acting regulatory elements and a portal to tools for in silico analysis of promoter sequences

Abstract: PlantCARE is a database of plant cis-acting regulatory elements, enhancers and repressors. Regulatory elements are represented by positional matrices, consensus sequences and individual sites on particular promoter sequences. Links to the EMBL, TRANSFAC and MEDLINE databases are provided when available. Data about the transcription sites are extracted mainly from the literature, supplemented with an increasing number of in silico predicted data. Apart from a general description for specific transcription factor sites, levels of confidence for the experimental evidence, functional information and the position on the promoter are given as well. New features have been implemented to search for plant cis-acting regulatory elements in a query sequence. Furthermore, links are now provided to a new clustering and motif search method to investigate clusters of co-expressed genes. New regulatory elements can be sent automatically and will be added to the database after curation. The PlantCARE relational database is available via the World Wide Web at http://sphinx.rug.ac.be:8080/PlantCARE/.

Resazurin microtiter assay plate: Simple and inexpensive method for detection of drug resistance in Mycobacterium tuberculosis

Abstract: A method for detecting multidrug-resistant Mycobacterium tuberculosis by using a reduction of resazurin is described. Eighty clinical isolates were evaluated against isoniazid and rifampin; results at 7 days were compared with those of the proportion method. Specificity and sensitivity were excellent. The method is simple, inexpensive, and rapid and might be used with other antituberculosis drugs.

Signal transduction during oxidative stress

Abstract: As an unfortunate consequence of aerobic life, active oxygen species (AOS) are formed by partial reduction of molecular oxygen. Plants possess a complex battery of enzymatic and non-enzymatic antioxidants that can protect cells from oxidative damage by scavenging AOS. It is becoming evident that AOS, which are generated during pathogen attack and abiotic stress situations, are recognized by plants as a signal for triggering defence responses. An overview of the literature is presented on the signalling role of AOS in plant defence responses, cell death, and development. Special attention is given to AOS and redox-regulated gene expression and the role of kinases and phosphatases in redox signal transduction.

Intravenous zoledronic acid in postmenopausal women with low bone mineral density.

Abstract: Background Bisphosphonates are effective agents for the management of osteoporosis. Their low bioavailability and low potency necessitate frequent administration on an empty stomach, which may reduce compliance. Gastrointestinal intolerance limits maximal dosing. Although intermittent intravenous treatments have been used, the optimal doses and dosing interval have not been systematically explored. Methods We studied the effects of five regimens of zoledronic acid, the most potent bisphosphonate, on bone turnover and density in 351 postmenopausal women with low bone mineral density in a one-year, randomized, double-blind, placebo-controlled trial. Women received placebo or intravenous zoledronic acid in doses of 0.25 mg, 0.5 mg, or 1 mg at three-month intervals. In addition, one group received a total annual dose of 4 mg as a single dose, and another received two doses of 2 mg each, six months apart. Lumbar-spine bone mineral density was the primary end point. Results There were similar increases in bone ...

The biotic ligand model : a historical overview

Abstract: During recent years, the biotic ligand model (BLM) has been proposed as a tool to evaluate quantitatively the manner in which water chemistry affects the speciation and biological availability of metals in aquatic systems. This is an important consideration because it is the bioavailability and bioreactivity of metals that control their potential to cause adverse effects. The BLM approach has gained widespread interest amongst the scientific, regulated and regulatory communities because of its potential for use in developing water quality criteria (WQC) and in performing aquatic risk assessments for metals. Specifically, the BLM does this in a way that considers the important influences of site-specific water quality. This journal issue includes papers that describe recent advances with regard to the development of the BLM approach. Here, the current status of the BLM development effort is described in the context of the longer-term history of advances in the understanding of metal interactions in the environment upon which the BLM is based. Early developments in the aquatic chemistry of metals, the physiology of aquatic organisms and aquatic toxicology are reviewed first, and the degree to which each of these disciplines influenced the development of water quality regulations is discussed. The early scientific advances that took place in each of these fields were not well coordinated, making it difficult for regulatory authorities to take full advantage of the potential utility of what had been learned. However, this has now changed, with the BLM serving as a useful interface amongst these scientific disciplines, and within the regulatory arena as well. The more recent events that have led to the present situation are reviewed, and consideration is given to some of the future needs and developments related to the BLM that are envisioned. The research results that are described in the papers found in this journal issue represent a distinct milestone in the ongoing evolution of the BLM approach and, more generally, of approaches to performing ecological assessments for metals in aquatic systems. These papers also establish a benchmark to which future scientific and regulatory developments can be compared. Finally, they demonstrate the importance and usefulness of the concept of bioavailability and of evaluative tools such as the BLM.

zt: A Sofware Tool for Simple and Partial Mantel Tests

Abstract: Different methods of data analysis (e.g. clustering and ordination) are based on distance matrices. In some cases, researchers may wish to compare several distance matrices with one another in order to test a hypothesis concerning a possible relationship between these matrices. However, this is not always self-evident. Usually, values in distance matrices are, in some way, correlated and therefore the usual assumption of independence between objects is violated in the classical tests approach. Furthermore, often, spurious correlations can be observed when comparing two distances matrices. A classic example is the comparison between genetic and environmental distances. Colonies that are in close proximity of each other tend to have similar environments and therefore there will be a positive correlation between environmental and geographical distances. Such colonies will also be more likely to exchange migrants so that genetic distances will be positively correlated with spatial distances. The consequence is that an observed positive association between genetic and environmental distances may be simply due to spatial effects. The most widely used method to account for distance correlations is a procedure known as the Mantel test (Mantel, 1967; Mantel and Valand, 1970 following the pioneering work of Daniels, 1944 ; Daniels and Kendall 1947). The simple Mantel test considers two matrices while an extension known as the partial Mantel test considers three matrices. These tools are widely used in different fields of research such as population genetics, ecology, anthropology, psychometrics and sociology.

An out-of-plane grating coupler for efficient butt-coupling between compact planar waveguides and single-mode fibers

Abstract: We have designed and fabricated an out-of-plane coupler for butt-coupling from fiber to compact planar waveguides. The coupler is based on a short second-order grating or photonic crystal, etched in a waveguide with a low-index oxide cladding. The coupler is optimized using mode expansion-based simulations. Simulations using a 2-D model show that up to 74% coupling efficiency between single-mode fiber and a 240-nm-thick GaAs-AlO/sub x/ waveguide is possible. We have measured 19% coupling efficiency on test structures.

Key roles of pH and calcium metabolism in microbial carbonate precipitation

Abstract: This paper reviews the general mechanismsof microbial carbonate precipitation and offersan alternative view on the role of calciummetabolism in this process, as well as on theoccurrence of species- and environment-specificcalcification.

Four qubits can be entangled in nine different ways

Abstract: We consider a single copy of a pure four-partite state of qubits and investigate its behavior under the action of stochastic local quantum operations assisted by classical communication (SLOCC). This leads to a complete classification of all different classes of pure states of four qubits. It is shown that there exist nine families of states corresponding to nine different ways of entangling four qubits. The states in the generic family give rise to Greenberger-Horne-Zeilinger-like entanglement. The other ones contain essentially two-or three-qubit entanglement distributed among the four parties. The concept of concurrence and 3-tangle is generalized to the case of mixed states of four qubits, giving rise to a seven-parameter family of entanglement monotones. Finally, the SLOCC operations maximizing all these entanglement monotones are derived, yielding the optimal single-copy distillation protocol.

The role of mitochondrial factors in apoptosis: a Russian roulette with more than one bullet.

Abstract: Mitochondria are 'life-essential' organelles for the production of metabolic energy in the form of ATP. Paradoxically mitochondria also play a key role in controlling the pathways that lead to cell death. This latter role of mitochondria is more than just a 'loss of function' resulting in an energy deficit but is an active process involving different mitochondrial proteins. Cytochrome c was the first characterised mitochondrial factor shown to be released from the mitochondrial intermembrane space and to be actively implicated in apoptotic cell death. Since then, other mitochondrial proteins, such as AIF, Smac/DIABLO, endonuclease G and Omi/HtrA2, were found to undergo release during apoptosis and have been implicated in various aspects of the cell death process. Members of the Bcl-2 protein family control the integrity and response of mitochondria to apoptotic signals. The molecular mechanism by which mitochondrial intermembrane space proteins are released and the regulation of mitochondrial homeostasis by Bcl-2 proteins is still elusive. This review summarises and evaluates the current knowledge concerning the complex role of released mitochondrial proteins in the apoptotic process.

Genome-Wide Analysis of Core Cell Cycle Genes in Arabidopsis

Abstract: Cyclin-dependent kinases and cyclins regulate with the help of different interacting proteins the progression through the eukaryotic cell cycle. A high-quality, homology-based annotation protocol was applied to determine the core cell cycle genes in the recently completed Arabidopsis genome sequence. In total, 61 genes were identified belonging to seven selected families of cell cycle regulators, for which 30 are new or corrections of the existing annotation. A new class of putative cell cycle regulators was found that probably are competitors of E2F/DP transcription factors, which mediate the G1-to-S progression. In addition, the existing nomenclature for cell cycle genes of Arabidopsis was updated, and the physical positions of all genes were compared with segmentally duplicated blocks in the genome, showing that 22 core cell cycle genes emerged through block duplications. This genome-wide analysis illustrates the complexity of the plant cell cycle machinery and provides a tool for elucidating the function of new family members in the future.

Auxin-Mediated Cell Cycle Activation during Early Lateral Root Initiation

Abstract: Lateral root formation can be divided into two major phases: pericycle activation and meristem establishment. In Arabidopsis, the first lateral root initiation event is spatially and temporally asynchronous and involves a limited number of cells in the xylem pericycle. To study the molecular regulation during pericycle activation, we developed a lateral root–inducible system. Successive treatments with an auxin transport inhibitor and exogenous auxin were used to prevent the first formative divisions and then to activate the entire pericycle. Our morphological and molecular data show that, in this inducible system, xylem pericycle activation was synchronized and enhanced to cover the entire length of the root. The results also indicate that the inducible system can be considered a novel in planta system for the study of synchronized cell cycle reactivation. In addition, the expression patterns of Kip-Related Protein2 (KRP2) in the pericycle and its ectopic expression data revealed that the cyclin-dependent kinase inhibitor plays a significant role in the regulation of lateral root initiation. KRP2 appears to regulate early lateral root initiation by blocking the G1-to-S transition and to be regulated transcriptionally by auxin.

Identification by redox proteomics of glutathionylated proteins in oxidatively stressed human T lymphocytes.

Abstract: Formation of mixed disulfides between glutathione and the cysteines of some proteins (glutathionylation) has been suggested as a mechanism through which protein functions can be regulated by the redox status. The aim of this study was to identify the proteins of T cell blasts that undergo glutathionylation under oxidative stress. To this purpose, we radiolabeled cellular glutathione with 35S, exposed T cells to oxidants (diamide or hydrogen peroxide), and performed nonreducing, two-dimensional electrophoresis followed by detection of labeled proteins by phosphorimaging and their identification by mass spectrometry techniques. We detected several proteins previously not recognized to be glutathionylated, including cytoskeletal proteins (vimentin, myosin, tropomyosin, cofilin, profilin, and the already known actin), enzymes (enolase, aldolase, 6-phosphogluconolactonase, adenylate kinase, ubiquitin-conjugating enzyme, phosphoglycerate kinase, triosephosphate isomerase, and pyrophosphatase), redox enzymes (peroxiredoxin 1, protein disulfide isomerase, and cytochrome c oxidase), cyclophilin, stress proteins (HSP70 and HSP60), nucleophosmin, transgelin, galectin, and fatty acid binding protein. Based on the presence of several protein isoforms in control cells, we suggest that enolase and cyclophilin are heavily glutathionylated under basal conditions. We studied the effect of glutathionylation on some of the enzymes identified in the present study and found that some of them (enolase and 6-phosphogluconolactonase) are inhibited by glutathionylation, whereas the enzymatic activity of cyclophilin (peptidylprolyl isomerase) is not. These findings suggest that protein glutathionylation might be a common mechanism for the global regulation of protein functions.

Cost and Profit Efficiency of Financial Conglomerates and Universal Banks in Europe

Abstract: In contrast to the United States, where the banking system has historically been fragmented, the Second Banking Directive allows European banks both to form financial conglomerates and hold equity stakes in nonfinancial companies. This paper analyzes the cost and profit efficiency of European financial conglomerates and universal banks. I find that conglomerates are more revenue efficient than their specialized competitors and that the degree of both cost and profit efficiency is higher in universal banks than in nonuniversal banks. These results indicate that the current trend toward further de-specialization may lead to a more efficient banking system. An investigation of the equity betas under varying business cycle conditions supports the hypothesis of superior monitoring capabilities on the part of universal banks. Finally, profit regressions suggest that operational efficiency has become the major determinant of bank profitability and that oligopolistic rents have become less prevalent in European banking.

A novel role for p120 catenin in E-cadherin function.

Abstract: Indirect evidence suggests that p120-catenin (p120) can both positively and negatively affect cadherin adhesiveness. Here we show that the p120 gene is mutated in SW48 cells, and that the cadherin adhesion system is impaired as a direct consequence of p120 insufficiency. Restoring normal levels of p120 caused a striking reversion from poorly differentiated to cobblestone-like epithelial morphology, indicating a crucial role for p120 in reactivation of E-cadherin function. The rescue efficiency was enhanced by increased levels of p120, and reduced by the presence of the phosphorylation domain, a region previously postulated to confer negative regulation. Surprisingly, the rescue was associated with substantially increased levels of E-cadherin. E-cadherin mRNA levels were unaffected by p120 expression, but E-cadherin half-life was more than doubled. Direct p120-E-cadherin interaction was crucial, as p120 deletion analysis revealed a perfect correlation between E-cadherin binding and rescue of epithelial morphology. Interestingly, the epithelial morphology could also be rescued by forced expression of either WT E-cadherin or a p120-uncoupled mutant. Thus, the effects of uncoupling p120 from E-cadherin can be at least partially overcome by artificially maintaining high levels of cadherin expression. These data reveal a cooperative interaction between p120 and E-cadherin and a novel role for p120 that is likely indispensable in normal cells.

The hidden duplication past of Arabidopsis thaliana

Abstract: Analysis of the genome sequence of Arabidopsis thaliana shows that this genome, like that of many other eukaryotic organisms, has undergone large-scale gene duplications or even duplications of the entire genome. However, the high frequency of gene loss after duplication events reduces colinearity and therefore the chance of finding duplicated regions that, at the extreme, no longer share homologous genes. In this study we show that heavily degenerated block duplications that can no longer be recognized by directly comparing two segments because of differential gene loss, can still be detected through indirect comparison with other segments. When these so-called hidden duplications in Arabidopsis are taken into account, many homologous genomic regions can be found in five to eight copies. This finding strongly implies that Arabidopsis has undergone three, but probably no more, rounds of genome duplications. Therefore, adding such hidden blocks to the duplication landscape of Arabidopsis sheds light on the number of polyploidy events that this model plant genome has undergone in its evolutionary past.

A confirmatory factor analysis of the Pain Catastrophizing Scale: invariant factor structure across clinical and non-clinical populations.

Abstract: This study examined the factor structure of the Pain Catastrophizing Scale in three different Dutch-speaking samples: 550 pain-free students, 162 chronic low back pain patients, and 100 fibromyalgia patients. Confirmatory factor analyses were used to compare three different models of pain catastrophizing (one factor, two oblique factors, three oblique factors), and to investigate the invariance of the factor structure across the three different samples. The results indicated that a three-factor oblique model with a four-item rumination factor, a three-item magnification factor, and a six-item helplessness factor provided the best fit to the data in the three samples. Furthermore, it was found that this model could be considered as invariant across three samples (pain-free students, chronic low back pain patients, and fibromyalgia patients) and across gender, indicating that the same processes are measured in different subgroups.

Abscisic acid determines basal susceptibility of tomato to Botrytis cinerea and suppresses salicylic acid-dependent signaling mechanisms.

Abstract: Abscisic acid (ABA) is one of the plant hormones involved in the interaction between plants and pathogens. In this work, we show that tomato (Lycopersicon esculentum Mill. cv Moneymaker) mutants with reduced ABA levels (sitiens plants) are much more resistant to the necrotrophic fungus Botrytis cinerea than wild-type (WT) plants. Exogenous application of ABA restored susceptibility to B. cinerea in sitiens plants and increased susceptibility in WT plants. These results indicate that ABA plays a major role in the susceptibility of tomato to B. cinerea. ABA appeared to interact with a functional plant defense response against B. cinerea. Experiments with transgenic NahG tomato plants and benzo(1,2,3)thiadiazole-7-carbothioic acid demonstrated the importance of salicylic acid in the tomato-B. cinerea interaction. In addition, upon infection with B. cinerea, sitiens plants showed a clear increase in phenylalanine ammonia lyase activity, which was not observed in infected WT plants, indicating that the ABA levels in healthy WT tomato plants partly repress phenylalanine ammonia lyase activity. In addition, sitiens plants became more sensitive to benzo(1,2,3)thiadiazole-7-carbothioic acid root treatment. The threshold values for PR1a gene expression declined with a factor 10 to 100 in sitiens compared with WT plants. Thus, ABA appears to negatively modulate the salicylic acid-dependent defense pathway in tomato, which may be one of the mechanisms by which ABA levels determine susceptibility to B. cinerea.

Consultation length in general practice: cross sectional study in six European countries

Abstract: Objectives: To compare determinants of consultation length discussed in the literature with those found in consultations with general practitioners from different European countries; to explore the determinants of consultation length, particularly the effect of doctors9 and patients9 perceptions of psychosocial aspects. Design: Analysis of videotaped consultations of general practitioners from the Eurocommunication study and of questionnaires completed by doctors and by patients. Setting: General practices in six European countries. Participants: 190 general practitioners and 3674 patients. Results: In a multilevel analysis with three levels (country, general practitioner, and patient), country and doctor variables contributed a similar amount to the total variance in consultation length (23% and 22%, respectively) and patient variables accounted for 55% of the variance. The variables used in the multilevel analysis explained 25% of the total variation. The country in which the doctor practised, combined with the doctors9 variables, was as important for the variance in consultation length as the variation between patients. Consultations in which psychosocial problems were considered important by the doctor and the patient lasted longer than consultations about biomedical problems only. The doctor9s perception had more influence in this situation than the patient9s. Consultation length is influenced by the patients9 sex (women got longer consultations), whether the practice was urban or rural, the number of new problems discussed in the consultation (the more problems the longer the consultation), and the patient9s age (the older the patient the longer the consultation). As a doctor9s workload increased, the length of consultations decreased. The general practitioner9s sex or age and patient9s level of education were not related to the length of consultation. Conclusion: Consultation length is determined by variables related to the doctor and the doctor9s country as well as by those related to patients. Women consulting in an urban practice with problems perceived as psychosocial have longer consultations than other patients.

A biotic ligand model predicting acute copper toxicity for Daphnia magna: the effects of calcium, magnesium, sodium, potassium, and pH.

Abstract: The extent to which Ca2+, Mg2+, Na+, K+ ions and pH independently mitigate acute copper toxicity for the cladoceran Daphnia magna was examined. Higher activities of Ca2+, Mg2+, and Na+ (but not K+) linearly increased the 48-h EC50 (as Cu2+ activity), supporting the concept of competitive binding of these ions and copper ions to toxic action or transport sites at the organism−water interface (e.g. fish gill, the biotic ligand). The increase of the EC50 (as Cu2+ activity) with increasing H+, however, seemed to suggest cotoxicity of CuOH+ rather than proton competition. Based on the biotic ligand model (BLM) concept, we developed a methodology to estimate stability constants for the binding of Cu2+, CuOH+, Ca2+, Mg2+, Na+, and H+ to the biotic ligand, solely based on toxicity data. Following values were obtained: log KCuBL = 8.02, log KCuOHBL= 7.45, log KCaBL = 3.47, log KMgBL = 3.58, log KNaBL = 3.19, and log KHBL ∼ 5.4. Further, we calculated that on average 39% of the biotic ligand sites need to be occup...

Proprioception and muscle strength in subjects with a history of ankle sprains and chronic instability

Abstract: OBJECTIVE: To examine if patients with chronic ankle instability or a history of ankle sprains without chronic instability have worse proprioception or less invertor and evertor muscle strength. DESIGN AND SETTING: We assessed proprioception and muscle strength on the Biodex isokinetic dynamometer in the laboratory of the Department of Sports Medicine, University Hospital Ghent. SUBJECTS: Subjects included 87 physical education students (44 men, 43 women, age = 18.33 +/- 1.25 years, mass = 66.09 +/- 8.11 kg, height = 174.11 +/- 8.57 cm) at the University of Ghent in Belgium. Their ankles were divided into 4 groups: a symptom-free control group, subjects with chronic ankle instability, subjects who had sustained an ankle sprain in the last 2 years without instability, and subjects who sustained an ankle sprain 3 to 5 years earlier without instability. MEASUREMENTS: Active and passive joint-position sense was assessed at the ankle, and isokinetic peak torque was determined for concentric and eccentric eversion and inversion movements at the ankle. RESULTS: Statistical analysis indicated significantly less accurate active position sense for the instability group compared with the control group at a position close to maximal inversion. The instability group also showed a significantly lower relative eversion muscle strength (% body weight). No significant differences were observed between the control group and the groups with past sprains without instability. CONCLUSIONS: We suggest that the possible cause of chronic ankle instability is a combination of diminished proprioception and evertor muscle weakness. Therefore, we emphasize proprioception and strength training in the rehabilitation program for ankle instability.

Water‐soluble organic compounds in biomass burning aerosols over Amazonia 1. Characterization by NMR and GC‐MS

Abstract: [1] As part of the European contribution to the Large-Scale Atmosphere-Biosphere Experiment in Amazonia (LBA-EUSTACH), aerosols were sampled at representative pasture and primary rainforest sites in Rondonia, Brazil, during the 1999 “burning season” and dry-to-wet season transition (September-October). Water-soluble organic compounds (WSOCs) within the samples were characterized using a combination of 1H Nuclear Magnetic Resonance (NMR) spectroscopy for chemical functional group analysis, and Gas Chromatography-Mass Spectrometry (GC-MS) for identification and quantification of individual low-molecular-weight compounds. The 1H NMR analysis indicates that WSOCs are predominantly aliphatic or oxygenated aliphatic compounds (alcohols, carboxylic acids, etc.), with a minor content of aromatic rings carrying carboxylic and phenolic groups. Levoglucosan (1,6-anhydro-β-D-glucose), a well-known cellulose combustion product, was the most abundant individual compound identified by GC-MS (0.04–6.90 μg m−3), accounting for 1–6% of the total carbon (TC) and 2–8% of the water-soluble organic carbon (WSOC). Other anhydrosugars, produced by hemicellulose breakdown, were detected in much smaller amounts, in addition to series of acids, hydroxyacids, oxoacids, and polyalcohols (altogether 2–5% of TC, 3–6% of WSOC). Most correlated well with organic carbon, black carbon, and potassium, indicating biomass burning to be the major source. A series of sugar alcohols (mannitol, arabitol, erythritol) and sugars (glucose, fructose, mannose, galactose, sucrose, trehalose) were identified as part of the natural background aerosol and are probably derived from airborne microbes and other biogenic material. The bulk of the WSOCs (86–91% WSOC) eluded analysis by GC-MS and may be predominantly high-molecular weight in nature.