bluuebunny/crossref_metadata_2025_split huggingface dataset:
A Gene Regulatory Network Model for Cell-Fate Determination duringArabidopsis thalianaFlower Development That Is Robust and Recovers Experimental Gene Expression Profiles[W]
Authors: Espinosa-Soto Carlos , Padilla-Longoria Pablo , Alvarez-Buylla Elena R. 
Published: November 2004

AbstractFlowers are icons in developmental studies of complex structures. The vast majority of 250,000 angiosperm plant species have flowers with a conserved organ plan bearing sepals, petals, stamens, and carpels in the center. The combinatorial model for the activity of the so-called ABC homeotic floral genes has guided extensive experimental studies in Arabidopsis thaliana and many other plant species. However, a mechanistic and dynamical explanation for the ABC model and prevalence among flowering plants is lacking. Here, we put forward a simple discrete model that postulates logical rules that formally summarize published ABC and non-ABC gene interaction data for Arabidopsis floral organ cell fate determination and integrates this data into a dynamic network model. This model shows that all possible initial conditions converge to few steady gene activity states that match gene expression profiles observed experimentally in primordial floral organ cells of wild-type and mutant plants. Therefore, the network proposed here provides a dynamical explanation for the ABC model and shows that precise signaling pathways are not required to restrain cell types to those found in Arabidopsis, but these are rather determined by the overall gene network dynamics. Furthermore, we performed robustness analyses that clearly show that the cell types recovered depend on the network architecture rather than on specific values of the model's gene interaction parameters. These results support the hypothesis that such a network constitutes a developmental module, and hence provide a possible explanation for the overall conservation of the ABC model and overall floral plan among angiosperms. In addition, we have been able to predict the effects of differences in network architecture between Arabidopsis and Petunia hybrida.
Structure-Function Analysis of the Presumptive Arabidopsis Auxin Permease AUX1[W]
Authors: Swarup Ranjan , Kargul Joanna , Marchant Alan , Zadik Daniel , Rahman Abidur , Mills Rebecca , Yemm Anthony , May Sean , Williams Lorraine , Millner Paul , Tsurumi Seiji , Moore Ian , Napier Richard , Kerr Ian D. , Bennett Malcolm J. 
Published: November 2004

AbstractWe have investigated the subcellular localization, the domain topology, and the amino acid residues that are critical for the function of the presumptive Arabidopsis thaliana auxin influx carrier AUX1. Biochemical fractionation experiments and confocal studies using an N-terminal yellow fluorescent protein (YFP) fusion observed that AUX1 colocalized with plasma membrane (PM) markers. Because of its PM localization, we were able to take advantage of the steep pH gradient that exists across the plant cell PM to investigate AUX1 topology using YFP as a pH-sensitive probe. The YFP-coding sequence was inserted in selected AUX1 hydrophilic loops to orient surface domains on either apoplastic or cytoplasmic faces of the PM based on the absence or presence of YFP fluorescence, respectively. We were able to demonstrate in conjunction with helix prediction programs that AUX1 represents a polytopic membrane protein composed of 11 transmembrane spanning domains. In parallel, a large aux1 allelic series containing null, partial-loss-of-function, and conditional mutations was characterized to identify the functionally important domains and amino acid residues within the AUX1 polypeptide. Whereas almost all partial-loss-of-function and null alleles cluster in the core permease region, the sole conditional allele aux1-7 modifies the function of the external C-terminal domain.
A Puromycin-Sensitive Aminopeptidase Is Essential for Meiosis inArabidopsis thaliana [W]
Authors: Saénchez-Moraén Eugenio , Jones Gareth H. , Franklin F. Christopher H. , Santos Juan Luis 
Published: November 2004

AbstractPuromycin-sensitive aminopeptidases (PSAs) participate in a variety of proteolytic events essential for cell growth and viability, and in fertility in a broad range of organisms. We have identified and characterized an Arabidopsis thaliana mutant (mpa1) from a pool of T-DNA tagged lines that lacks PSA activity. This line exhibits reduced fertility, producing shorter siliques (fruits) bearing a lower number of seeds compared with wild-type plants. Cytogenetic characterization of meiosis in the mutant line reveals that both male and female meiosis are defective. In mpa1, early prophase I appears normal, but after pachytene most of the homologous chromosomes are desynaptic, thus, by metaphase I a high level of univalence is observed subsequently leading to abnormal chromosome segregation. Wild-type plants treated with specific inhibitors of PSA show a very similar desynaptic phenotype to that of the mutant line. A fluorescent PSA-specific bioprobe, DAMPAQ-22, reveals that the protein is maximally expressed in wild-type meiocytes during prophase I and is absent in mpa1. Immunolocalization of meiotic proteins showed that the meiotic recombination pathway is disrupted in mpa1. Chromosome pairing and early recombination appears normal, but progression to later stages of recombination and complete synapsis of homologous chromosomes are blocked.
A Mechanism Related to the Yeast Transcriptional Regulator Paf1c Is Required for Expression of the ArabidopsisFLC/MAFMADS Box Gene Family[W]
Authors: Oh Sookyung , Zhang Hua , Ludwig Philip , van Nocker Steven 
Published: November 2004

AbstractThe Arabidopsis thaliana VERNALIZATION INDEPENDENCE (VIP) gene class has multiple functions in development, including repression of flowering through activation of the MADSbox gene FLC. Epigenetic silencing of FLC plays a substantial role in the promotion of flowering through cold (vernalization). To better understand how VIP genes influence development, we undertook a genetic and molecular study of the previously uncharacterized VIP5 and VIP6 genes. We found that loss of function of these genes also resulted in downregulation of other members of the FLC/MAF gene family, including the photoperiodic pathway regulator MAF1/FLM. We cloned VIP5 and VIP6 through mapping and transcriptional profiling. Both proteins are closely related to distinct components of budding yeast Paf1C, a transcription factor that assists in establishment and maintenance of transcription-promotive chromatin modifications such as ubiquitination of H2B by Bre1/Rad6 and methylation of histone H3 lysine-4 by the trithorax-related histone methylase Set1. Genetic analysis and coimmunoprecipitation experiments suggest that VIP5 and VIP6 function in the same mechanism as the previously described VIP3 and VIP4. Our findings suggest that an evolutionarily conserved transcriptional mechanism plays an essential role in the maintenance of gene expression in higher eukaryotes and has a central function in flowering.
Rapid hip bone loss in active Crohn's disease patients receiving short‐term corticosteroid therapy
Authors: Tobias J. H. , Sasi M. R. , Greenwood R. , Probert C. S. J. 
Published: November 2004

SummaryBackground : Uncertainty over whether corticosteroids cause bone loss in patients with Crohn's disease may reflect their short, intermittent use.Aim : We investigated whether a 2‐month course of prednisolone is associated with detectable bone loss.Methods : Fifteen patients with active Crohn's disease and 19 controls with inactive Crohn's disease were recruited. Bone mineral density of the lumbar spine and hip was measured at baseline and 2 and 8 months.Results : At 2 months, significant bone loss was found in patients with active disease (femoral neck −2.7%, P < 0.002; Ward's triangle −3.9%, P < 0.01). Although bone mineral density was still lower at 8 months, these differences were no longer significant (−1.3% and −3.4%, femoral neck and Ward's triangle, respectively). No significant change in hip bone mineral density was observed in controls. Previous corticosteroid use was not significantly associated with baseline bone mineral density, although significant independent associations were observed between weight, site of disease and lumbar spine bone mineral density, and between dietary calcium deficiency and femoral neck and Ward's triangle bone mineral density.Conclusion : Significant bone loss at the hip can be detected in patients receiving corticosteroid treatment for 2 months for active Crohn's disease ; however, it remains unclear whether this is because of disease activity or its treatment. This rapid bone loss may represent a risk factor for fracture and justify bone protective therapy.
The new DR‐70 immunoassay detects cancer of the gastrointestinal tract: a validation study
Authors: Kerber A. , Trojan J. , Herrlinger K. , Zgouras D. , Caspary W. F. , Braden B. 
Published: November 2004

SummaryBackground : Malignant cells characteristically possess high levels of plasminogen activator, which induce local fibrinolysis. The DR‐70 immunoassay is a newly developed test, which quantifies fibrin degradation products in serum by a proprietary antibody.Aim : To evaluate the DR‐70 immunoassay as a detection assay for the presence of gastrointestinal cancers.Methods : We prospectively collected blood sera of 85 patients with histologically proven tumour and 100 healthy blood donors. Ten microlitres of the sera was used for the DR‐70 immunoassay. Nineteen patients had a hepatocellular and 10 cholangiocellular carcinoma, 13 cancer of the pancreas, 30 colorectal cancer, 10 stomach cancer and three cancer of the oesophagus.Results : Receiver–operator curve analysis revealed <0.7 μg/mL as the best cut‐off value to distinguish between patients with cancer and healthy controls. Using this cut‐off value, the DR‐70 immunoassay showed a good clinical performance with a sensitivity of 91% and a specificity of 93%. Patients with advanced tumour spread showed significantly higher DR‐70 values than those with early‐stage tumours (P < 0.0003).Conclusion : The DR‐70 immunoassay reliably differs between cancer patients and healthy controls. Therefore, it promises to become a useful test for the detection of cancer in clinical practice.
Clinical and functional responses to salbutamol inhaled via different devices in asthmatic patients with induced bronchoconstriction
Authors: Lavorini Federico , Geri Pietro , Luperini Martina , Maluccio Nazzarena M. , Mariani Laura , Marmai Cecilia , Pistolesi Massimo , Fontana Giovanni A. 
Published: November 2004

AimsThis study aimed at evaluating changes in airway patency, lung volumes and perception of breathing discomfort intensity following salbutamol administration via the Diskus dry‐powder inhaler (DPI) or a pressurized metered‐dose inhaler with the Volumatic valved holding chamber (pMDI + Volumatic) in asthmatic patients with methacholine‐induced bronchoconstriction.MethodsOn six different study days, 18 patients inhaled methacholine until forced expiratory volume in 1 s (FEV1) decreased by approximately 35% of baseline. Following placebo, 200 and 400 µg of salbutamol through the pMDI + Volumatic or the Diskus, changes in FEV1, volume‐adjusted mean forced expiratory flow from 25 to 75% of the forced vital capacity (isoFEF25−75), lung volumes and breathing discomfort intensity, assessed by visual analogue scale (VAS) score, were repeatedly measured over a 60‐min observation period.ResultsInduced bronchoconstriction was accompanied by obvious reductions in lung volumes and increases in VAS score. After salbutamol administration, FEV1 and VAS score changes were similar in all experimental conditions. However, following 400 µg salbutamol via pMDI + Volumatic, isoFEF25−75 values increased up to 4.48 l s−1 (95% confidence interval 4.06, 4.90), a significantly (P < 0.01) higher value than those attained in all other experimental conditions. Independently of the salbutamol dose, lung volumes rose to significantly (P < 0.01) higher levels in pMDI + Volumatic than in Diskus trials. The low salbutamol dose via the pMDI + Volumatic and the high dose via the DPI increased isoFEF25−75 and lung volumes to similar extents.ConclusionsSalbutamol via the pMDI + Volumatic provides greater isoFEF25−75 and lung volume increases in asthmatic patients with induced bronchoconstriction; salbutamol‐induced changes in VAS scores poorly reflect those in small airway patency. The lack of differences in FEV1 increases observed after 200 and 400 µg salbutamol may reflect attainment of the flat portion of the dose–response curve using either device.
Internet based clinical trial protocols – as applied to a study of warfarin pharmacogenetics
Authors: Lindh Jonatan D. , Kublickas Marius , Westgren Magnus , Rane Anders 
Published: November 2004

AimsTo describe and evaluate the use of an Internet‐based study protocol in a multicentre study of genetic risk factors in anticoagulant treatment.MethodsA web‐based study protocol, similar to existing anticoagulation medical record systems, was developed for entry of clinical data. It was also supplied with a separate interface for study monitoring. Measures were taken to assure the confidentiality of transferred data. In addition, software modifications were made to enable automated transfer of clinical data from an existing medical record system to the study database.ResultsThe system has been in use since March 2002, and at present 39 centres have included 909 patients with a dropout rate of 2.8%. The need for education of participating clinicians has been satisfactorily provided for by means of written instructions and telephone support.ConclusionsOur study demonstrates the usability of Internet‐based data acquisition techniques in a full‐scale multicentre clinical trial. The main advantages of such a protocol are automated data validation and standardization, fast data transfer independent of geographical distance, user feedback, synchronization of protocol updates and automatic data formatting facilitating statistical analyses. Safety and accessibility are possibly cumbersome areas and should be addressed duly.
Detection of p53 dysfunction by flow cytometry in chronic lymphocytic leukaemia
Authors: Carter A. , Lin K. , Sherrington P. D. , Pettitt A. R. 
Published: November 2004

SummaryIn chronic lymphocytic leukaemia (CLL) cells, functional impairment of the p53 pathway is detectable by Western blotting as impaired up‐regulation of p21 (a transcriptional target of p53) in response to ionizing radiation (IR). The type A defect is characterized by baseline p53 overexpression and is associated with TP53 mutation. The type B defect is characterized by impaired IR‐induced p53 up‐regulation and is associated with inactivation of the ataxia telangiectasia‐mutated gene (ATM). Both abnormalities are strongly associated with adverse clinical outcome. In the present study, flow cytometry was found to be an effective alternative to Western blotting in the detection of p53 dysfunction in CLL.
CD40 stimulation of B‐cell chronic lymphocytic leukaemia cells enhances the anti‐apoptotic profile, but also Bid expression and cells remain susceptible to autologous cytotoxic T‐lymphocyte attack
Authors: Kater Arnon P. , Evers Ludo M. , Remmerswaal Ester B. M. , Jaspers Annelieke , Oosterwijk Michiel F. , van Lier René A. W. , van Oers Marinus H. J. , Eldering Eric 
Published: November 2004

SummaryTo enhance the poor antigen‐presenting capacity of B‐cell chronic lymphocytic leukaemia (B‐CLL), CD40 triggering has been considered as an active immunotherapy. However, CD40 stimulation also has an anti‐apoptotic effect and may further impair the dysregulated response of B‐CLL to apoptotic stimuli. Therefore, we measured the expression of virtually all regulators of apoptosis before and after CD40 stimulation. These findings were correlated with sensitivity for chemotherapy‐ and death‐receptor‐induced apoptosis and T‐cell‐mediated killing. CD40 stimulation enhanced the constitutive anti‐apoptotic profile of B‐CLL cells by upregulation of Bcl‐xL and Bfl‐1 and downregulation of the BH3‐only protein Harakiri. Unexpectedly, the BH3‐only protein Bid was strongly induced. Functionally, CD40‐stimulated B‐CLL cells became resistant to drug‐induced apoptosis and, despite upregulation of CD95 and Bid, were not sensitive to CD95L. In contrast, autologous T cell killing, triggered by loading CLL cells with viral (CMV) peptides, was very efficient both before and after CD40 stimulation. Upon CTL interaction, CLL targets underwent mitochondrial depolarization and caspase‐3 activation. Thus, despite an increased anti‐apoptotic profile, CD40 triggered B‐CLL cells remain excellent targets for resident cytotoxic T cells. These data support therapeutic exploitation of CD40 stimulation in B‐CLL, provided that a strong CTL component is induced.
Clinical features, diagnosis, treatment and molecular studies in paediatric Cushing's syndrome due to primary nodular adrenocortical hyperplasia
Authors: Storr H. L. , Mitchell H. , Swords F. M. , Main K. M. , Hindmarsh P. C. , Betts P. R. , Shaw N. J. , Johnston D. I. , Clark A. J. L. , Reznek R. H. , Grossman A. B. , Savage M. O. 
Published: November 2004

Summarybackground  Primary nodular adrenocortical hyperplasia (PNAH) is a well recognized, but infrequently studied cause of paediatric Cushing's syndrome (CS).objective  To assess presentation, diagnosis, radiological imaging, treatment and molecular analysis of patients with childhood‐onset CS due to PNAH.patients  Four males and two females (median age 12·9 years, range 10·9–16·9 years) were studied.results  All had growth failure (mean height SDS −1·2; range −2·5–0·0), weight gain [mean body mass index (BMI) SDS 3·5; range 2·5–4·6] and clinical virilization, while five had hypertension [mean systolic blood pressure (SBP) 130 mmHg, diastolic blood pressure (DBP) 83 mmHg]. One patient had generalized lentigines, one had a tibial chondromyxomatous cyst and two had facial freckling. One patient had a family history of primary nodular adrenocortical disease. The diagnosis of CS was based on elevation of sleeping midnight serum cortisol and urinary free cortisol excretion, and impaired suppression of cortisol on both low‐ and high‐dose dexamethasone suppression tests (DST). All patients had undetectable plasma ACTH with absent responses of both plasma ACTH and serum cortisol to an intravenous (i.v.) corticotrophin‐releasing hormone (CRH) test. Computed tomography or magnetic resonance imaging showed normal or small adrenals, with nodules in two patients. All patients underwent bilateral adrenalectomy, performed by open (n = 2) or laparoscopic surgery (n = 4) at a mean of 0·4 years (range 0·2–0·8 years) from diagnosis. Hypercortisolaemia was treated preoperatively by metyrapone alone 0·50–0·75 g/day (n = 4), metyrapone 0·75–1·50 g/day + o’p'DDD/mitotane 1–2 g/day (n = 1), or ketoconazole (n = 1). Adrenal histology showed nodular cortical hyperplasia with shrinkage of intervening cortical tissue and pigmentation, present in four patients. Molecular analysis of the type 1‐α regulatory subunit of protein kinase A (PRKAR1A) gene revealed a novel germline mutation in one patient. Postadrenalectomy, three patients, had catch‐up growth with height velocities increasing from 3·0, 3·9 and 2·5–8·9, 8·3 and 9·0 cm/years, respectively. All six are well at a follow‐up (mean 4·0 years; range 0·5–10·8 years).conclusions  PNAH was associated with cushingoid features, virilization and hypertension with a lack of cortisol suppression on high DST, undetectable plasma ACTH and absent cortisol and ACTH responses to CRH. Adrenals were normal or small on imaging. PRKAR1A gene analysis may be helpful in the assessment of these patients.
Characterization of a promoter polymorphism in the glucocorticoid receptor gene and its relationship to three other polymorphisms
Authors: Van Rossum Elisabeth F. C. , Roks Petronella H. M. , De Jong Frank H. , Brinkmann Albert O. , Pols Huib A. P. , Koper Jan W. , Lamberts Steven W. J. 
Published: November 2004

Summaryobjective  Sensitivity to glucocorticoids within the normal population is highly variable and partly determined by polymorphisms in the glucocorticoid receptor (GR) gene (NR3C1). We investigated the exact sequence alteration of a TthIIII polymorphism in the GR gene, whether it is associated with glucocorticoid sensitivity, and its relationship to 3 polymorphisms of the GR gene (N363S, BclI, ER22/23EK).design  Two dexamethasone (DEX) suppression tests were performed with 1 and 0·25 mg DEX, respectively.patients  We genotyped a random subgroup of 209 participants of the Rotterdam Study, a population‐based study in the elderly.measurements  Anthropometric parameters, cortisol, insulin and glucose levels, and lipid concentrations were measured.results  We identified the TthIIII polymorphism as a C to T mutation, 3807 bp upstream from the mRNA start site. We found 39·7% CC‐carriers, 44·5% CT‐carriers, and 15·8 % TT‐carriers. No differences were found between TthIIII genotypes in sensitivity to DEX, baseline cortisol, insulin, glucose or cholesterol levels, or in anthropometric variables. However, all ER22/23EK‐carriers also carried the TthIIII T‐allele, and carriers of both these polymorphisms had a significantly smaller cortisol suppression after 1 mg DEX, lower fasting insulin levels, and lower total and low‐density lipoprotein (LDL) cholesterol levels than TthIIII T carriers without the ER22/23EK variant and noncarriers. No interaction was found between the TthIIII variant and N363S or BclI polymorphisms.conclusions  The TthIIII polymorphism is not functional by itself. However, the ER22/23EK polymorphism is without exception linked to the TthIIII T polymorphism and this haplotype is associated with a relative resistance to glucocorticoids, and a healthy metabolic profile.
Associations of insulin‐like growth factors, insulin‐like growth factor binding proteins and acid‐labile subunit with coronary heart disease
Authors: Fischer Frank , Schulte Helmut , Mohan Subburaman , Tataru Mira‐Christine , Köhler Ekkehart , Assmann Gerd , Von Eckardstein Arnold 
Published: November 2004

Summaryobjective  IGFs and their binding proteins (IGFBPs) are produced both systemically and locally by cells of the cardiovascular system. As growth promoters, they may play a role in atherosclerosis.design  Case–control, cross‐sectional.patients  A total of 95 nondiabetic male patients with coronary heart disease (CHD) and 92 probands from the Prospective Cardiovascular Münster (PROCAM) who were below the age of 60 years and matched by age, body mass index (BMI) and smoking habitsmeasurements  We analysed the strength and independence of associations of angiographically assessed presence of CHD with BMI, systolic and diastolic blood pressure, total, high‐density lipoprotein (HDL) and LDL cholesterol, triglycerides, lipoprotein(a), apolipoproteins A‐I and B, total and free IGF‐I, IGF‐II, IGFBP‐1, IGFBP‐3, IGFBP‐5, acid‐labile subunit (ALS), insulin, C‐peptide, testosterone, DHEAS and sex hormone binding globulin.results  Using multivariate statistical analysis, the presence of CHD had significant positive associations with total IGF‐I, IGFBP‐5, ALS and IGFBP‐3. These associations were independent of each other as well as of traditional risk factors, insulin and sex hormones.conclusion  These observations may indicate a pathogenetic role of the GH/IGF axis in coronary atherosclerosis.