AthaMap web tools for database-assisted identification of combinatorial cis-regulatory elements and the display of highly conserved transcription factor binding sites in Arabidopsis thaliana

The AthaMap database generates a map of cis-regulatory elements for the Arabidopsis thaliana genome. AthaMap contains more than 7.4 x 10(6) putative binding sites for 36 transcription factors (TFs) from 16 different TF families. A newly implemented functionality allows the display of subsets of higher conserved transcription factor binding sites (TFBSs). Furthermore, a web tool was developed that permits a user-defined search for co-localizing cis-regulatory elements. The user can specify individually the level of conservation for each TFBS and a spacer range between them. This web tool was employed for the identification of co-localizing sites of known interacting TFs and TFs containing two DNA-binding domains. More than 1.8 x 10(5) combinatorial elements were annotated in the AthaMap database. These elements can also be used to identify more complex co-localizing elements consisting of up to four TFBSs. The AthaMap database and the connected web tools are a valuable resource for the analysis and the prediction of gene expression regulation at http://www.athamap.de.

Development of a multipoint model for sulfur in proteins: a new parametrization scheme to reproduce high-level ab initio interaction energies

To properly represent weak hydrogen bonds to sulfur in biological systems, a new multipoint model of atomic sulfur for the amino acid methionine is introduced. This is of particular importance for the description of ligand-protein interactions. The parametrization is performed by fitting the nonbonding parameters of dimethyl sulfide to high level ab initio interaction energy surfaces of the dimethyl sulfide-methanol system and incorporating them in the GROMACS force field. Two examples demonstrate the performance of the new model, the molecular dynamics simulations of the hRAR receptor and of alpha-lytic protease. In hRAR the origin of the discrimination between the R- and S-enantiomers of the synthetic ligand BMS 184394 is explained, and in the simulation of the alpha-lytic protease it is shown that no artificial long range disorders are introduced by the new parametrization.

Flow profiling of a surface-acoustic-wave nanopump

The flow profile in a capillary gap and the pumping efficiency of an acoustic micropump employing surface acoustic waves is investigated both experimentally and theoretically. Ultrasonic surface waves on a piezoelectric substrate strongly couple to a thin liquid layer and generate a quadrupolar streaming pattern within the fluid. We use fluorescence correlation spectroscopy and fluorescence microscopy as complementary tools to investigate the resulting flow profile. The velocity was found to depend on the applied power approximately linearly and to decrease with the inverse third power of the distance from the ultrasound generator on the chip. The found properties reveal acoustic streaming as a promising tool for the controlled agitation during microarray hybridization.

Physiology: does gut hormone PYY3-36 decrease food intake in rodents?

Batterham et al. report that the gut peptide hormone PYY3-36 decreases food intake and body-weight gain in rodents, a discovery that has been heralded as potentially offering a new therapy for obesity. However, we have been unable to replicate their results. Although the reasons for this discrepancy remain undetermined, an effective anti-obesity drug ultimately must produce its effects across a range of situations. The fact that the findings of Batterham et al. cannot easily be replicated calls into question the potential value of an anti-obesity approach that is based on administration of PYY3-36.

Cardiac ECMO for biventricular hearts after paediatric open heart surgery

OBJECTIVE

To delineate predictors of hospital survival in a large series of children with biventricular physiology supported with extracorporeal membrane oxygenation (ECMO) after open heart surgery.

RESULTS

81 children were placed on ECMO after open heart surgery. 58% (47 of 81) were transferred directly from cardiopulmonary bypass to ECMO. Hospital survival was 49% (40 of 81) but there were seven late deaths among these survivors (18%). Factors that improved the odds of survival were initiation of ECMO in theatre (64% survival (30 of 47)) rather than the cardiac intensive care unit (29% survival (10 of 34)) and initiation of ECMO for reactive pulmonary hypertension. Important adverse factors for hospital survival were serious mechanical ECMO circuit problems, renal support, residual lesions, and duration of ECMO.

CONCLUSIONS

Hospital survival of children with biventricular physiology who require cardiac ECMO is similar to that found in series that include univentricular hearts, suggesting that successful cardiac ECMO is critically dependent on the identification of hearts with reversible ventricular dysfunction. In our experience of postoperative cardiac ECMO, the higher survival of patients cannulated in the operating room than in the cardiac intensive care unit is due to early effective support preventing prolonged hypoperfusion and the avoidance of a catastrophic cardiac arrest.

Acute Otitis Externa: Efficacy and Tolerability of N-Chlorotaurine, a Novel Endogenous Antiseptic Agent

OBJECTIVE

The study's objective was to test the tolerability and efficacy of the endogenous antiseptic N-chlorotaurine (NCT) in comparison with a standard clinical treatment according to a phase IIb clinical trial protocol.

STUDY DESIGN

The antimicrobial agent NCT was compared with the antibiotic component drops Otosporin (containing neomycin, polymyxin B, and hydrocortisone) for topical treatment of acute otitis externa in a randomized and rater-blinded clinical study.

METHODS

Fifty patients suffering from acute otitis externa were divided into two groups according to a randomized list. The test group was treated with 1 mL of 1% aqueous NCT solution, the reference group with 1 mL of Otosporin. The substances were applied to the external ear canal at one daily session until the signs of infection disappeared. Efficacy and tolerability were evaluated daily by visual analogue scale and a six-step infection score. In addition, smears were analyzed to identify the causative pathogens.

RESULTS

Both medications were equally well tolerated by the patients. The treatment was successful for all patients of the NCT group, whereas in one patient from the reference group, the infection did not disappear. The inflammation score improved more rapidly in the NCT group, which resulted in an earlier termination of the therapy. This difference became highly significant on days 4 to 7 (P <.01 each). Time needed for disappearance of inflammation (score 0) was 5.6 +/- 1.6 (mean +/- SD, range 3-9) days in the NCT group and 7.4 +/- 1.6 (range 4-10) days in the Otosporin group (P <.001). As expected, microbiologic cultures from ear swabs revealed Pseudomonas aeruginosa (58%) followed by Staphylococcus aureus (18%) as the main causative pathogens.

CONCLUSIONS

NCT appears to be well tolerated and more effective than the therapy using antibiotic component drops. Because of its endogenous nature and its higher efficacy, NCT appears to be a good choice for topical treatment of acute otitis externa.

[Minimally invasive, safe treatment of the neurogenic bladder with botulinum-A-toxin in children with myelomeningocele]

PURPOSE

The efficacy and durability of botulinum-A toxin in the treatment of detrusor hyperreflexia in myelomeningocele (MMC) children was evaluated prospectively.

MATERIALS AND METHODS

A total of 15 children (10 male and 5 female, mean age 5.8 years), all on clean intermittent catheterisation (CIC) due to MMC, were "non responders" to orally and intravesically administered anticholinergic medication. Pretreatment assessment included a videourodynamic evaluation, incontinence scoring and a mercaptoacetyltriglycine-3 renal scan. We injected from 10 U/kg up to a maximum of 360 U botulinum-A toxin at 25-40 sites of the detrusor, sparing the trigone. Follow-up was 24 months. All children had a urodynamic reevaluation with assessment of bladder capacity and incontinence score at 3, 9 and 12 months.

RESULTS

Mean bladder reflex volume increased from 72.00 +/- 28.12 ml to 298 +/- 32.45 ml (p < 0.001). The maximal detrusor pressure decreased from 78.76 +/- 23.14 cm H(2)O to 42.76 +/- 24.34 cm H(2)O (p < 0.001). Maximal bladder capacity increased from 136.34 +/- 45.71 ml to 297.02 +/- 87.17 ml (p < 0.001). Detrusor compliance increased from 18.29 +/- 27.19 ml/cm H(2)O to 51.17 +/- 38.17 ml/mmH(2)O (p < 0.001). While 10 patients became completely dry between CIC, the remaining 2 patients improved from score 3 to 1. Results at 9 months were similar to the ones at 3 months. The mean efficacy and durability of the toxin was 10.5 months after the first intravesical injection.

CONCLUSIONS

Botulinum-A toxin is a safe alternative in the management of detrusor hyperreflexia in MMC children. Preliminary results are promising concerning urodynamic parameters and continence.

AthaMap: an online resource for in silico transcription factor binding sites in the Arabidopsis thaliana genome

Gene expression is controlled mainly by the binding of transcription factors to regulatory sequences. To generate a genomic map for regulatory sequences, the Arabidopsis thaliana genome was screened for putative transcription factor binding sites. Using publicly available data from the TRANSFAC database and from publications, alignment matrices for 23 transcription factors of 13 different factor families were used with the pattern search program Patser to determine the genomic positions of more than 2.4 x 10(6) putative binding sites. Due to the dense clustering of genes and the observation that regulatory sequences are not restricted to upstream regions, the prediction of binding sites was performed for the whole genome. The genomic positions and the underlying data were imported into the newly developed AthaMap database. This data can be accessed by positional information or the Arabidopsis Genome Initiative identification number. Putative binding sites are displayed in the defined region. Data on the matrices used and on the thresholds applied in these screens are given in the database. Considering the high density of sites it will be a valuable resource for generating models on gene expression regulation. The data are available at http://www.athamap.de.

PathoPlant: a database on plant-pathogen interactions

Pathogen recognition and signal transduction during plant pathogenesis is essential for the activation of plant defense mechanisms. To facilitate easy access to published data and to permit comparative studies of different pathogen response pathways, a database is indispensable to give a broad overview of the components and reactions so far known. PathoPlant has been developed as a relational database to display relevant components and reactions involved in signal transduction related to plant-pathogen interactions. On the organism level, the tables 'plant', 'pathogen' and 'interaction' are used to describe incompatible interactions between plants and pathogens or diseases. On the molecular level, plant pathogenesis related information is organized in PathoPlant's main tables 'molecule', 'reaction' and 'location'. Signal transduction pathways are modeled as consecutive sequences of known molecules and corresponding reactions. PathoPlant entries are linked to associated internal records as well as to entries in external databases such as SWISS-PROT, GenBank, PubMed, and TRANSFAC. PathoPlant is available as a web-based service at http://www.pathoplant.de.

CL/RAMP2 and CL/RAMP3 produce pharmacologically distinct adrenomedullin receptors: a comparison of effects of adrenomedullin22-52, CGRP8-37 and BIBN4096BS

Adrenomedullin (AM) has two known receptors formed by the calcitonin receptor-like receptor (CL) and receptor activity-modifying protein (RAMP) 2 or 3: we report the effects of the antagonist fragments of human AM and CGRP (AM22-52 and CGRP8-37) in inhibiting AM at human (h), rat (r) and mixed species CL/RAMP2 and CL/RAMP3 receptors transiently expressed in Cos 7 cells or endogenously expressed as rCL/rRAMP2 complexes by Rat 2 and L6 cells. AM22-52 (10 microM) antagonised AM at all CL/RAMP2 complexes (apparent pA2 values: 7.34+/-0.14 (hCL/hRAMP2), 7.28+/-0.06 (Rat 2), 7.00+/-0.05 (L6), 6.25+/-0.17 (rCL/hRAMP2)). CGRP8-37 (10 microM) resembled AM22-52 except on the rCL/hRAMP2 complex, where it did not antagonise AM (apparent pA2 values: 7.04+/-0.13 (hCL/hRAMP2), 6.72+/-0.06 (Rat2), 7.03+/-0.12 (L6)). On CL/RAMP3 receptors, 10 microM CGRP8-37 was an effective antagonist at all combinations (apparent pA2 values: 6.96+/-0.08 (hCL/hRAMP3), 6.18+/-0.18 (rCL/rRAMP3), 6.48+/-0.20 (rCL/hRAMP3)). However, 10 microM AM22-52 only antagonised AM at the hCL/hRAMP3 receptor (apparent pA2 6.73+/-0.14). BIBN4096BS (10 microM) did not antagonise AM at any of the receptors. Where investigated (all-rat and rat/human combinations), the agonist potency order on the CL/RAMP3 receptor was AM approximately betaCGRP>alphaCGRP. rRAMP3 showed three apparent polymorphisms, none of which altered its coding sequence. This study shows that on CL/RAMP complexes, AM22-52 has significant selectivity for the CL/RAMP2 combination over the CL/RAMP3 combination. On the mixed species receptor, CGRP8-37 showed the opposite selectivity. Thus, depending on the species, it is possible to discriminate pharmacologically between CL/RAMP2 and CL/RAMP3 AM receptors.

Genotyping of Clostridium perfringens Isolated from Domestic and Exotic Ruminants and Swine

Clostridium perfringens types A, B, C, D and E are known to cause severe enteritis/enterotoxaemia and diseases (especially caused by type A) belonging to the gas oedema complex in many species. Samples from the small intestine as well as faeces of domestic and exotic animals suffering from enterotoxaemic signs or having died within days after first occurance of toxaemia were submitted for typing C. perfringens toxovars by multiplex PCR. The following species have been investigated: domestic sheep (Ovis ammon; n = 10), domestic goat (Capra aegagrus hircus; n = 26), Japanese serow (Capricornis sumatraensis; n = 4), lechwe waterbuck (Hydrotragus leche; n = 1), blackbuck (Antilope cervicapra; n = 1), European reindeer (Rangifer tarandus tarandus; n = 4), domestic swine (Sus scrofa; n = 52), and collared peccary (Tayassu albirostris; n = 1). Interestingly, the predominant C. perfringens toxovar in domestic sheep was type A. This toxovar could also be diagnosed in all reindeer, in three Japanese serows, one lechwe waterbuck and most pigs (n = 47), the majority of those being at suckling age. Type D was the most prevalent toxovar (n = 18) in domestic goats, but also types A and E could be identified as pathogens in this species. Type C could only be found in domestic swine (n = 5) and in one case of clostridiosis in a Japanese serow. Two cases of enterotoxaemia in goats, one case in reindeer, and a single case in blackbuck and collared peccary were caused by C. perfringens type E. Genotyping of C. perfringens is recommended before starting vaccination programmes as it could be shown, that the importance of specific toxovars has been underestimated in specific species and/or age groups.

Development and potential of non-peptide antagonists for calcitonin-gene-related peptide (CGRP) receptors: evidence for CGRP receptor heterogeneity

Calcitonin-gene-related peptide (CGRP) is a 37-amino-acid vasodilatory peptide, of which two isoforms, alpha CGRP and beta CGRP, have been described. The use of C-terminal fragments of CGRP peptide, such as human alpha CGRP-(8-37), has led to the pharmacological subdivision of CGRP receptors into CGRP-1 [high potency for binding of human alpha CGRP-(8-37)] and CGRP-2 (lower potency) receptors. We have recently developed BIBN4096BS, the first non-peptide CGRP antagonist, which has sub-nanomolar affinity for primate CGRP receptors. The use of BIBN4096BS has led to the discovery of further functional CGRP receptor heterogeneity in rat tissues. To further exploit BIBN4096BS as a pharmacological tool, we used BIBN4096BS in pig left anterior descending coronary vessels and cerebral basilar arteries, and compared functional with molecular data, characterizing CGRP receptor components. Our data show that, apart from a subdivision into CGRP-1 and -2 receptors, BIBN4096BS reveals additional functional differences between the actions of alpha CGRP and beta CGRP. However, evidence for CGRP receptor heterogeneity on a molecular level is scarce.

Expression of somatostatin receptor types 1-5 in 81 cases of gastrointestinal and pancreatic endocrine tumors. A correlative immunohistochemical and reverse-transcriptase polymerase chain reaction analysis

Somatostatin receptors (SSTRs) have been extensively mapped in human tumors by means of autoradiography, reverse-transcriptase polymerase chain reaction (RT-PCR), in situ hybridization (ISH) and immunohistochemistry (IHC). We analyzed the SSTR type 1-5 expression by means of RT-PCR and/or IHC in a series of 81 functioning and non-functioning gastroenteropancreatic (GEP) endocrine tumors and related normal tissues. Moreover, we compared the results with clinical, pathological and hormonal features. Forty-six cases (13 intestinal and 33 pancreatic) were studied for SSTR 1-5 expression using RT-PCR, IHC with antibodies to SSTR types 2, 3, 5 and ISH for SSTR2 mRNA. The vast majority of tumors expressed SSTR types 1, 2, 3 and 5, while SSTR4 was detected in a small minority. Due to the good correlation between RT-PCR and IHC data on SSTR types 2, 3, and 5, thirty-five additional GEP endocrine tumors were studied with IHC alone. Pancreatic insulinomas had an heterogeneous SSTR expression, while 100% of somatostatinomas expressed SSTR5 and 100% gastrinomas and glucagonomas expressed SSTR2. Pre-operative biopsy material showed an overlapping immunoreactivity with that of surgical specimens, suggesting that the SSTR status can be detected in the diagnostic work-up. It is concluded that SSTRs 1-5 are heterogeneously expressed in GEP endocrine tumors and that IHC is a reliable tool to detect SSTR types 2, 3 and 5 in surgical and biopsy specimens.

Titrating the expression of a Gi protein-coupled receptor using an ecdysone-inducible system in CHO-K1 cells

Changes in receptor density are often associated with pathological conditions. For example, high levels of the G protein-coupled somatostatin receptor, sst2, have been detected in a number of malignant cell types, a characteristic feature that is routinely utilised as a diagnostic tool. However, how the increased receptor expression affects cellular function through alterations in G protein-coupling or changes in the intensity or duration of activated signalling pathways is poorly understood. The current report details the use of an ecdysone-inducible expression system in CHO-K1 cells, whereby the consequence of modulating the level of human sst2 receptor expression on specific transduction events can be examined. A time- and concentration-dependent induction of sst2 receptor expression was attained by exposure of cells to the ecdysteroid-inducing agent, muristerone A (MuA). Increases in sst2 receptor expression were determined by immunoassay, immunoblotting and immunocytochemical analysis. Maximal sst2 receptor expression was obtained after treatment of cells with 7 microM MuA for 24 h. Functionality of the sst2 receptor was assessed by immunoblot analysis of phosphorylated forms of MAP kinase. Following receptor activation, time-dependent increases in the level of MAP kinase phosphorylation were shown to correlate with the degree of sst2 receptor induction. Confirmation of receptor activation was determined by visualisation of ligand-induced redistribution of sst2 receptors from the plasma membrane to discrete intracellular compartments. However, in a series of further studies, both immunocytochemical and fluorescence-activated cell sorting (FACS) analyses demonstrated that over a prolonged period, stable receptor expression could not be maintained in CHO-K1 cells using this expression system. Thus, routine analysis of the sst2 receptor expressing cell population is required to derive comparable results between assays, especially when some assays provide information from the whole cell population whilst others are based at the single cell level. On the basis of these observations we conclude that, providing such quality control measurements are taken, the ecdysone inducible expression system is a useful tool to modulate functional sst2 receptor expression in an in vitro environment over short time periods.

Expression of somatostatin receptor types 2, 3 and 5 in biopsies and surgical specimens of human lung tumours. Correlation with preoperative octreotide scintigraphy

The increasingly popular use of somatostatin analogs in clinical practice for both diagnostic and therapeutic purposes prompted extensive investigations on somatostatin receptor (sst) expression in human tumors by autoradiography, nucleic acid analysis and, recently, immunohistochemistry (IHC). The currently employed radiotracer for scintigraphy (Octreoscan) is octreotide, a somatostatin analog having a high affinity for sst types 2, 3, and 5. In this study on 25 patients, we compared sst 2, 3, and 5 expression in surgical and biopsy specimens of lung tumors, as revealed by immunohistochemical and reverse transcriptase polymerase chain reaction (RT-PCR), with the octreoscan outcome (which was positive in 20/25 cases). By IHC, the tumors mainly expressed sst2 (17/25, 68%) at the cell membrane level, while sst 3 and 5 were detected in a fraction of cases (24% and 20%, respectively). Comparing RT-PCR and IHC data, a correlation was found in 83.3% of cases, while octreoscan findings and sst expression were correlated in 22/25 cases (88%). In addition, cytological and biopsy specimens expressed the same sst type found in the corresponding surgical sample, thus indicating that a cell membrane sst immunoreactivity in a biopsy reliably predicts the tumor-receptor profile before its resection. Finally, sst expression was not restricted to neuroendocrine lung tumors, but was also a feature of some non-neuroendocrine carcinomas, although to a lesser extent. The occasional expression of sst subtypes in intratumoral lymphocytes, endothelia and necrotic areas is an additional feature to be considered in the interpretation of Octreoscan findings, since the in vivo procedure does not allow to define the sst cellular distribution. IHC can therefore be usefully coupled to radionuclear investigations to better characterize the sst cellular location and subtype in lung tumors.

Mosses share mitochondrial group II introns with flowering plants, not with liverworts

Extant bryophytes are regarded as the closest living relatives of the first land plants, but relationships among the bryophyte classes (mosses, liverworts and hornworts) and between them and other embryophytes have remained unclear. We have recently found that plant mitochondrial genes with positionally stable introns are well suited for addressing questions of plant phylogeny at a deep level. To explore further data sets we have chosen to investigate the mitochondrial genes nad4 and nad7, which are particularly rich in intron sequences. Surprisingly, we find that in these genes mosses share three group II introns with flowering plants, but none with the liverwort Marchantia polymorpha or other liverworts investigated here. In mitochondria of Marchantia, nad7 is a pseudogene containing stop codons, but nad7 appears as a functional mitochondrial gene in mosses, including the isolated genus Takakia. We observe the necessity for strikingly frequent C-to-U RNA editing to reconstitute conserved codons in Takakia when compared to other mosses. The findings underline the great evolutionary distances among the bryophytes as the presumptive oldest division of land plants. A scenario involving differential intron gains from fungal sources in what are perhaps the two earliest diverging land plant lineages, liverworts and other embryophytes, is discussed. With their positionally stable introns, nad4 and nad7 represent novel marker genes that may permit a detailed phylogenetic resolution of early clades of land plants.

Effect of delayed sternal closure after cardiac surgery on respiratory function in ventilated infants

OBJECTIVE

Studies examining the effect of sternal closure on respiratory function have not been published, and currently there is little evidence to guide ventilation management immediately after closure. The aim of this study was to establish the impact of delayed sternal closure on expired tidal volume, respiratory system compliance, and CO2 elimination immediately after the procedure in infants who had undergone open heart surgery.

DESIGN

Prospective study of respiratory function before and after delayed sternal closure.

SETTING

Cardiac intensive care unit, Great Ormond Street Hospital, London.

PATIENTS

Seventeen infants (median age, 2 wks) with open median sternotomy incisions after cardiac surgery. Data were collected between August 1998 and March 2000.

INTERVENTIONS

Respiratory function was measured continuously for 30 mins before and after delayed sternal closure in paralyzed ventilated infants.

MEASUREMENTS AND RESULTS

Four babies were excluded from the study because they required either immediate increase in ventilation after delayed sternal closure (n = 3) or removal of pericardial blood collection (n = 1). In the remaining 13 infants, expired tidal volume and CO2 elimination decreased significantly (p < .005) by a mean of 17% and 29%, respectively, after sternal closure. In five of the remaining 13 patients, the magnitude of tracheal tube leak increased by > or = 10% after delayed sternal closure, thereby invalidating recorded changes in respiratory system compliance. Of the eight infants in whom there was a minimal change in leak, respiratory system compliance decreased significantly (p < .05) by a mean of 19%.

CONCLUSIONS

This study supports the hypothesis that respiratory function may be compromised after delayed sternal closure and that ventilatory support should be increased to counteract the anticipated decrease in tidal volume. Extra vigilance should be applied in monitoring blood gases after delayed sternal closure to assess clinical responses to sternal closure or changes in ventilatory support. Accurate assessment of change in respiratory system compliance after any therapeutic intervention may be precluded by changes in tracheal tube leak during the procedure.

Presence of sst2(a) receptor immunoreactivity in rat ependyma and tanycytes

Somatostatin sst2(a) receptor was observed, by immunofluorescence, in ependymal cells and in tanycytes of the wall of the ventricle and the hypothalamic recess of the male rat median eminence. Strong immunoreactivity for the receptor protein was observed in lateral tanycytes (alpha-type) while a moderate signal was seen in medial tanycytes (beta-type). In high magnification the immunoreactive material, of moderate intensity, had a coarse granular appearance. Only few of the alpha-tanycytes also displayed immunoreactive GFAP. The apical portion of the ependymal cells as well as of tanycytes contained immunoreactive S-100 (alphabeta). Since rather high levels of somatostatin are demonstrated to occur in the cerebrospinal fluid of the third ventricle, it is suggested that somatostatin via the sst2(a) receptor may regulate the physiology of tanycytes.