Identification of virus-encoded microRNAs

RNA silencing processes are guided by small RNAs that are derived from double-stranded RNA. To probe for function of RNA silencing during infection of human cells by a DNA virus, we recorded the small RNA profile of cells infected by Epstein-Barr virus (EBV). We show that EBV expresses several microRNA (miRNA) genes. Given that miRNAs function in RNA silencing pathways either by targeting messenger RNAs for degradation or by repressing translation, we identified viral regulators of host and/or viral gene expression.

MicroRNA targets in Drosophila

A computational method for whole-genome prediction of microRNA target genes is presented. Application of this method to the Drosophila melanogaster, Drosophila pseudoobscura and Anopheles gambiae genomes identifies several hundred target genes potentially regulated by one or more known microRNAs.

Background

The recent discoveries of microRNA (miRNA) genes and characterization of the first few target genes regulated by miRNAs in Caenorhabditis elegans and Drosophila melanogaster have set the stage for elucidation of a novel network of regulatory control. We present a computational method for whole-genome prediction of miRNA target genes. The method is validated using known examples. For each miRNA, target genes are selected on the basis of three properties: sequence complementarity using a position-weighted local alignment algorithm, free energies of RNA-RNA duplexes, and conservation of target sites in related genomes. Application to the D. melanogaster, Drosophila pseudoobscura and Anopheles gambiae genomes identifies several hundred target genes potentially regulated by one or more known miRNAs.

Results

These potential targets are rich in genes that are expressed at specific developmental stages and that are involved in cell fate specification, morphogenesis and the coordination of developmental processes, as well as genes that are active in the mature nervous system. High-ranking target genes are enriched in transcription factors two-fold and include genes already known to be under translational regulation. Our results reaffirm the thesis that miRNAs have an important role in establishing the complex spatial and temporal patterns of gene activity necessary for the orderly progression of development and suggest additional roles in the function of the mature organism. In addition the results point the way to directed experiments to determine miRNA functions.

Conclusions

The emerging combinatorics of miRNA target sites in the 3' untranslated regions of messenger RNAs are reminiscent of transcriptional regulation in promoter regions of DNA, with both one-to-many and many-to-one relationships between regulator and target. Typically, more than one miRNA regulates one message, indicative of cooperative translational control. Conversely, one miRNA may have several target genes, reflecting target multiplicity. As a guide to focused experiments, we provide detailed online information about likely target genes and binding sites in their untranslated regions, organized by miRNA or by gene and ranked by likelihood of match. The target prediction algorithm is freely available and can be applied to whole genome sequences using identified miRNA sequences.

Comparative protein structure modeling by iterative alignment, model building and model assessment

Comparative or homology protein structure modeling is severely limited by errors in the alignment of a modeled sequence with related proteins of known three-dimensional structure. To ameliorate this problem, we have developed an automated method that optimizes both the alignment and the model implied by it. This task is achieved by a genetic algorithm protocol that starts with a set of initial alignments and then iterates through re-alignment, model building and model assessment to optimize a model assessment score. During this iterative process: (i) new alignments are constructed by application of a number of operators, such as alignment mutations and cross-overs; (ii) comparative models corresponding to these alignments are built by satisfaction of spatial restraints, as implemented in our program MODELLER; (iii) the models are assessed by a variety of criteria, partly depending on an atomic statistical potential. When testing the procedure on a very difficult set of 19 modeling targets sharing only 4-27% sequence identity with their template structures, the average final alignment accuracy increased from 37 to 45% relative to the initial alignment (the alignment accuracy was measured as the percentage of positions in the tested alignment that were identical to the reference structure-based alignment). Correspondingly, the average model accuracy increased from 43 to 54% (the model accuracy was measured as the percentage of the C(alpha) atoms of the model that were within 5 A of the corresponding C(alpha) atoms in the superposed native structure). The present method also compares favorably with two of the most successful previously described methods, PSI-BLAST and SAM. The accuracy of the final models would be increased further if a better method for ranking of the models were available.

Tools for comparative protein structure modeling and analysis

The following resources for comparative protein structure modeling and analysis are described (http://salilab.org): MODELLER, a program for comparative modeling by satisfaction of spatial restraints; MODWEB, a web server for automated comparative modeling that relies on PSI-BLAST, IMPALA and MODELLER; MODLOOP, a web server for automated loop modeling that relies on MODELLER; MOULDER, a CPU intensive protocol of MODWEB for building comparative models based on distant known structures; MODBASE, a comprehensive database of annotated comparative models for all sequences detectably related to a known structure; MODVIEW, a Netscape plugin for Linux that integrates viewing of multiple sequences and structures; and SNPWEB, a web server for structure-based prediction of the functional impact of a single amino acid substitution.

Femoral shaft fractures in children--a comparison of treatment

Between April 1986 and March 1997, 83 femoral-shaft fractures in children 4-8 years old were treated at Christian Medical College and Hospital, Ludhiana, India. Among 35 patients with a minimum of 12 months follow-up, 14 were treated with Hamilton-Russell (HR) skin traction and 14 with proximal tibial skeletal traction. The group treated with HR traction had a shorter duration of (a) hospital stay (average 16.8 days versus 29.7 days for skeletal traction, p=0.02), (b) time to fracture consolidation (average 8.8 weeks versus 10.8 weeks for skeletal traction, p=0.04), and (c) return to normal activities (average 12.2 weeks versus 17.2 weeks for skeletal traction, p=0.03). At final follow-up (minimum 1 year), there were no significant differences in functional outcomes. Conservative management is still a gold standard for treatment of closed femoral shaft fractures in children 4-8 years of age. There appears to be no advantage to skeletal traction over skin traction in this age group.

[Outpatient geriatric rehabilitation: an evaluation of two models assessing trends of medical outcomes]

In Germany, complex and intensified outpatient geriatric rehabilitation is currently scarcely practised, mainly in model projects. The evaluation of these projects is exclusively conducted in uncontrolled studies. In our project "AMBRA", two different organisational models of geriatric rehabilitation are compared: a mobile rehabilitation team based at a geriatric hospital department and an outpatient rehabilitation centre run by GPs trained in geriatrics. Outcomes were assessed in terms of capability of self-care (Barthel-Index), mobility (Tinetti-Test, Timed "Up & Go"-Test, TUG), and depression (Geriatric Depression Scale, GDS). They were documented at three points in time (start of rehabilitation, end of rehabilitation, 6 months after end of rehabilitation) and analysed by multivariate analyses of variance (repeated measurements). 162 complete patients histories were taken in the first 18 months of the project. They show significant improvements in capability of self-care and mobility (both Tinetti-Test and TUG) between the beginning and the end of rehabilitation (adjusted for age, sex, cognitive function, diagnosis, rehabilitation model). On a medium-term basis, these results remained stable (TUG declined, however). Average GDS values did not change significantly. There were no significant sex- or age-related effects. The patients' cognitive function influenced changes in the results of the Barthel-Index and the Tinetti-Test. Patients with skeletal diseases showed less favourable trends in the Barthel-Index as did patients with cognitive impairments caused by vascular disease in the TUG, but these patients also benefited in the course of the model rehabilitation procedures. Differences in trends between patient groups of the two models were observed in the Barthel-Index. 96 % of patients previously living at home were still living there at the end of rehabilitation, 91 % were still living there 6 months after the end of rehabilitation. At the end of rehabilitation, 67 % of patients described an improvement of their personal situation associated with the rehabilitation procedure. Six months later, 82 % described an improvement or a stabilisation of their personal situation. Our results show positive medium-term rehabilitation trends concerning medical and subjective outcomes. In order to analyse effectiveness, we will have to wait for the results of a regional control group which is being recruited.

[Outpatient geriatric rehabilitation - the structural and process quality of a geriatric mobile service team and a community-based outpatient center]

The trial "Outpatient Geriatric Rehabilitation (AMBRA)" has been launched to compare two outpatient rehabilitation models close to their place of residence or at home: a mobile rehabilitation team based at a geriatric hospital department and a community-based outpatient rehabilitation center run by GPs. Primary analyses concerning structural and process quality of the models are presented in this paper. They refer to medical features and factors associated with care which were assessed at the beginning of the rehabilitation procedures and during intervention. The models include 60 patients attended by the mobile rehabilitation team and 76 patients attended by the outpatient rehabilitation centre. The patients are suffering from multiple illnesses and are limited in their daily activities. Both teams co-ordinate interdisciplinary rehabilitation programs with an average of 50 therapeutic units per patient under medical supervision. The programs' focus is on physiotherapy and occupational therapy and, if indicated, on logotherapy. Psychosocial and health promotional offers are hardly integrated into the procedures. The mobile rehabilitation team on average cares for patients with better cognitive functions (Mini-Mental State Examination) but worse abilities to cope in daily life (Barthel index) than the outpatient rehabilitation team. These differences between rehabilitation groups remain significant after multivariate consideration of sociodemographic, morbidity and process factors. However, differences in mobility (Tinetti Test) can be explained by these variables. The future comparison of results of the rehabilitation programs must therefore consider the different baseline levels and determinants between both groups.

Gastrointestinal stromal tumors: clinicopathological and immunohistochemical features

OBJECTIVES

To study the clinicopathological and immunohistochemical features of gastrointestinal stromal tumors (GISTs) in Kuwait.

MATERIALS AND METHODS

Hematoxylin- and eosin-stained sections of primary gastrointestinal mesenchymal tumors were reviewed. Immunohistochemical staining was performed using a panel of antibodies to determine muscle and neural differentiation, the incidence of CD117 and CD34 expression, as well as bcl-2 and cytokeratin expression. Each stain was interpreted as negative or positive. The staining intensity of positive cases was graded as weak, moderate or strong.

RESULTS

The age range was 25-80 with an average age of 54 and a male:female ratio of 3:2. The stomach was the most common site for these tumors, followed by the small intestine. Histologically, 46% were classified as malignant and 54% were benign. Most of the malignant tumors occurred in males, particularly in the stomach or small intestine. There was no significant difference in patient age between malignant and benign tumors. The most sensitive markers were muscle-specific actin for muscle differentiation and glial fibrillary acidic protein for neural differentiation. CD117 expression was seen in 81% and CD34 in 54% of all tumors.

CONCLUSIONS

The results of this study show that the stomach is the most common site for these tumors, that malignant tumors are more likely to occur in the small intestine than in the stomach, and that there is no difference between benign and malignant tumors with regard to age. Our findings are comparable to those of other workers, although our male:female ratio was slightly higher.

Caspase-mediated cleavage of actin-binding and SH3-domain-containing proteins cortactin, HS1, and HIP-55 during apoptosis

Reorganization of the actin cytoskeleton occurs during apoptosis. We found that actin-binding and Src homology 3 (SH3)-domain-containing proteins cortactin, hematopoietic-specific protein 1 (HS1), and hematopoietic progenitor kinase 1-interacting protein of 55 kDa (HIP-55, also called SH3P7 and Abp1) were degraded in a caspase-dependent manner during apoptosis. Cortactin, HS1, and HIP-55 were direct substrates of caspase 3. Cortactin and HS1 have two clusters of potential caspase cleavage sites; one is in their actin-binding domains, and the other is close to their carboxy-terminal SH3 domains. HIP-55 has one caspase recognition site, EHID(361). The HIP-55 (D361A) mutant was resistant to caspase cleavage. Cleavage of HIP-55 by caspases dissociated its actin-binding domain from its SH3 domain. The cleavage of these actin-binding and SH3 domain-containing proteins may affect cell signaling to and from the actin cytoskeleton and may be involved in the morphological change of cells during apoptosis.

Evidence for altered basal ganglia and cortical functions in transient idiopathic dystonia

Idiopathic dystonia with onset in the first year of life has been described as a transient movement disorder, in contrast to other forms of idiopathic dystonia We report on a girl who showed, from her 5th month, episodes of dystonic postures of her neck and arm, which lasted for seconds and occurred several times a day. Neurologic findings and the psychomotor development were and remained normal. Neurometabolic screening tests and cerebral magnetic resonance imaging showed normal results. Functional cerebral imaging showed decreased perfusion of the basal ganglia and the left temperomesial cortex using single photon emission computed tomography (SPECT with technetium 99m hexamethylpropyleneamine oxime [99mTc-HMPAO]) and decreased glucose metabolism in the basal ganglia and the cerebellum using positron emission tomography (PET with [18F]fluorodeoxyglucose [18FDG]). Follow-up revealed that the episodes disappeared at the age of 16 months. The findings of PET and SPECT give evidence of an alteration in basal ganglia function but also in functions of other central nervous system regions, which may, however, be temporary.

Depth-dependent analysis of membranes using benzophenone-based phospholipids

Any attempt to probe the membrane hydrophobic core with chemical reagents necessitates the use of reactive intermediates like carbenes and nitrenes, which can insert into C-H bonds. Several photoactivable reagents based on carbenes and nitrenes have been reported. However, the high reactivity of these reagents, often leads to very low insertion yields. We report here a high degree of cross-linking (35-40%) achieved with three benzophenone-based phospholipids and analyze the carbon functionalization data using a multiple Gaussian function. These phospholipids are so designed so as to permit depth-dependent labeling in membranes. Single bilayer vesicles were prepared from these phospholipids and dimyristoylphosphatidylcholine. The cross-linked product was isolated and characterized by mass spectroscopy. The results obtained indicated that the cross-linked product was dominated by dimeric product formed by intermolecular cross-linking. The Gaussian analysis used here provides insight into the relative depths of the probes inside the membrane.

Free fat interpositional graft in acute physeal injuries: the anticipatory Langenskiöld procedure

Free fat graft interposition has been used extensively in management of physeal injuries with established growth disturbances. The use of this technique as part of the management of acute physeal injuries has not been reported. Here we report on its application in acute physeal injuries, where it has prevented the formation of an anticipated physeal arrest.

Assessment of different methods for staining Helicobacter pylori in endoscopic gastric biopsies

The recent implication of Helicobacter pylori in the pathogenesis of gastritis-peptic ulcer syndrome and its relevance for the development of upper gastrointestinal malignancy warrant efficient methods for the detection and demonstration of the organism in biopsy specimens. We have compared 5 staining methods, namely, haematoxylin and eosin (H & E), immunohistochemistry (IHC), the silver staining HpSS, the alcian yellow-toluidine blue (Leung) method (A-Y) and Genta staining, for the demonstration of the organism in gastric biopsies taken from antrum, body and fundus of 118 patients who presented to our hospital with upper gastrointestinal symptoms. We found no significant differences in the efficacy of H & E, IHC, HpSS and A-Y in the demonstration of H. pylori in all 3 gastric sites. The least reproducible stain in our hands was the Genta stain. We conclude that H & E is adequate for the initial assessment of gastric biopsies in symptomatic upper gastrointestinal patients. This is because it is a well-tested, cheap and easy staining method, requiring a relatively short period of time to perform, with highly reproducible results. It has an added advantage of enabling simultaneous assessment of morphological changes accompanying H. pylori infection. When the density of the organism is expected to be low, we recommend addition of HpSS staining because of its high sensitivity and low cost. The disadvantages of the other staining methods (IHC, A-Y and Genta) are discussed.

Metabolism of levormeloxifene, a selective oestrogen receptor modulator, in the Sprague-Dawley rat, Cynomolgus monkey and postmenopausal woman

1. The metabolic fate of levormeloxifene in the Sprague-Dawley rat, Cynomolgus monkey and postmenopausal volunteer has been investigated. 2. Two doses of [14C]levormeloxifene, 0.7 and 50 mg/kg, were given to the male and female rat and monkey, and a single 20-mg dose to the postmenopausal volunteer. 3. The primary route of excretion in all three species was the faeces. Metabolism was similar in all three species, with demethylation forming the major metabolite in the rat and postmenopausal volunteer. One of the major metabolites in the monkey involved an oxidative ring opening of a pyrrole ring. 4. The main site of metabolism of levormeloxifene is the liver and the majority of the drug and its metabolites is excreted via the faecal route. Metabolic pathways appear to be similar in the three species studied.

Heat-shock protein 72/73 and impaired wound healing in diabetic and hypercortisolemic states

BACKGROUND

Impaired wound healing is a well-documented phenomenon in experimental and clinical diabetes. Emerging evidence favors the involvement of glucocorticoids (GCs) in the pathogenesis of this diabetic complication. Recent data indicated that a heat-shock protein (HSP) with a molecular weight of about 70 kd is expressed in wound healing and it is under the control of the hypothalamic-pituitary-adrenal axis. In view of these findings, the current study was designed to examine the influence of diabetes and the hypercortisolemic state on the expression of HSP 72/73 during wound healing.

METHODS

Induction of diabetes was achieved by the intravenous injection of streptozotocin at a dose of 55 mg/kg. Subcutaneously implanted polyvinyl alcohol (PVA) sponges were used as a wound healing model. Control and diabetic animals received, respectively, subcutaneous 30-day timed-release pellets of GC (200 mg) and RU 486 (25 mg). Corresponding animals received placebo pellets. Expression of HSP 72/73 within the PVA sponges was assayed with use of Western blotting and immunohistochemical techniques.

RESULTS

GCs caused a Cushing-like syndrome with weight loss and adrenal atrophy. A pronounced accumulation of constitutive HSP 72/73 was observed in the cytoplasm of various cell types including fibroblasts, macrophages, and endothelium of nondiabetic controls. The PVA sponge contents of HSP 72/73 were decreased as a function of diabetes. A similar phenomenon was seen in control animals receiving high doses of GCs. Partial normalization of the associated hyperglycemic and hypercortisolemic states of diabetes with insulin (hyperglycemia) and the GC receptor block RU 486 (hypercortisolemia) ameliorated the diabetes-related decrease in PVA sponge contents of HSP 72/73.

CONCLUSIONS

The current study provides evidence that both diabetes and the hypercortisolemic state are associated with a reduction in PVA sponge content of HSP 72/73. An amelioration of these changes was achieved by the institution of RU 486 therapy. Although our data may point to the possibility that the diabetes-related decrease in HSP 72/73 is mediated at least in part by GCs, a confirmation regarding this premise awaits further investigation.

Th1 dominance in the immune response to live Salmonella typhimurium requires bacterial invasiveness but not persistence

Factors responsible for the predictable generation of Th1 or Th2 immune responses to microorganisms in vivo are not well characterized, although the ability of antigen presenting cells (APC) to provide co-stimulation, the kinetics of MHC-peptide ligand generation as well as the cytokine environment are all considered important factors for the differential Th1/Th2 priming of T cells. Our earlier findings of an IFN-gamma-dominant, Th1-type response to live Salmonella typhimurium (Stm) and a Th2-type response to killed Stm suggested that persistence of viable bacteria might be an important factor in the generation of IFN-gamma-dominant responses. Using genetically susceptible and resistant strains of mice to limit bacterial replication and persistence in vivo, we show that mice of the lty(r) genotype, capable of a 10-fold better clearance of Stm, mount an IFN-gamma-dominant immune response following immunization with live Stm similar to that in the lty(s) strain. Further, metabolically defective mutants of Stm, aroA and purA, when used in the live form, also elicit IFN-gamma-dominant immune responses similar to the wild-type Stm strain despite their inability to proliferate in vivo. While a laboratory strain of Escherichia coli, which is antigenically cross-reactive but non-invasive, elicits hardly any IFN-gamma in immune responses, an invasive strain of E. coil induces an IFN-gamma-dominant response. These data together indicate that, while entry of bacteria into macrophages is likely to be critical for the generation of IFN-gamma-dominant immune responses, their persistence is not.

Characterisation of inflammatory cells in benign prostatic hyperplasia

Inflammation is a common finding in benign prostatic hyperplasia (BPH) and may be classified as acute, chronic active or chronic inactive prostatitis. The aim of the present study was to localise the different types of inflammatory cells in prostatic lesions to determine the sequence of events in the cellular reaction. We have carried out immunohistological characterisation of the inflammatory cells, using CD45RO and CD3 antibodies to detect T-lymphocytes, CD20 antibodies to detect B-lymphocytes, CD68 to detect macrophages, kappa and lambda immunoglobulin light chains, and antibodies against prostate specific antigen (PSA) and prostate specific acid phosphatase (PSAP). Macrophages accumulated in the lumen and glandular epithelial layers of damaged prostatic glands and were found in the periglandular cuff of inflammatory cells in acute and chronic active prostatitis. Lymphocytes also accumulated in large numbers in the glandular epithelial layers and around the glands, indicating an association with macrophages. B-lymphocytes were scanty, if at all present, in acute and chronic active prostatitis, but were prominent within well-organised follicle centres in chronic active prostatitis. Cells positive for light chains were few and scattered in prostatic tissue. PSA and PSAP activity was lost in recently damaged prostatic glandular epithelium and reappeared only in regenerating secretory epithelium, indicating leakage as a result of damage. We suggest that the initial response to prostatic injury is cellular, and probably related to leakage into the periglandular tissues of PSA, PSAP and other antigenic molecules normally present in prostatic secretion. Macrophages respond, followed by recruitment of T-lymphocytes which participate in the inflammatory response and accumulate around the damaged glands. B-cell activity appears to be a late event.

Absorption and excretion of radioactivity after intravaginal administration of an advanced delivery system of 14C-flutrimazole vaginal cream to postmenopausal women

In order to improve the effectiveness of treatment of vaginal yeast infections, flutrimazole, (CAS 119006-77-8), a broad spectrum local imidazolic fungicide, has been formulated in an advanced delivery system (Site Release, here in after briefly referred to as SR) designed to improve vaginal retention of the drug. To determine the extent of absorption of 14C-flutrimazole from this formulation, the absorption and excretion of total radioactivity have been studied in healthy postmenopausal female volunteers after intravaginal administration of approximately 5 g of SR Vaginal Cream containing 2% 14C-flutrimazole. Concentrations of unchanged flutrimazole have also been measured in plasma and urine, using a validated gas chromatography-mass spectrometry method. The rate of absorption was slow, with a mean peak plasma radioactivity concentration, Cmax, of 56 ng equivalents/ml, achieved at a mean Tmax of 28 h. Corresponding parameters for flutrimazole were 1.94 ng/ml at 24 h. At 24 h post-dose, unchanged flutrimazole represented only 3% of plasma total radioactivity which indicates that flutrimazole is extensively metabolised in man. Total radioactivity and unchanged flutrimazole were eliminated from plasma with terminal half-lives of 37 and 22 h, respectively. From the proportion of the radioactive dose excreted in urine and faeces, the maximal extent of absorption indicated for the intravaginal dose was about 8%, which is similar to that observed with other imidazolic compounds administered by this route. Thus, the formulation achieves the aim of prolonged drug action through the maintenance of therapeutic concentrations of the drug at the site of infection without notably increased absorption.